Micrornas in Retinal Development

VS04CH02_Hindges ARI 14 August 2018 11:4

Annual Review of Vision Science MicroRNAs in Retinal Development

Thomas A. Reh1 and Robert Hindges2

1Department of Biological Structure, University of Washington, Seattle, Washington 98195, USA; email: [email protected] 2Centre for Developmental Neurobiology, MRC Centre for Neurodevelopmental Disorders, King’s College London, London SE1 1UL, United Kingdom; email: [email protected]

Annu. Rev. Vis. Sci. 2018. 4:25–44 Keywords First published as a Review in Advance on retina, microRNA, Dicer, development, retinal cells, cell differentiation, June 11, 2018 axon guidance The Annual Review of Vision Science is online at Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org vision.annualreviews.org Access provided by University of Washington on 07/31/19. For personal use only. Abstract https://doi.org/10.1146/annurev-vision-091517- The small RNA regulatory molecules called microRNAs (miRNAs) play key 034357 roles in the development of most organisms. The expression of many dif- Copyright c 2018 by Annual Reviews. ferent miRNAs has been described in the developing and mature vertebrate All rights reserved retina. The ability of miRNAs to regulate a diversity of messenger RNA targets allows them to have effects on many different developmental processes, but the functions of only a few miRNAs have been documented to date. De- velopmental transitions between cell states appear to be particularly sensitive to miRNA loss of function, as evidenced by speciﬁc miRNA knockdowns or from global perturbations in miRNA levels (e.g., Dicer deletion). However, we are still in only the very early stages of understanding the range of cellular functions miRNAs control during development.

25 VS04CH02_Hindges ARI 14 August 2018 11:4

1. BACKGROUND MicroRNAs (miRNAs) are small noncoding RNA molecules that control gene expression through posttranscriptional regulation. They recognize complementary sequences on messenger RNA molecules (mRNAs), which then leads to either (a) destabilization of the mRNA and acceleration of its destruction or (b) interference with the mRNA translation machinery (Bartel 2004). Most miRNAs are transcribed by RNA polymerase II to generate primary miRNAs, or pri-miRNAs, which may contain multiple miRNAs (Figure 1). These long transcripts are then processed while

miRNA gene Protein-coding gene Nucleus

RNA Pol II Pri-miRNA mRNA CapExon 1 Exon 2 AAAAA Cap AAAAAA Splicing Pre-miRNA CapExon 1 Exon 2 AAAA DGCR8 Mature mRNA

Drosha x Editing x x

Exportin-5

Translational repression Ago Dicer RISC TRBP Cytoplasm miRNA* degradation mRNA degradation

Figure 1 Biogenesis of microRNAs (miRNAs). Canonical pathway (left): miRNA genes are transcribed by RNA polymerase II (Pol II) to give rise to long primary transcripts [primary miRNAs (pri-miRNAs)], which form

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org hairpin structures. This step is subject to regulation by transcriptional activators or inhibitors (not shown). Access provided by University of Washington on 07/31/19. For personal use only. Still in the nucleus, pri-miRNAs are then processed by a protein complex containing the ribonuclease III Drosha and DGCR8, resulting in a 60–70-nucleotide stem/loop structure [precursor miRNAs (pre-miRNAs)]. Furthermore, in some cases, pre-miRNA sequences can be subject to base modifications by specific RNA editing. The pre-miRNAs are then exported to the cytosol with the help of Exportin-5 through a GTP-dependent process. There, the pre-miRNAs are further processed by the Dicer-TRBP ∗ complex to yield a 21–24-nucleotide-long miRNA:miRNA duplex molecule. Finally, after destruction of ∗ one strand [most of the time, the passenger strand, denoted with an asterisk ( )], mature miRNAs are loaded into an RNA-induced silencing complex (RISC) that includes Argonaute (Ago). The miRNA then binds to the 3 untranslated regions of specific messenger RNA (mRNA) targets and, depending on its seed sequence, leads either to translational repression or to the cleavage and degradation of the target. Mirtron pathway (right): Pre-miRNAs can also be generated through an alternative, Drosha-independent pathway. Here, miRNA sequences are located in introns of primary mRNA transcripts generated by RNA Pol II. Their expression pattern is therefore exactly following the mirtron-harboring gene. The miRNA sequence is subsequently spliced out from the primary transcript by the spliceosome and then enters the canonical pathway. Additional abbreviation: DGCR8, DiGeorge syndrome critical region 8.

26 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

still in the nucleus by the DiGeorge syndrome critical region 8 (DGCR8) protein and the ribonuclease Drosha to form shorter, about 70-nucleotide-long precursor miRNAs (pre-miRNAs) that are subsequently exported to the cytoplasm by Exportin-5. The pre-miRNAs are further reduced to 21–23-nucleotide double-stranded mature miRNAs by the endoribonuclease Dicer, complexed to TRBP. The mature miRNA becomes part of the RNA-induced silencing complex (RISC), containing Argonaute (Ago) as a key component, to effect gene silencing of mRNA targets through binding to complementary sequences in their 3 untranslated region (UTR) (Figure 1). In addition to this canonical pathway described, some alternative mechanisms to generate miRNAs exist, bypassing, for example, Drosha or Dicer processing (Ha & Kim 2014). Although initially considered primarily as translational repressors (Olsen & Ambros 1999), miRNAs were also shown to cause mRNA degradation (Bagga et al. 2005, Lim et al. 2005), and more recent evidence indicates that in mammalian cells, mRNA degradation accounts for most of the repression mediated by miRNA, with a smaller contribution from translation repression (Eichhorn et al. 2014). A given miRNA recognizes its targets by base pairing via a short sequence, known as the seed sequence (6–8 nucleotides), at the 5 end. Early target prediction programs were largely based on the complementation of this short seed region with a potential target mRNA. These target prediction databases typically report thousands of targets for a particular miRNA. The vast majority of these predicted targets have not been confirmed by biological and biochemical experiments, and many may not be actual targets; however, they serve as a source of potential targets for confirmatory studies. To experimentally determine mRNA targets, researchers can use antibodies to Ago to precipi- tate the complex with miRNAs and their targets [CLIP (crosslinking and immunoprecipitation)], and this has provided additional insight into the mechanisms of miRNA-mediated gene silencing (Chi et al. 2009). Directly sequencing the miRNA:mRNA complexes, using, for example, AGO-CLIP, PAR (photoactivatable ribonucleoside–enhanced)-CLIP, CLEAR (covalent ligation of endogenous Ago-bound RNAs)-CLIP, and CLASH (crosslinking, ligation, and sequencing of hybrids), has shown that most mRNAs (a) are typically paired with two or more miRNAs, making combinatorial regulation likely, and (b) are frequently paired in a noncanonical manner, suggesting that the potential targets available for an miRNA may be substantially different than those identified by seed matches (Chi et al. 2009, Hafner et al. 2010, Helwak et al. 2013, Moore et al. 2015). For example, one AGO-CLIP study found 7-mer and 8-mer seeds in only about half the Ago-bound sites. There are several levels of redundancy in miRNA:target regulation. First, each miRNA can target many mRNAs. Second, many mRNAs can be targeted by several miRNAs. Third, miRNAs

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org are frequently in families of related molecules, and so several family members can target the same

Access provided by University of Washington on 07/31/19. For personal use only. site on an mRNA. These considerations make it sometimes difficult to discern the roles of specific miRNAs in a given biological process. Knockout studies that delete all members of a given miRNA family are rare, though miRNA sponges (see Section 3) can be used to reduce several family members simultaneously. However, since many mRNAs are best targeted by a combination of different miRNAs, loss-of-function studies typically require antagonism of multiple miRNA family members of multiple miRNA families. Focused overexpression studies of miRNAs are also complicated by the diversity of targets and the additional effects on several biological processes that are outside the focus of the specific study. These considerations have made making progress in the field more difficult than doing so in the analysis of protein-coding genes, which is a more well-established discipline; nevertheless, significant advancement has been made in the identification of miRNAs expressed in the retina during development, in mature retina, and in retinal disease.

www.annualreviews.org • MicroRNAs in Retinal Development 27 VS04CH02_Hindges ARI 14 August 2018 11:4

2. CHARACTERIZING miRNA EXPRESSION IN DEVELOPING RETINA Several studies have characterized miRNA expression in the developing retina in a variety of species, including ﬁsh, frogs, and mice, using a variety of methods, such as microarrays, reverse transcription polymerase chain reaction (RT-PCR), in situ hybridization, NanoString technology, and miRNA sensors (Arora et al. 2010, Damiani et al. 2008, Decembrini et al. 2009, Deo et al. 2006, Georgi & Reh 2010, Hackler et al. 2010, Karali et al. 2010, La Torre et al. 2013, Wohl & Reh 2016, Xu et al. 2007). Although there are many differences among species and across the methods of analyses, in the particular miRNAs that have been reported, many of the most highly expressed miRNAs are common to both the diverse species and the particular methods used. For example, in a microarray study of the developing frog retina, the most highly expressed miRNAs include let- 7c, miR-183, and miR-125b, and these same miRNAs are highly expressed in developing mouse retina as well (Decembrini et al. 2009, Georgi & Reh 2010, Hackler et al. 2010, La Torre et al. 2013). Table 1 lists some of the most commonly reported miRNAs found in developing retina.

