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In Vivo Atoh1 Targetome Reveals How a Proneural Transcription Factor Regulates Cerebellar Development

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In Vivo Atoh1 Targetome Reveals How a Proneural Transcription Factor Regulates Cerebellar Development In vivo Atoh1 targetome reveals how a proneural transcription factor regulates cerebellar development Tiemo J. Klischa,b,c,1, Yuanxin Xid,1, Adriano Floraa,c, Liguo Wangd, Wei Lid,2, and Huda Y. Zoghbia,b,c,e,2 aDepartment of Molecular and Human Genetics, bThe Howard Hughes Medical Institute, dDivision of Biostatistics, The Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, and eDepartments of Neuroscience and Pediatrics, and Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030; and cThe Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX 77030 Contributed by Huda Y. Zoghbi, January 5, 2011 (sent for review November 16, 2010) The proneural, basic helix–loop–helix transcription factor Atoh1 later CGPs (around P5) are already committed (23). Atoh1 is governs the development of numerous key neuronal subtypes, expressed in the proliferating CGPs at both times, providing an such as cerebellar granule and brainstem neurons, inner ear hair ideal opportunity to study its various functions. cells, and several neurons of the proprioceptive system, as well as We took a three-pronged approach to define Atoh1 targets. diverse nonneuronal cell types, such as Merkel cells and intestinal First, we determined an Atoh1 DNA-binding signature by iden- secretory lineages. However, the mere handful of targets that have tifying genomic Atoh1 binding sites with in vivo ChIP using the been identified barely begin to account for Atoh1’s astonishing Atoh1 FLAG-tagged knock-in mouse model (17). Second, we range of functions, which also encompasses seemingly paradoxical generated a CGP chromatin signature by identifying the global activities, such as promoting cell proliferation and medulloblas- histone H3 lysine 4 methylation status (Histone-seq). Third, we toma formation in the cerebellum and inducing cell cycle exit and established an Atoh1 expression signature in CGPs by mapping suppressing tumorigenesis in the intestine. We used a multipronged gene expression differences between WT and Atoh1-null cere- approach to create a comprehensive, unbiased list of over 600 direct bellar tissue (RNA-seq). Analysis of these results identified Atoh1 target genes in the postnatal cerebellum. We found that hundreds of Atoh1 targets. By analyzing this Atoh1 “targetome,” Atoh1 binds to a 10 nucleotide motif (AtEAM) to directly regulate we found that Atoh1’s function in CGP development is much genes involved in migration, cell adhesion, metabolism, and other broader than anticipated. previously unsuspected functions. This study expands current thinking about the transcriptional activities driving neuronal dif- Results ferentiation and provides a framework for further neurodevelop- We took advantage of the Atoh1-floxed conditional knockout mental studies. mouse model (24), as well as a hormonally inducible CrePR allele knocked into the Atoh1 locus (Atoh1CrePR) that has a re- transcriptional regulation | chromatin immunoprecipitation | deep stricted and low recombination activity in CGPs (25). This mouse sequencing | E-box motif model enables us to delete Atoh1 specifically in the cycling progenitors of the outer external granule layer (EGL). We fl roneural transcription factors play a key role in the specifi- crossed Atoh1CrePR/ ox mice with mice carrying the Cre-inducible Pcation of a multitude of neural progenitors in the developing YFP gene in the Rosa locus (R26YFP) (26). After activation of fl brain. Several studies have suggested that the dozen or so pro- Cre by RU486, specific cells in RosaYFP/YFP;Atoh1CrePR/ ox ani- Δ neural genes, which encode a family of closely related basic mals (designated here as Atoh1 ) lose Atoh1 expression and turn helix–loop–helix (bHLH) transcription factors (1), are able to be on the reporter gene. We deleted Atoh1 either at P0 or P5 and responsible for such protean developmental programs by acti- used the inward migration of differentiating CGPs as a read-out vating “secondary” transcription factors, which over time induce for differentiation (27). Twenty-four hours after Cre recom- effector genes (2, 3). Unfortunately, it has been difficult to bination, we collected the tissue and counted YFP+ cells with identify the direct target genes of these proneural factors, which respect to their position to the cerebellar surface. YFP+ cells can exert an impressive range of effects. located in the EGL were classified as undifferentiated, and For example, Atoh1, the mouse homolog of Drosophila atonal YFP+ cells in the internal granule layer (IGL) were classified as (4, 5), governs the differentiation of key populations of the ner- differentiated (Fig. 1). After Atoh1 deletion at P0, a large vous system (cerebellar granule and brainstem neurons, inner ear number of cells remained undifferentiated (Fig. 