Table 1 Highly expressed microRNAs in developing retina MicroRNA References hsa-miR-18a Georgi & Reh (2010), Hackler et al. (2010) mmu-let-7a Georgi & Reh (2010), Hackler et al. (2010), La Torre et al. (2013), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-let-7c Georgi & Reh (2010), Hackler et al. (2010), La Torre et al. (2013), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-let-7e Hackler et al. (2010), Georgi & Reh (2010), Loscher et al. (2007), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-let-7f Georgi & Reh (2010), Hackler et al. (2010), La Torre et al. (2013), Shen et al. (2008), Xu et al. (2007) mmu-miR-101a Georgi & Reh (2010), Shen et al. (2008) mmu-miR-106b Georgi & Reh (2010), La Torre et al. (2013), Loscher et al. (2007), Shen et al. (2008), Xu et al. (2007) mmu-miR-124 Arora et al. (2007), Georgi & Reh (2010), Hackler et al. (2010), Kapsimali et al. (2007), Karali et al. (2007), La Torre et al. (2013), Loscher et al. (2007), Makarev et al. (2006), Ryan et al. (2006), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-miR-125a-5p Georgi & Reh (2010), Hackler et al. (2010), Loscher et al. (2007), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-miR-125b Georgi & Reh (2010), Hackler et al. (2010), Kapsimali et al. (2007), La Torre et al. (2013), Loscher et al. (2007), Makarev et al. (2006), Ryan et al. (2006), Xu et al. (2007), Shen et al. (2008), Wohl & Reh (2016) Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org

Access provided by University of Washington on 07/31/19. For personal use only. mmu-miR-136 Georgi & Reh (2010), Hackler et al. (2010), Loscher et al. (2007) mmu-miR-16 Georgi & Reh (2010), Hackler et al. (2010), La Torre et al. (2013), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-miR-17 Georgi & Reh (2010), Hackler et al. (2010), Shen et al. (2008) mmu-miR-182 Georgi & Reh (2010), Hackler et al. (2010), Jin et al. (2009), Kapsimali et al. (2007), Karali et al. (2007), La Torre et al. (2013), Loscher et al. (2007), Loscher et al. (2008), Ryan et al. (2006), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-miR-183 Georgi & Reh (2010), Hackler et al. (2010), Jin et al. (2009), Kapsimali et al. (2007), La Torre et al. (2013), Loscher et al. (2007), Loscher et al. (2008), Ryan et al. (2006), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) ∗ mmu-miR-183 Georgi & Reh (2010), Hackler et al. (2010) mmu-miR-191 Georgi & Reh (2010), Hackler et al. (2010), Loscher et al. (2007), Shen et al. (2008), Xu et al. (2007) (Continued)

28 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

Table 1 (Continued) MicroRNA References ∗ mmu-miR-200b Georgi & Reh (2010), Hackler et al. (2010) mmu-miR-26a Georgi & Reh (2010), Hackler et al. (2010), Ryan et al. (2006), Shen et al. (2008), Shi et al. (2009), Xu et al. (2007) mmu-miR-204 Georgi & Reh (2010), Hackler et al. (2010), Wohl & Reh (2016) mmu-miR-26b Georgi & Reh (2010), Loscher et al. (2007), Shen et al. (2008), Xu et al. (2007) mmu-miR-30a Hackler et al. (2010), Xu et al. (2007) mmu-miR-690 Georgi & Reh (2010), Hackler et al. (2010) mmu-miR-691 Georgi & Reh (2010), Hackler et al. (2010), Loscher et al. (2007) mmu-miR-709 Georgi & Reh (2010), Hackler et al. (2010) mmu-miR-720 Georgi & Reh (2010), Wohl & Reh (2016) mmu-miR-7a Arora et al. (2007), Georgi & Reh (2010), Hackler et al. (2010), Li & Carthew (2005), Xu et al. (2007) mmu-miR-7b Arora et al. (2007), Georgi & Reh (2010), Li & Carthew (2005) mmu-miR-9 Georgi & Reh (2010), Hackler et al. (2010), Kapsimali et al. (2007), Karali et al. (2007), La Torre et al. (2013), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-miR-9∗ Georgi & Reh (2010), Hackler et al. (2010), Loscher et al. (2007), Shen et al. (2008), Xu et al. (2007) mmu-miR-93 Georgi & Reh (2010), Hackler et al. (2010) mmu-miR-96 Georgi & Reh (2010), Hackler et al. (2010), Jin et al. (2009), Kapsimali et al. (2007), Loscher et al. (2007), Loscher et al. (2008), Shen et al. (2008), Wohl & Reh (2016), Xu et al. (2007) mmu-miR-99b Xu et al. (2007), Hackler et al. (2010), Georgi & Reh (2010), Wohl & Reh (2016)

∗Denotes passenger strand.

Most of these studies have assayed miRNAs from total retinal samples, and so the miRNAs that are reported are likely expressed either in an abundant cell type, like photoreceptors or progenitor cells, or in multiple cell types. Some of the studies have documented differences between species that might be real developmental differences or, alternatively, may reﬂect relative differences in cell numbers. For example, mice have a relative abundance of photoreceptors compared with frogs, and so the miRNAs from the photoreceptor-expressed miR-182/183/96 cluster are more abundant in mouse retinas. Some of the most commonly reported miRNAs in developing retina are also present in other regions of the developing central nervous system (CNS), like let-7 family members, miR-9, and miR-125, but there are many miRNAs speciﬁcally expressed in developing retina (Figure 2). In addition, in several studies, it has been noted that miRNAs derived from a Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org

Access provided by University of Washington on 07/31/19. For personal use only. common genomic cluster tend to be coexpressed with similar developmental profiles. An example is the mouse miRNA cluster containing miR-106a, miR-130b, miR-17, miR-18a, miR-19a, miR- 20a, miR-20b, and miR-93; these were all reported to be expressed in embryonic mouse retina and coordinately regulated (Hackler et al. 2010). Localization of miRNAs to specific cell types has been evaluated using several different approaches. In situ hybridization has been carried out for some of the most abundant miRNAs and provides cellular resolution (Deo et al. 2006, Xu et al. 2007). A complementary approach using miRNA sensors has also been made for several miRNAs and again provides cellular resolution (La Torre et al. 2013). Both approaches show miR-183 expression in photoreceptors, for example. Laser capture microdissection (LCM) and fluorescence-activated cell sorting (FACS) have also been used to localize miRNA expression to specific cell types. LCM was used to localize miR-204 to the inner nuclear layer (Hackler et al. 2010), and this finding was confirmed and refined to show specific expression in the Muller¨ glia by FACS and NanoString analysis (Wohl &

www.annualreviews.org • MicroRNAs in Retinal Development 29 VS04CH02_Hindges ARI 14 August 2018 11:4

lt lt

5 5

1 1 18 18 15 1

Brain E15 Brain E15 Brain Adu Brain Adu E E E E E P1 E P1 P5 P1 P5 P12 P5 P12 Adult P12 Adult Adult Adult miR-34a miR-132 mmu-miR-103 miR-29c miR-29a mmu-miR-106a miR-24 miR-23b mmu-miR-106b miR-23a miR-22 mmu-miR-130a miR-29b miR-27b mmu-miR-130b miR-129-3p miR-27a miR-143 mmu-miR-135a miR-338-3p miRNAs common miR-138 to brain and retina mmu-miR-146b miR-127 miR-151-5p mmu-miR-153 miR-193 let-7e mmu-miR-15b miR-98 let-7d mmu-miR-17 let-7c let-7b mmu-miR-18a let-7a miR-136 mmu-miR-19a let-7i miR-124 miR-26a mmu-miR-19b miR-195 miR-148a mmu-miR-207 miR-140 miR-181a mmu-miR-20a miR-183* miRNAs specific miR-183 mmu-miR-20b miR-182 to mature retina miR-96 mmu-miR-212 miR-181b miR-210 mmu-miR-25 miR-204 miR-452 miR-713 mmu-miR-301a miR-33 miR-181a-1* mmu-miR-32 miR-542 miR-292-5p mmu-miR-489 miR-744 miR-689 mmu-miR-551b miR-290-5p miRNAs expressed Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org miR-15a in developing retina mmu-miR-689 Access provided by University of Washington on 07/31/19. For personal use only. miR-423-5p miR-320 mmu-miR-700 miR-677 miR-301a mmu-miR-92b miR-130b miR-374 miR-32 mmu-miR-93

Figure 2 (a) Comparison of brain and retinal miRNAs during development. Microarray study of the retina and brain to show common and unique microRNAs (miRNAs). Some miRNAs are present in neurons in both brain and retina and show increases from embryonic tissues to adult neural tissues. Many members of the let-7 family fall into this class. However, there are also miRNAs that are speciﬁc to retina either in adults (e.g., miR-183) or during development (miR-130b). (b) Some of the key miRNAs in developing retina include the miR-106b–93–25 and miR-17–18a–19a/b–20a–92 clusters that regulate mitotic proliferation in many tissues. Violet indicates high expression, while green indicates low levels of expression. Figure adapted from Hackler et al. (2010).

30 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

Reh 2016). A further approach to localize miRNAs has relied on analysis of miRNA expression after changes in retinal cellular composition: Georgi & Reh (2010) used a Notch inhibitor to force the differentiation of progenitor cells into neurons to identify progenitor-specific miRNAs, while Hackler et al. (2010) analyzed miRNAs in Nrl mutant mice to identify rod-specific miRNAs. The various approaches to localization of miRNAs have all provided information for some of the more abundant miRNAs, but for most of the miRNAs in the developing retina, we still do not know exactly which cells express them. However, recent advances in single-cell transcriptomics should provide a more complete picture of the miRNAs expressed in specific retinal cell populations during development.

3. DETERMINING THE FUNCTIONAL ROLE FOR miRNAs IN DEVELOPING RETINA: DICER DELETION One approach to determine the role of miRNAs in retinal development has been to target the enzymes required for miRNA processing (Figure 1). The most popular target to date has been Dicer, since knockout or knockdown of this enzyme will prevent mature miRNAs from being produced. Several studies in mice, zebrafish, and Xenopus frogs have examined the effects of Dicer deletion or knockdown in the developing retina (Akhtar et al. 2015, Damiani et al. 2008, Davis et al. 2011, Decembrini et al. 2009, Georgi & Reh 2010, Iida et al. 2011, La Torre et al. 2013, Maiorano & Hindges 2013, Pinter & Hindges 2010) (Table 2). Given the large numbers of miRNAs in the developing retina, diversity of cell types, and potentially very large number of targets for each miRNA, it is surprising that the retina develops as well as it does without functional Dicer. However, several clear phenotypes have emerged from these studies, highlighting those developmental processes that are most sensitive to a reduction in miRNA levels. Reduction in eye size and retinal cell number has been observed in nearly every study (Table 2). This is likely a consequence of increased cell death, as most studies have observed a higher rate of apopotosis. Several studies have specifically shown loss in retinal ganglion cells (RGCs), but other cell types also appear to be affected. A reduction in mitotic proliferation has also been noted in some studies, though this is variable and dependent on the specific line of Cre recombinase–expressing mice or knockdown strategy in other species. Other, more specific phenotypes have also been documented, particularly alterations in cell fate determination and axon guidance of RGC axons, and these are discussed below. Deletion of Dicer in mature cells has less dramatic immediate consequences; however, apoptosis is observed over a longer time course. Inhibition of miRNA production, specifically in photoreceptors with a rod-specific Dicer

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org conditional deletion, leads to rod cell death beginning around 8 weeks postnatal and causing a

Access provided by University of Washington on 07/31/19. For personal use only. near complete loss by 14 weeks (Sundermeier et al. 2014). Although the increase in apoptosis observed after Dicer deletion may be due to relatively nonspecific dysregulation of gene expression, which can trigger cell death pathways, there is also evidence for miRNAs being important regulators of apoptosis genes in the retina. Sanuki et al. (2011) generated a loss-of-function mouse mutant of miR-124a by targeted disruption of Rncr3, the transcript that produces miR-124a. Rncr3−/− mice had smaller brains and other abnormalities. In the retina, the cone photoreceptors were specifically affected and underwent cell death over several weeks. One target of miR-124a is Lhx2, and the increase in this gene in the Rncr3 knockout mouse cones was implicated in the observed cell death. However, deletion of specific miRNAs can also directly elicit apoptosis, suggesting that loss of Dicer may lead to a loss in miRNAs that specifically repress cell death pathways. Walker & Harland (2009) found, for example, that miR-24a represses apoptosis in the developing Xenopus retina; knockdown of miR-24a results in an increase in apoptosis, while proliferation and other developmental processes

www.annualreviews.org • MicroRNAs in Retinal Development 31 VS04CH02_Hindges ARI 14 August 2018 11:4

Table 2 Summary of Dicer deletion studiesa Aberrant retinal Study Deletion phenotype detected Proliferation changes Apoptosis changes Damiani et al. 2008 Chx10-Cre; Dicerfl/fl Rosettes/Retinal No change Pychnotic nuclei degeneration present Iida et al. 2011 Dkk3-Cre; Dicerfl/fl Brn3-positive RGCs PH3-positive cells Caspase-3 increase not increase unchanged quantified Decembrini et al. Dicer KO using Otx2 and Otx5b bipolar BrdU-positive cells TUNEL increase 2008 morpholino approach cells increase increase (Xenopus) Georgi & Reh 2010 Alpha-Pax6-Cre; Brn3-positive RGCs Slight decline in Caspase-3 increase Dicerfl/fl increase; bipolar cells, PH3-positive cells rods, and Muller¨ glia decrease Pinter & Hindges Rx-Cre; Dicerfl/fl Eye size decreases; RGC Proliferation not assayed Caspase-3 increase 2010 axon guidance problems Davis et al. 2011 Alpha-Pax6-Cre and Brn3-positive RGCs Ki67 not quantified Caspase-3 increase tryp2-Cre; Dicerfl/fl increase; amacrine, rods, and Muller¨ glia decrease Maiorano & Alpha-Pax6-Cre; Loss of all Dicer−/− Ki67 relative to Dicer+ Caspase-3 relative to + Hindges 2013 Dicerfl/fl RGCs by P8 retinal area assessed Dicer retinal area assessed Akhtar et al. 2015 Dicer mutation Small eye, lethal Proliferation not Cell death not assessed (zebrafish) assessed

aDeletion of Dicer leads to a variety of developmental defects depending on the method of knockout/knockdown and the species used in the study. Nearly all studies have reported some cell death and changes in the relative numbers of retinal cell types. Abbreviations: KO, knockout; RGC, retinal ganglion cell; TUNEL, terminal deoxynucleotidyl transferase dUTP nick end labeling.

were not affected. In addition, miR-24a directly represses translation of the proapoptotic factors Apaf1 and Caspase-9 via binding sites in their 3 UTRs. A role for miRNAs in speciﬁcally inhibiting cell death pathways was also elegantly demonstrated by Zhu et al. (2011). By creating a mouse model where a sponge for the photoreceptor-enriched miRNA cluster composed of miR-96, miR-182, and miR-183 is expressed under the opsin promoter, they found that the Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org

Access provided by University of Washington on 07/31/19. For personal use only. photoreceptors were more susceptible to light-damage-induced stress. In this case, Caspase-2 was normally targeted by these miRNAs, and this inhibition was blocked by the introduced sponge. The fact that particular miRNAs can affect apoptotic pathways may provide a way to reduce or delay degeneration of speciﬁc retinal cells in progressive degenerative diseases, such as glaucoma or retinitis pigmentosa, and the possibility of developing miRNA-based therapies for these diseases has been proposed (Sundermeier & Palczewski 2016).

4. ROLE OF miRNAs IN EARLY EYE DEVELOPMENT AND EYE-FIELD SPECIFICATION Although miRNAs have been shown to be important in a number of early developmental events in vertebrate embryos, most studies of miRNAs in the eye have been conducted after the period of eye- field specification. Nevertheless, there is evidence that miRNAs also play a role in the early events of eye morphogenesis. Knockdown of miR-204 in medaka fish causes microphthalmia, abnormal

32 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

lens development, and altered patterning of the retina along the dorsal-ventral axis (Conte et al. 2010). These phenotypes are mediated primarily by an increase in the expression of the Meis2 transcription factor. In addition, overexpression of a mutant form of miR-204 (associated with ocular coloboma) also results in microphthalmia in the fish (Conte et al. 2015). Pax6, an eye-field transcription factor, is also important in the regulation of expression of miR-204, which suppresses the neuronal gene Sox11 in the lens (Shaham et al. 2013). The network between miR-204, Pax6, and Meis2 is thus a critical link in the diversification and patterning of the ocular tissues early in development.