1A); Atoh1 de- hair cells, and numerous components of the proprioceptive and letion at P5 had less effect on differentiation, as most Atoh1-null interoceptive systems) (6–10), as well as diverse nonneuronal cell cells migrated into the IGL (Fig. 1B). types (e.g., Merkel cells and intestinal secretory lineages) (11–14). To quantify the data, we generated a differentiation index by Although studies based on candidate gene approaches have calculating the ratio of cells located in the IGL relative to the revealed a few putative targets of Atoh1 (10, 15–18), this handful EGL. The differentiation index at P0 was much lower than at P5, of targets barely begins to account for this astonishing range of suggesting that at an early time point many cells require Atoh1 to functions, which encompasses seemingly paradoxical activities, such as promoting cell proliferation (and medulloblastoma) in the cerebellum and promoting cell cycle exit and suppressing Author contributions: T.J.K., W.L., and H.Y.Z. designed research; T.J.K. and A.F. performed tumorigenesis in the intestine (17, 19, 20). research; Y.X., L.W., and W.L. contributed new reagents/analytic tools; T.J.K., Y.X., A.F., To better understand Atoh1’s role in neurogenesis, we set out L.W., W.L., and H.Y.Z. analyzed data; and T.J.K., A.F., W.L., and H.Y.Z. wrote the paper. fl to identify its molecular functions by defining its direct target The authors declare no con ict of interest. genes in vivo in the cerebellar granule neuron precursors (CGP), Data deposition: All primary sequence data of RNA-seq, Histone-seq, and Atoh1 ChIP-seq fi have been deposited in the National Center for Biotechnology Information Gene Expres- a key population in the developing brain. The CGPs are speci ed sion Omnibus repository, www.ncbi.nlm.nih.gov/geo (accession no. GSE22111). during early embryonic development [embryonic day (E) 11–14] 1 fi T.J.K. and Y.X. contributed equally to this work. and, after a clonal expansion during the rst postnatal week in 2 To whom correspondence may be addressed. E-mail: [email protected] or hzoghbi@bcm. mouse, differentiate to give rise to the granule cells of the cere- edu. bellum (21, 22). Interestingly, postnatal day 0 (P0) CGPs are not This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. completely committed to a neuronal fate, although the majority of 1073/pnas.1100230108/-/DCSupplemental. 3288–3293 | PNAS | February 22, 2011 | vol. 108 | no. 8 www.pnas.org/cgi/doi/10.1073/pnas.1100230108 Downloaded by guest on September 27, 2021 and sequence saturation (Fig. S2 E and F and Dataset S1). Interestingly, Atoh1 binding peaks were highly correlated with H3K4me1 but not H3K4me3 (Fig. 2 A and B, Fig. S1 B and C, and Dataset S1), indicating that most Atoh1 binding regions were located in enhancer regions. As a third criterion, we wanted to analyze the gene-expression changes associated with the loss of Atoh1. Because Atoh1-null mice die at birth (9), we could not use P5 cerebella but compared the transcriptional profiles of E18.5 WT and Atoh1-null cere- bellar tissue instead. Having obtained high-quality data [as judged by its high reproducibility (Fig. S1D), equal transcript coverage, and high sequence saturation (Fig. S3 A–C and Dataset S1)], we created a differentially expressed transcript list and identified 4,064 differentially expressed transcripts with an adjusted P value less than 0.01, of which most were down- regulated in the Atoh1-null tissue (Fig. S3D and Dataset S3). Importantly, the overall histone methylation status of the gene bodies at P5 was highly enriched in the RNA transcripts iden- tified at E18.5 compared with transcripts that are not expressed, suggesting that these transcripts are still actively transcribed (Fig. 2 C and D). Fig. 1. Loss of Atoh1 leads to an early differentiation halt. (A and B) Using CrePR/flox YFP/YFP Atoh1 ;Rosa mice, we depleted Atoh1 by administrating RU486 Atoh1 E-Box Associated Motif Characterizes the Atoh1 Genomic to the cerebellum at P0 (A)orP5(B) and collected the cerebellum 24 h later. In the 20-μm sagittal sections, Atoh1-depleted cells were visualized by YFP ex- Signature. Because proneural factors bind to a loose E-Box pression (green channel). Nuclei are stained with DAPI (blue channel). (Scale consensus sequence, CANNTG (29), we searched for this motif bars, 50 μm.) (C) Quantification of differentiating cells measured by their in our target regions. We could identify at least one E-Box in location. Shown is the ratio of cells located in the IGL in respect to the EGL. 91% (17,568) of Atoh1-bound regions, consistent with the idea that these could be true Atoh1-binding sites. Little is known differentiate (Fig. 1C). To confirm that these results are caused by Atoh1 deletion from dividing CGPs situated on the outer EGL, we used an organotypic culture system in which we applied GFP- containing or Cre-IRES-GFP adenoviruses on the surface of fl fl cultured Atoh1 ox/ ox P0 or P5 cerebella to infect only the out- ermost cell layers of the EGL (Fig.
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