5. miRNAs AND DEVELOPMENTAL TIMING The various types of retinal neurons, and the Muller¨ glia, are generated by mitotically active cells, known as retinal progenitors (RPs). These cells are capable of many rounds of cell division and express many of the same transcription factors present in the eye-field cells, along with proneural and neural differentiation genes, such as Ascl1 and Neurog2. In all vertebrates, the RPs generate the various types of neurons in a relatively conserved sequence (Figure 3a). Ganglion cells, cone photoreceptors, and horizontal cells are “born” from RP cell divisions early in retinal development, whereas most amacrine cells, rod photoreceptors, bipolar cells, and Muller¨ glia are produced by the RPs in the second half of histogenesis (Livesey & Cepko 2001a, Reh & Cagan 1994). In mammals and birds, the RP cells can be further classified by differences in their expression of particular genes; for example, mouse progenitor cells present in early embryonic stages of retinal neurogenesis express Prtg, while RP cells from later embryonic stages and postnatal retina express Sox9 and Ascl1 (Brzezinski et al. 2011, Georgi & Reh 2010, La Torre et al. 2013, Livesey & Cepko 2001b). The so-called early retinal progenitors (ERPs) and late retinal progenitors (LRPs) can be further characterized by their response to mitogenic factors: ERPs do not respond to EGF (epidermal growth factor), while this is a potent mitogen for LRPs (Anchan et al. 1991, Lillien & Cepko 1992). The competence for production of different types of neurons also changes as the retina develops: Most of the rods, bipolar cells, and Muller¨ glia are produced by Ascl1-positive LRPs, but ERPs produce the RGCs (Brzezinski et al. 2011). A great deal has been learned over the past 25 years about the transcription factors that specify the various types of retinal neurons and the Muller¨ glia; however, the factors that define the temporal sequence of neuronal production are only beginning to be elucidated. The timing of events in retinal development is an example of a strict developmental sequence. Often, these sequences are controlled by a timing mechanism, and changes in that timing can produce very different phenotypic outcomes. The very different number of vertebrae in snakes Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org and birds is an example of where relatively small heterochronic changes in development (like the Access provided by University of Washington on 07/31/19. For personal use only. time it takes to make each somite) can dramatically affect the morphology of an animal (Keyte & Smith 2014). miRNAs have been associated with developmental timing since their discovery in Caenorhabditis elegans. In a series of remarkable publications, Ambros & Horvitz (1984) defined the heterochronic pathway in these simple organisms by screening for mutants that affected the pattern of postembryonic cell divisions in the seam cell lineages. Ambros and colleagues went on to identify the first miRNA, lin-4, as one of these key regulators of timing (Lee et al. 1993), and subsequently let-7 and lin-28 were discovered as part of this pathway (Moss et al. 1997, Wightman et al. 1993). These genes make up the core heterochronic pathway in C. elegans, and since these first components were identified, several additional proteins and miRNAs have been added to the pathway (Moss & Romer-Seibert 2014). In mice, normal developmental timing also requires miRNAs. In Dicer conditional knockout (CKO) mice, one of the most dramatic phenotypes is an inhibition of the normal change in competence of the RPs, from producing so-called early generated cell types, like RGCs, to

www.annualreviews.org • MicroRNAs in Retinal Development 33 VS04CH02_Hindges ARI 14 August 2018 11:4

CON AMA a RGC HOR ROD

BIP ERP LRP LRP MUL Dicer Ascl1+

E12 E14 E16 P2

bc Dicer+/– Dicer CKO E14 P1 let-7a Nbl miR-106b let-7f GCL Brn3 let-7c miR-720 let-7d miR-125b Nbl miR-9 let-7b GCL Ascl1 let-7g

d e Brn3mCherry Nrl-GFP mCherry Nbl

mCherry mCherry GCL RGCL

NBL Nbl LP-miRNAs Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org GCL

Access provided by University of Washington on 07/31/19. For personal use only. RGCL lin-28 OE/mCherry

miR-125 lin-28 let-7 miR-9 Prtg1

Development

(Caption appears on following page)

34 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

Figure 3 (Figure appears on preceding page) (a) Simpliﬁed model of retinal neurogenesis. An early retinal progenitor (ERP) that does not express Ascl1 generates retinal ganglion cells (RGCs) at early stages of embryonic development (E12), but as development proceeds, the ERP gives rise to late retinal progenitors (LRPs), which express Ascl1 and have the potential to generate the other types of retinal cells. Abbreviations: CON, cone photoreceptors; HOR, horizontal cells; AMA, amacrine cells; ROD, rod photoreceptors; BIP, bipolar cells; MUL, Muller¨ glia. (b) Conditional deletion of Dicer in mouse retina using the alpha-Pax6-Cre line prevents the transition from ERP to LRP cells, and as a result, Ascl1 is not expressed in the progenitors and they generate excess Brn3-positive ganglion cells [seen in the ganglion cell layer (GCL) and migrating in the neuroblastic layer (Nbl)]. Abbreviation: CKO, conditional knockout. (c) Heatmap of microRNA (miRNA) levels in mouse retina at two stages of development (red = high; green = low). Several miRNAs increase substantially in LRPs (P1), compared with ERPs (E14), including members of the let-7 family, miR-9, and miR-125b. (d)The RNA-binding protein lin-28 prevents the transition from ERP to LRP. Overexpression of the let-7 inhibitor, lin-28, in developing mouse retina phenocopies the Dicer conditional deletion, showing an increase in Brn3-positive ganglion cell production at an age when these cells are no longer produced in the wild-type mouse; mCherry is used to show the region of transfection in the control and lin-28-transfected retinas. Abbreviations: OE, overexpression; RGCL, retinal ganglion cell layer. (e) Overexpression of let-7, miR-125, and miR-9, collectively named LP-miRNAs, in early embryonic retina accelerates the transition of ERPs to LRPs, as shown by the early onset of Nrl-GFP-positive rod photoreceptors. mCherry is used to show the region of transfection. ( f ) Model of heterochronic gene regulation by miRNAs during retinal development. Many of these same molecules were discovered for their role in the regulation of developmental timing in Caenorhabditis elegans. Panels a–e modiﬁed from La Torre et al. (2013).

producing late fates, like glia and rod photoreceptors (Davis et al. 2011, Georgi & Reh 2010, La Torre et al. 2013). ERP markers (Prtg, Fgf15, lin-28) continue to be expressed into late embryonic and postnatal stages of retinal development, while LRP markers, like Ascl1 and Sox9, are never expressed by the RPs after Dicer deletion (Ascl1 in Figure 3b). Although Otx2-positive cells continue to be produced in the Dicer CKO mouse retina, they do not express markers of rods (rhodopsin) or bipolar cells. Instead, there is an overproduction of the ganglion cells, and this persists long past the normal developmental competence window for ganglion cell production (Brn3 in Figure 3b). La Torre et al. (2013) FACS purified the cells with Dicer deletion, since the Cre recombinase carried a reporter. They then carried out a study of the mRNAs most significantly affected by the loss of Dicer in developing retinal cells. They found that many of the genes normally in early born cell types and their progenitors, like Lgr5 and Onecut1, 2,and3, increased in the Dicer- negative cells, while genes associated with LRPs, like Fabp7, Ascl1,andSox9, were reduced in the cells, consistent with the immunolabeling results. One gene that was particularly increased was Prtg, a gene previously identified in early progenitors of the spinal cord. Further western Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org

Access provided by University of Washington on 07/31/19. For personal use only. blot and immunolabeling studies demonstrated that this gene is expressed in ERPs but absent in these cells in retina from later stages. Another gene of interest was lin-28, a core component of the C. elegans heterochronic pathway. The RNA-binding protein lin-28 interferes with the production of functional let-7 by binding the pre-miR form. In the developing retina, lin-28 is expressed with a similar time course and distribution as Prtg. To better understand how these genes were regulated by the loss in specific miRNAs caused by the Dicer deletion, the authors also profiled miRNAs in the developing retinas. They found a specific set of miRNAs that was more prominently expressed in P0 retina than in E14 retina (Figure 3c) and were able to determine which of these were expressed in progenitors by their response to forced differentiation by Notch inhibition. This allowed them to define a set of early- progenitor miRNAs and a set of LRP miRNAs (LRP-miRNAs). They found, using RT-PCR and miRNA sensors, that LRP-miRNAs increase in RPs over the transition from early to late stages of neurogenesis. They focused on members of the let-7 family, miR-9, and miR-125.

www.annualreviews.org • MicroRNAs in Retinal Development 35 VS04CH02_Hindges ARI 14 August 2018 11:4

Using an antagomir knockdown approach to test the function of LRP-miRNAs, the authors showed that knocking down just three miRNAs—let-7, miR-9, and miR-125—phenocopies the Dicer CKO. Further, overexpression of these three LRP-miRNAs as mature miRNA mimics in Dicer CKO retinas rescued the phenotype and allowed progenitors to adopt a late-progenitor pattern of gene expression (La Torre et al. 2013). Even more interesting, overexpression of LRP- miRNA mimics in wild-type retina can actually accelerate developmental timing in this system (Figure 3e). The authors also were able to show that both Prtg and lin-28 are targets of the LRP- miRNAs, accounting for their downregulation, as progenitors transition from the early to late state. Moreover, these two genes, when overexpressed, can also retard normal developmental timing in theretina(Figure 3d,f ). There is evidence that the components of the heterochronic pathway continue to regulate the timing of key events in maturation and even lifespan. For example, lin-4 mutants age at an increased rate, while lin-14 mutants age more slowly than wild-type animals (Boehm & Slack 2005, 2006). Both let-7b and let-7e are more highly expressed in old human skeletal muscle than in young muscle (Drummond et al. 2011). Genome-wide association studies have found that polymorphisms near the LIN28B locus are associated with precocious puberty in girls (He et al. 2009, Ong et al. 2009, Sulem et al. 2009). Thus, this fundamental biological timing pathway may be involved in other aspects of development, maturation, and aging (Moss & Romer-Seibert 2014). Studies in nonmammalian vertebrates provide further insight into the potential mechanisms by which miRNAs regulate developmental timing of cell differentiation. In Xenopus, knockdown of Dicer, using morpholios, produces defects in retinal lamination and cell cycle exit. The translation of Xotx5b and Xotx2, two transcription factors important for bipolar cell fate, is increased, though mRNA for these genes was not affected (Decembrini et al. 2009). By screening highly expressed, developmentally regulated miRNAs, researchers found that miR-129, miR-155, miR-214, and miR-222 target Xotx2 as well as Vsx1, another gene required for bipolar cells. Inactivation of these miRNAs with antisense oligonucleotides results in an increase in bipolar cells (Decembrini et al. 2009) similar to that observed in the Dicer knockdown. These researchers concluded that these speciﬁc miRNAs couple cell cycle exit with bipolar cell fate, as previous data showed a relation between cell cycle length and miRNA expression. It appears that a different set of miRNAs control developmental timing in mice and frogs, since the miRNAs in this study were different from those studied in developmental timing in mouse retina. Nevertheless, let-7c and miR-125b were also reported to be among the top miRNAs expressed in developing frog retina, so it is possible that similar mechanisms as those described in mice also regulate frog retinal development. Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org

Access provided by University of Washington on 07/31/19. For personal use only. 6. miRNA REGULATION OF NOTCH SIGNALING Notch is a key developmental regulator of retinal neurogenesis. In mice, both Notch1 and Notch3 are expressed by RPs. Several lines of evidence, from genetic to small molecule inhibitors, have shown that loss in Notch signaling leads to an increase in neurons at the expense of glia in the retina and elsewhere in the CNS. In addition, in the retina, both ERPs and LRPs require Notch; inhibition of Notch signaling at any stage of development produces characteristic phenotypes (Nelson et al. 2007, 2009). Loss of miRNAs in the Dicer CKO mouse retina leads to a reduction in expression in several components of the Notch signaling pathway by P0, including Hes5, the Notch ligand, Dll3, and Notch1 itself, leading to a generalized decrease in Notch signaling (Georgi & Reh 2011). The loss in Notch signaling does not appear to be responsible for the effects of Dicer deletion on progenitor competence, however, since this was not rescued by crossing the Dicer CKO mice with Notch– intracellular domain (ICD)-expressing mice. Although the Notch signaling defect was rescued in

36 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

these mice, the defect in gliogenesis was still present, and the normally late-generated cell types, like rods and bipolar cells, were still absent, while ganglion cells were still overproduced. These results suggest that Notch signaling is regulated by a different set of miRNAs than those that control progenitor competence. One potential mechanism by which miRNAs regulate Notch signaling comes from a study in zebrafish. Olena et al. (2015) surveyed developing zebrafish retina and found 12 miRNAs expressed at 2 days postfertilization (dpf ) and 23 miRNAs at 5 dpf. From in situ localization experiments, 3 miRNAs—miR-9, miR-124, and miR-216a—were expressed specifically in the developing eye. Overexpression of miR-216a led to retinal phenotypes consistent with reduced Notch signaling: a decrease in Muller¨ glia and an increase in photoreceptors (Olena et al. 2015). Although several components of the Notch pathway have miRNA recognition elements (MREs) for miR-216a, they focused on SNX5, a gene required for Delta endocytosis and Notch ICD internalization. Knockdown of miR-216a causes an increase in Muller¨ glial differentiation, with fewer photoreceptors, and this effect can be partly rescued by overexpression of SNX5. It is not known whether miR-216 plays a similar role in mice, and it is not highly expressed in developing mouse retina (Georgi & Reh 2010); however, another miRNA, miR-7a, may regulate Notch signaling in developing mouse RPs. Transfection of an miR-7a decoy causes a loss in Muller¨ glia, while overexpression of miR-7a causes an increase in these cells. This appears to be via a direct targeting of Notch 3 (Baba et al. 2015). It is unlikely that the reduction in Notch 3 accounts for the more general loss in Notch signaling observed in the Dicer CKO mouse, and thus it is likely that other miRNAs are normally important in regulating this very important developmental signal.

7. miRNAs AND ESTABLISHING VISUAL CONNECTIVITY Recent findings have shown that miRNAs play essential roles in the establishment of connectivity in the visual system. Although most of the data is relevant to axon guidance and synapse formation outside the retina per se, we discuss here some core findings concentrating on the vertebrate visual system. RGCs are the only neurons projecting out of the retina to form long-range connections with targets in the brain proper. On their journey, they encounter several choice points where they need to make pathfinding decisions in order to innervate the appropriate targets, including the optic chiasm at the midline (Erskine & Herrera 2014). The first indication that miRNAs impact long-range axon guidance decisions came from studies by Pinter & Hindges (2010), who used a conditional Dicer deletion approach in mice. To delete

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org Dicer from the developing retina, the authors used an Rx-Cre mouse line, where the Cre recombi-

Access provided by University of Washington on 07/31/19. For personal use only. nase is driven by promoter elements from the eye-field transcription factor retinal-homeobox gene Rx (Swindell et al. 2006). In mice, Rx is normally expressed from E7.5 onward in the anterior neural plate and becomes subsequently restricted to the retina and ventral forebrain by E10.5 (Mathers et al. 1997). The degree of visual overlap between the two eyes directly determines the magnitude of stereovision and is reflected in the relative proportions of ipsi- and contralaterally projecting axons at the optic chiasm (Herrera et al. 2003). In mice, with only a limited visual overlap, about 95% of all RGC axons cross the midline, whereas the remaining 5% stay ipsilaterally (Drager & Olsen 1980). Pinter & Hindges (2010) showed that upon deletion of Dicer, RGC axons exhibit a strong pathfinding phenotype at the optic chiasm, with many axons failing to cross the midline (Figure 4a). Instead, they either stayed ipsilaterally or extended aberrantly into the ventral di- encephalon (Pinter & Hindges 2010). Furthermore, a significant portion of axons was found to turn into the contralateral optic stalk and extend to the contralateral eye. The authors found that, in parallel with these projection errors, axons were generally defasciculated, not only within the

www.annualreviews.org • MicroRNAs in Retinal Development 37 VS04CH02_Hindges ARI 14 August 2018 11:4

Ipsilateral Contralateral optic tract optic tract 3 2

Optic chiasm 1 4

Lens

b miR-124 miR-204 miR-134 miR-182

Expression AAAA Lens Timing Branching RGC RGC Fasciculation RGC RGC Local translation

Figure 4 Roles of microRNAs during axon outgrowth. (a) Summary of phenotypes occurring in conditional Dicer mutant mice in combination with the Rx-Cre lines. In wild-type or heterozygous Dicer mutant mice (left), the neural retina encapsulates the lens, and retinal ganglion cell axons (red) extend toward the midline, forming the optic nerve. At the optic chiasm, most of the axons cross to the contralateral side (contralateral optic tract), whereas only 3–5% stay on the ipsilateral side (ipsilateral optic tract). The axons form tight fasciculated axon bundles at the point of crossing and when extending into the optic tracts. In homozygous Dicer mutants (right), four major defects are observed: () a small eye, with the lens being only about 50% encapsulated by the retina; () an increased ipsilateral projection; () ﬁbers extend further than the optic chiasm, and after crossing the midline, they form a parallel optic tract; and () a signiﬁcant proportion of axons extend aberrantly into the contralateral eye (adapted from Pinter & Hindges 2010). (b) Examples of individual miRNAs affecting the correct timing of axon guidance receptor expression at the growth cone, fasciculation, axon branching, and the local translation of messenger RNAs involved in axon guidance responses.

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org retina failing to form a tight optic fiber layer but also at the optic chiasm, leading to the forma- Access provided by University of Washington on 07/31/19. For personal use only. tion of a secondary optic tract on the contralateral side. Although this defasciculation phenotype points toward a cell-autonomous effect, the study could not clearly determine whether the axon pathfinding defects at the midline are based on altered sensitivity of the growing RGC axons or a change of the chiasm cells (or a combination of both) as the Rx promoter leads to Cre expression both in the retina and at the chiasm (Pinter and Hindges 2010). Rx-Cre+/Dicer mutant mice die at birth, which made it impossible to study the role of Dicer, and thus miRNAs, in the process of later axon targeting—for example, during the process of topographic mapping. In addition to studies eliminating most of the miRNAs through Dicer deletions, more recent studies have identified the roles of individual miRNAs to control the process of retinal axon outgrowth and targeting. In Xenopus, miR-124 was shown to control the precise timing of sensitivity of RGC growth cones to Sema3A during the formation of the visual projections (Baudet et al. 2011) (Figure 4b). The authors showed that a knockdown of miR-124 leads to the

38 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

downregulation of the Sema3A receptor neuropilin1. This is achieved indirectly through coR- EST, which was identified as a novel miR-204 target that controls Nrp1 expression. A different study identified possible targets of miR-204, which has important function during eye development, using an RNA sequencing approach upon overexpression and knockdown of this miRNA (Conte et al. 2014). The resulting list contains a substantial number of molecules associated with axon guidance, including Eph receptors and their ephrin ligands (Reber et al. 2007). Knockdown of miR-204 in medaka resulted in defasciculation of RGC axons as well as aberrant growth into different retinal layers and mistargeting along the optic pathways (Conte et al. 2014) (Figure 4b). These defects were rescued by the knockdown of either EphB2 or ephrin-B3, suggesting that the regulation of these molecules through miR-204 is critical for the correct axon pathfinding of RGC axons. These studies demonstrate nicely the intricate network of factors that are controlled by individual microRNAs to ensure the correct spatiotemporal presence of axon guidance cues needed to form a fully functioning visual system. Once RGC axons have reached the target area, a multistep process, including axon branching, remodeling, and synapse formation, takes place to finally form the appropriate connections (Hindges et al. 2002). An important regulator of RGC axon branching is brain-derived neu- rotrophic factor (BDNF)/TrkB signaling (Feldheim & O’Leary 2010). Consistent with a role of microRNAs in this process, Marler et al. (2008) showed that BDNF-induced branching is dependent on the presence of miR-132 (Figure 4b). Here, the authors demonstrate that in both the mouse and the chick, miR-132 is highly expressed in RGCs during the developmental window when RGC axons grow into their targeting area and refine their termination zones through branching and synaptogenesis (Hindges et al. 2002, Yates et al. 2001). Overexpression of miR- 134 leads to increase of branching, while a knockdown decreases BDNF-mediated branching. This process is achieved through the interaction of miR-134 with its target Rho family GTPase- activating protein p250GAP, an inhibitor of Rac, which in turn is a branch-promoting protein. During the refinement phase of RGC axon mapping, BDNF in the target induces the expression of miR-132, which then leads to a reduction of p250GAP levels and thus increase of branching activity through activation of Rac (Marler et al. 2008). This interaction of miR-132 with p250GAP was also shown in different contexts—for example, in dorsal root ganglion axons, where it promotes axon extension (Hancock et al. 2014). An important mechanism of axon guidance, branching, and target selection is the local translation of mRNAs (Jung et al. 2014, Shigeoka et al. 2016). Interestingly, several screens using different neuronal populations have shown that miRNAs are not restricted to the cell soma and that they are also found in axons (Natera-Naranjo et al. 2010, Sasaki et al. 2014), in combination

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org with the presence of RISC (Hengst et al. 2006). This suggested a possible role of miRNAs in

Access provided by University of Washington on 07/31/19. For personal use only. controlling the levels of locally translated proteins. Indeed, a recent profiling study in growing Xenopus RGC axons identified a number of miRNAs present in axons and even the growth cone, with miR-182 being the most abundant axonal miRNA (Bellon et al. 2017). Using a loss of function approach, the authors could show that miR-182 is important for the appropriate targeting of RGC axons in the optic tectum. Further experiments revealed that this change in targeting precision was dependent on the action of Slit2. The authors found that miR-182 regulates the responsiveness of growth cones to Slit2 through controlling the local translation of cofilin 1 (Cfl1), an important regulator of the cytoskeleton. In normal conditions, miR-182 binds to the 3 UTR of Cfl1 and represses its local translation. However, upon Slit2 stimulation (through its receptors Robo2 and Robo3), the miR-182 repression is released and allows the production of Cfl1 and thus the necessary cytoskeletal changes for a growth- cone repulsive response. Interestingly, this mechanism of modulating growth-cone responsiveness seems to be very specific, as the sensitivity to a different repulsive cue, Sema3A, was unchanged

www.annualreviews.org • MicroRNAs in Retinal Development 39 VS04CH02_Hindges ARI 14 August 2018 11:4

(Bellon et al. 2017). This suggests an even more intricate system to activate and modulate the responses of growth cones to external signals through miRNAs. In addition to the ﬁndings about miRNAs during axon guidance/targeting discussed here, there are a number of studies from outside the visual system showing the involvement of miRNAs in this process (Iyer et al. 2014). Similarly, miRNAs have also been found to control further steps during the establishment of neural circuits, including dendritogenesis and synapse formation (Rajman & Schratt 2017), and it is very likely that this also includes these processes within the retina or along the visual pathway.

8. CONCLUSIONS Posttranscriptional regulatory mechanisms play an important role during the development and functional assembly of the retina. This includes the action of miRNAs found to be expressed at different stages of eye development. Although much progress has been made to unravel their functions, one particular difficulty has been that most of these noncoding molecules are more likely acting to fine-tune the protein output of a cell as compared to leading to a complete switch (with some exceptions). In addition, the fact that many miRNAs act in combination with each other to bind individual target mRNAs demonstrates the necessity to understand their role in a combinatory fashion. Nevertheless, recent experimental advances—for example, multiplex gene targeting or simple base editing using CRISPR/Cas (clustered regularly interspaced short palin- dromic repeats/CRISPR-associated proteins) approaches, together with the progress in single-cell sequencing and proteomics—will certainly be helpful to the field and efforts to identify the function of miRNAs in the eye in much more detail.

SUMMARY POINTS 1. MicroRNAs (miRNAs) are critical for controlling key developmental timing events in the developing retina, such as the sequential generation of speciﬁc cell fates. 2. Some of the components of the well-characterized heterochronic pathway of miRNAs and RNA-binding proteins are also important regulators of developmental timing in mouse retinal neurogenesis, showing the deep conservation of this early role. 3. miRNAs play important roles at various steps during the establishment of visual system connectivity. Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org Access provided by University of Washington on 07/31/19. For personal use only.

FUTURE ISSUES 1. Cell-type-speciﬁc deletions of Dicer or other genes necessary for microRNA (miRNA) processing have the potential to reveal other developmental requirements for these regulators in neurons and glia. 2. Single-cell analyses of miRNA expression in the eye have the potential to reveal possible roles in the generation of retinal cell subtypes. 3. Little is known about the role of miRNAs in regulating synaptogenesis in the retina. Given the evidence for miRNA regulation in synaptogenesis in other systems, it would be very interesting to assess this, particularly for the formation of speciﬁc visual circuits.

40 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

DISCLOSURE STATEMENT The authors are not aware of any afﬁliations, memberships, funding, or ﬁnancial holdings that might be perceived as affecting the objectivity of this review.

ACKNOWLEDGMENTS Work in the authors’ laboratories is supported by a National Eye Institute grant (NEI R01EY021482 to T.A.R.), the Foundation Fighting Blindness (TA-RM-0614–0650-UWA to T.A.R.), the Paul G. Allen Family Foundation (Frontiers Program to T.A.R.), the Medical Re- search Council (G0601182 to R.H.), the Wellcome Trust (087883/Z/08/Z to R.H.), and the Biotechnology and Biological Sciences Research Council (BB/M000664/1 to R.H.).

LITERATURE CITED Akhtar S, Patnaik SR, Kotapati Raghupathy R, Al-Mubrad TM, Craft JA, Shu X. 2015. Histological characterization of the Dicer1 mutant zebrafish retina. J. Ophthalmol. 2015:309510 Ambros V, Horvitz HR. 1984. Heterochronic mutants of the nematode Caenorhabditis elegans. Science 226:409– 16 Anchan RM, Reh TA, Angello J, Balliet A, Walker M. 1991. EGF and TGF-αstimulate retinal neuroepithelial cell proliferation in vitro. Neuron 6:923–36 Arora A, Guduric-Fuchs J, Harwood L, Dellett M, Cogliati T, Simpson DA. 2010. Prediction of microRNAs affecting mRNA expression during retinal development. BMC Dev. Biol. 10:1 Arora A, McKay GJ, Simpson DA. 2007. Prediction and verification of miRNA expression in human and rat retinas. Investig. Ophthalmol. Vis. Sci. 48:3962–67 Baba Y, Aihara Y, Watanabe S. 2015. MicroRNA-7a regulates Muller¨ glia differentiation by attenuating Notch3 expression. Exp. Eye Res. 138:59–65 Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli AE. 2005. Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell 122:553–63 Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–97 Baudet ML, Zivraj KH, Abreu-Goodger C, Muldal A, Armisen J, et al. 2011. miR-124 acts through CoREST to control onset of Sema3A sensitivity in navigating retinal growth cones. Nat. Neurosci. 15:29–38 Bellon A, Iyer A, Bridi S, Lee FCY, Ovando-Vazquez´ C, et al. 2017. miR-182 regulates Slit2-mediated axon guidance by modulating the local translation of a specific mRNA. Cell Rep. 18:1171–86 Boehm M, Slack F. 2005. A developmental timing microRNA and its target regulate life span in C. elegans. Science 310:1954–57 Boehm M, Slack FJ. 2006. MicroRNA control of lifespan and metabolism. Cell Cycle 5:837–40

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org Brzezinski JAT, Kim EJ, Johnson JE, Reh TA. 2011. Ascl1 expression defines a subpopulation of lineage- Access provided by University of Washington on 07/31/19. For personal use only. restricted progenitors in the mammalian retina. Development 138:3519–31 Chi SW, Zang JB, Mele A, Darnell RB. 2009. Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps. Nature 460:479–86 Conte I, Carrella S, Avellino R, Karali M, Marco-Ferreres R, et al. 2010. miR-204 is required for lens and retinal development via Meis2 targeting. PNAS 107:15491–96 Conte I, Hadfield KD, Barbato S, Carrella S, Pizzo M, et al. 2015. MiR-204 is responsible for inherited retinal dystrophy associated with ocular coloboma. PNAS 112:E3236–45 Conte I, Merella S, Garcia-Manteiga JM, Migliore C, Lazarevic D, et al. 2014. The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance. Nucleic Acids Res. 42:7793–806 Damiani D, Alexander JJ, O’Rourke JR, McManus M, Jadhav AP, et al. 2008. Dicer inactivation leads to progressive functional and structural degeneration of the mouse retina. J. Neurosci. 28:4878–87 Davis N, Mor E, Ashery-Padan R. 2011. Roles for Dicer1 in the patterning and differentiation of the optic cup neuroepithelium. Development 138:127–38

www.annualreviews.org • MicroRNAs in Retinal Development 41 VS04CH02_Hindges ARI 14 August 2018 11:4

Decembrini S, Bressan D, Vignali R, Pitto L, Mariotti S, et al. 2009. MicroRNAs couple cell fate and developmental timing in retina. PNAS 106:21179–84 Deo M, Yu J-Y, Chung K-H, Tippens M, Turner DL. 2006. Detection of mammalian microRNA expression by in situ hybridization with RNA oligonucleotides. Dev. Dyn. 235:2538–48 Drager UC, Olsen JF. 1980. Origins of crossed and uncrossed retinal projections in pigmented and albino mice. J. Comp. Neurol. 191:383–412 Drummond MJ, McCarthy JJ, Sinha M, Spratt HM, Volpi E, et al. 2011. Aging and microRNA expression in human skeletal muscle: a microarray and bioinformatics analysis. Physiol. Genom. 43:595–603 Eichhorn SW, Guo H, McGeary SE, Rodriguez-Mias RA, Shin C, et al. 2014. mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol. Cell 56:104–15 Erskine L, Herrera E. 2014. Connecting the retina to the brain. ASN Neuro 6:1759091414562107 Feldheim DA, O’Leary DD. 2010. Visual map development: bidirectional signaling, bifunctional guidance molecules, and competition. Cold Spring Harb. Perspect. Biol. 2:a001768 Georgi SA, Reh TA. 2010. Dicer is required for the transition from early to late progenitor state in the developing mouse retina. J. Neurosci. 30:4048–61 Georgi SA, Reh TA. 2011. Dicer is required for the maintenance of notch signaling and gliogenic competence during mouse retinal development. Dev. Neurobiol. 71:1153–69 Ha M, Kim VN. 2014. Regulation of microRNA biogenesis. Nat. Rev. Mol. Cell Biol. 15:509–24 Hackler L Jr., Wan J, Swaroop A, Qian J, Zack DJ. 2010. MicroRNA proﬁle of the developing mouse retina. Investig. Ophthalmol. Vis. Sci. 51:1823–31 Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, et al. 2010. Transcriptome-wide identiﬁcation of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141:129–41 Hancock ML, Preitner N, Quan J, Flanagan JG. 2014. MicroRNA-132 is enriched in developing axons, locally regulates Rasa1 mRNA, and promotes axon extension. J. Neurosci. 34:66–78 He C, Kraft P, Chen C, Buring JE, Pare´ G, et al. 2009. Genome-wide association studies identify loci associated with age at menarche and age at natural menopause. Nat. Genet. 41:724–28 Helwak A, Kudla G, Dudnakova T, Tollervey D. 2013. Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153:654–65 Hengst U, Cox LJ, Macosko EZ, Jaffrey SR. 2006. Functional and selective RNA interference in developing axons and growth cones. J. Neurosci. 26:5727–32 Herrera E, Brown L, Aruga J, Rachel RA, Dolen G, et al. 2003. Zic2 patterns binocular vision by specifying the uncrossed retinal projection. Cell 114:545–57 Hindges R, McLaughlin T, Genoud N, Henkemeyer M, O’Leary DD. 2002. EphB forward signaling controls directional branch extension and arborization required for dorsal-ventral retinotopic mapping. Neuron 35:475–87 Iida A, Shinoe T, Baba Y, Mano H, Watanabe S. 2011. Dicer plays essential roles for retinal development by regulation of survival and differentiation. Investig. Ophthalmol. Vis. Sci. 52:3008–17 Iyer AN, Bellon A, Baudet M-L. 2014. microRNAs in axon guidance. Front. Cell Neurosci.8:78

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org Jin ZB, Hirokawa G, Gui L, Takahashi R, Osakada F, et al. 2009. Targeted deletion of miR-182, an abundant Access provided by University of Washington on 07/31/19. For personal use only. retinal microRNA. Mol. Vis. 15:523–33 Jung H, Gkogkas CG, Sonenberg N, Holt CE. 2014. Remote control of gene function by local translation. Cell 157:26–40 Kapsimali M, Kloosterman WP, de Bruijn E, Rosa F, Plasterk RH, Wilson SW. 2007. MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system. Genome Biol. 8:R173 Karali M, Peluso I, Gennarino VA, Bilio M, Verde R, et al. 2010. miRNeye: a microRNA expression atlas of the mouse eye. BMC Genom. 11:715 Karali M, Peluso I, Marigo V, Banfi S. 2007. Identification and characterization of microRNAs expressed in the mouse eye. Investig. Ophthalmol. Vis. Sci. 48:509–15 Keyte AL, Smith KK. 2014. Heterochrony and developmental timing mechanisms: changing ontogenies in evolution. Semin. Cell Dev. Biol. 34:99–107 La Torre A, Georgi S, Reh TA. 2013. Conserved microRNA pathway regulates developmental timing of retinal neurogenesis. PNAS 110:E2362–70

42 Reh · Hindges VS04CH02_Hindges ARI 14 August 2018 11:4

Lee RC, Feinbaum RL, Ambros V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–54 Li X, Carthew RW. 2005. A microRNA mediates EGF receptor signaling and promotes photoreceptor differentiation in the Drosophila eye. Cell 123:1267–77 Lillien L, Cepko C. 1992. Control of proliferation in the retina: temporal changes in responsiveness to FGF and TGFα. Development 115:253–66 Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, et al. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769–73 Livesey FJ, Cepko CL. 2001a. Vertebrate neural cell-fate determination: lessons from the retina. Nat. Rev. Neurosci. 2:109–18 Livesey R, Cepko C. 2001b. Neurobiology: developing order. Nature 413:471–73 Loscher CJ, Hokamp K, Kenna PF, Ivens AC, Humphries P, et al. 2007. Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa. Genome Biol. 8:R248 Loscher CJ, Hokamp K, Wilson JH, Li T, Humphries P, et al. 2008. A common microRNA signature in mouse models of retinal degeneration. Exp. Eye Res. 87:529–34 Maiorano NA, Hindges R. 2013. Restricted perinatal retinal degeneration induces retina reshaping and cor- related structural rearrangement of the retinotopic map. Nat. Commun. 4:1938 Makarev E, Spence JR, Del Rio-Tsonis K, Tsonis PA. 2006. Identification of microRNAs and other small RNAs from the adult newt eye. Mol. Vis. 12:1386–91 Marler KJ, Becker-Barroso E, Martinez A, Llovera M, Wentzel C, et al. 2008. A TrkB/EphrinA interaction controls retinal axon branching and synaptogenesis. J. Neurosci. 28:12700–12 Mathers PH, Grinberg A, Mahon KA, Jamrich M. 1997. The Rx homeobox gene is essential for vertebrate eye development. Nature 387:603–7 Moore MJ, Scheel TK, Luna JM, Park CY, Fak JJ, et al. 2015. miRNA–target chimeras reveal miRNA 3 -end pairing as a major determinant of Argonaute target specificity. Nat. Commun. 6:8864 Moss EG, Lee RC, Ambros V. 1997. The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA. Cell 88:637–46 Moss EG, Romer-Seibert J. 2014. Cell-intrinsic timing in animal development. Wiley Interdiscip. Rev. Dev. Biol. 3:365–77 Natera-Naranjo O, Aschrafi A, Gioio AE, Kaplan BB. 2010. Identification and quantitative analyses of micro- RNAs located in the distal axons of sympathetic neurons. RNA 16:1516–29 Nelson BR, Hartman BH, Georgi SA, Lan MS, Reh TA. 2007. Transient inactivation of Notch signaling synchronizes differentiation of neural progenitor cells. Dev. Biol. 304:479–98 Nelson BR, Hartman BH, Ray CA, Hayashi T, Bermingham-McDonogh O, Reh TA. 2009. Acheate-scute like 1 (Ascl1) is required for normal Delta-like (Dll) gene expression and Notch signaling during retinal development. Dev. Dyn. 238:2163–78 Olena AF, Rao MB, Thatcher EJ, Wu SY, Patton JG. 2015. miR-216a regulates snx5, a novel notch signaling

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org pathway component, during zebraﬁsh retinal development. Dev. Biol. 400:72–81

Access provided by University of Washington on 07/31/19. For personal use only. Olsen PH, Ambros V. 1999. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216:671–80 Ong KK, Elks CE, Li S, Zhao JH, Luan J, et al. 2009. Genetic variation in LIN28B is associated with the timing of puberty. Nat. Genet. 41:729–33 Pinter R, Hindges R. 2010. Perturbations of microRNA function in mouse dicer mutants produce retinal defects and lead to aberrant axon pathfinding at the optic chiasm. PLOS ONE 5:e10021 Rajman M, Schratt G. 2017. MicroRNAs in neural development: from master regulators to fine-tuners. Development 144:2310–22 Reber M, Hindges R, Lemke G. 2007. Eph receptors and ephrin ligands in axon guidance. Adv. Exp. Med. Biol. 621:32–49 Reh TA, Cagan RL. 1994. Intrinsic and extrinsic signals in the developing vertebrate and fly eyes: viewing vertebrate and invertebrate eyes in the same light. Perspect. Dev. Neurobiol. 2:183–90 Ryan DG, Oliveira-Fernandes M, Lavker RM. 2006. MicroRNAs of the mammalian eye display distinct and overlapping tissue specificity. Mol. Vis. 12:1175–84

www.annualreviews.org • MicroRNAs in Retinal Development 43 VS04CH02_Hindges ARI 14 August 2018 11:4

Sanuki R, Onishi A, Koike C, Muramatsu R, Watanabe S, et al. 2011. miR-124a is required for hippocampal axogenesis and retinal cone survival through Lhx2 suppression. Nat. Neurosci. 14:1125–34 Sasaki Y, Gross C, Xing L, Goshima Y, Bassell GJ. 2014. Identification of axon-enriched microRNAs localized to growth cones of cortical neurons. Dev. Neurobiol. 74:397–406 Shaham O, Gueta K, Mor E, Oren-Giladi P, Grinberg D, et al. 2013. Pax6 regulates gene expression in the vertebrate lens through miR-204. PLOS Genet. 9:e1003357 Shen J, Yang X, Xie B, Chen Y, Swaim M, et al. 2008. MicroRNAs regulate ocular neovascularization. Mol. Ther. 16:1208–16 Shi L, Ko ML, Ko GY-P. 2009. Rhythmic expression of microRNA-26a regulates the L-type voltage-gated calcium channel α1C subunit in chicken cone photoreceptors. J. Biol. Chem. 284:25791–803 Shigeoka T, Jung H, Jung J, Turner-Bridger B, Ohk J, et al. 2016. Dynamic axonal translation in developing and mature visual circuits. Cell 166:181–92 Sulem P, Gudbjartsson DF, Rafnar T, Holm H, Olafsdottir EJ, et al. 2009. Genome-wide association study identifies sequence variants on 6q21 associated with age at menarche. Nat. Genet. 41:734–38 Sundermeier TR, Palczewski K. 2016. The impact of microRNA gene regulation on the survival and function of mature cell types in the eye. FASEB J. 30:23–33 Sundermeier TR, Zhang N, Vinberg F, Mustafi D, Kohno H, et al. 2014. DICER1 is essential for survival of postmitotic rod photoreceptor cells in mice. FASEB J. 28:3780–91 Swindell EC, Bailey TJ, Loosli F, Liu C, Amaya-Manzanares F, et al. 2006. Rx-Cre, a tool for inactivation of gene expression in the developing retina. Genesis 44:361–63 Walker JC, Harland RM. 2009. microRNA-24a is required to repress apoptosis in the developing neural retina. Genes Dev. 23:1046–51 Wightman B, Ha I, Ruvkun G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75:855–62 Wohl SG, Reh TA. 2016. The microRNA expression profile of mouse Muller¨ glia in vivo and in vitro. Sci. Rep. 6:35423 Xu S, Witmer PD, Lumayag S, Kovacs B, Valle D. 2007. MicroRNA (miRNA) transcriptome of mouse retina and identification of a sensory organ-specific miRNA cluster. J. Biol. Chem. 282:25053–66 Yates PA, Roskies AL, McLaughlin T, O’Leary DD. 2001. Topographic-specific axon branching controlled by ephrin-As is the critical event in retinotectal map development. J. Neurosci. 21:8548–63 Zhu Q, Sun W, Okano K, Chen Y, Zhang N, et al. 2011. Sponge transgenic mouse model reveals important roles for the microRNA-183 (miR-183)/96/182 cluster in postmitotic photoreceptors of the retina. J. Biol. Chem. 286:31749–60 Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org Access provided by University of Washington on 07/31/19. For personal use only.

44 Reh · Hindges VS04_TOC ARI 21 August 2018 11:58

Annual Review of Vision Science Contents Volume 4, 2018

A Life in Vision John E. Dowling pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp1 MicroRNAs in Retinal Development Thomas A. Reh and Robert Hindges pppppppppppppppppppppppppppppppppppppppppppppppppppppppppp25 Microglia in the Retina: Roles in Development, Maturity, and Disease Sean M. Silverman and Wai T. Wong pppppppppppppppppppppppppppppppppppppppppppppppppppppp45 Plasticity of Retinal Gap Junctions: Roles in Synaptic Physiology and Disease John O’Brien and Stewart A. Bloomﬁeld pppppppppppppppppppppppppppppppppppppppppppppppppppp79 Retinal Vasculature in Development and Diseases Ye Sun and Lois E.H. Smith ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp101 Parallel Processing of Rod and Cone Signals: Retinal Function and Human Perception William N. Grimes, Adree Songco-Aguas, and Fred Rieke ppppppppppppppppppppppppppppppp123 Elementary Motion Detection in Drosophila: Algorithms and Mechanisms Helen H. Yang and Thomas R. Clandinin ppppppppppppppppppppppppppppppppppppppppppppppppp143 Neural Mechanisms of Motion Processing in the Mammalian Retina Wei Wei ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp165

Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org Vision During Saccadic Eye Movements Access provided by University of Washington on 07/31/19. For personal use only. Paola Binda and Maria Concetta Morrone pppppppppppppppppppppppppppppppppppppppppppppppp193 Corollary Discharge Contributions to Perceptual Continuity Across Saccades Robert H. Wurtz pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp215 Visual Function, Organization, and Development of the Mouse Superior Colliculus Jianhua Cang, Elise Savier, Jad Barchini, and Xiaorong Liu pppppppppppppppppppppppppppp239 Thalamocortical Circuits and Functional Architecture Jens Kremkow and Jose-Manuel Alonso pppppppppppppppppppppppppppppppppppppppppppppppppppp263 VS04_TOC ARI 21 August 2018 11:58

Linking V1 Activity to Behavior Eyal Seidemann and Wilson S. Geisler pppppppppppppppppppppppppppppppppppppppppppppppppppp287 A Tale of Two Visual Systems: Invariant and Adaptive Visual Information Representations in the Primate Brain Yaoda Xu ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp311 Blindness and Human Brain Plasticity Ione Fine and Ji-Min Park ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp337 How Visual Cortical Organization Is Altered by Ophthalmologic and Neurologic Disorders Serge O. Dumoulin and Tomas Knapen ppppppppppppppppppppppppppppppppppppppppppppppppppp357 The Organization and Operation of Inferior Temporal Cortex Bevil R. Conway ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp381 Invariant Recognition Shapes Neural Representations of Visual Input Andrea Tacchetti, Leyla Isik, and Tomaso A. Poggio pppppppppppppppppppppppppppppppppppppp403 Shape from Contour: Computation and Representation James Elder pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp423 Geometry of Pictorial Relief Jan J. Koenderink, Andrea J. van Doorn, and Johan Wagemans ppppppppppppppppppppppp451 Color Perception: Objects, Constancy, and Categories Christoph Witzel and Karl R. Gegenfurtner pppppppppppppppppppppppppppppppppppppppppppppp475 Motion Perception: From Detection to Interpretation Shin’ya Nishida, Takahiro Kawabe, Masataka Sawayama, and Taiki Fukiage pppppppp501

Errata An online log of corrections to Annual Review of Vision Science articles may be found at http://www.annualreviews.org/errata/vision Annu. Rev. Vis. Sci. 2018.4:25-44. Downloaded from www.annualreviews.org Access provided by University of Washington on 07/31/19. For personal use only.