View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by MPG.PuRe Review Special Issue: Organogenesis Long noncoding RNAs in organogenesis: making the difference 1 2,3 Phillip Grote and Bernhard G Herrmann 1 Institute of Cardiovascular Regeneration, Center for Molecular Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany 2 Max Planck Institute for Molecular Genetics, Department of Developmental Genetics, Ihnestr. 63-73, 14195, Berlin, Germany 3 Charite´ – University Medicine Berlin, Institute for Medical Genetics, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany A large proportion of the cellular transcriptome of higher alleles of the cardiac transcription factor coding genes vertebrates consists of non-protein coding transcripts, Nkx2-5 (NK2 homeobox 5), Gata4 (GATA binding protein among them the long noncoding RNAs (lncRNAs). 4), and Tbx5 (T-box 5) are functional. If one is dysfun- Although lncRNAs are functionally extremely divergent, ctional or lacking, congenital heart disease lesions develop many ncRNAs have been shown to interact with chro- [1–3]. Hence, the development of a vital organism not only matin modifying complexes and/or with transcriptional depends on the accurate temporal and spatial control of regulators. Via such interactions, many lncRNAs are gene activation, but also, at least for some critical devel- involved in controlling the activity and expression level opmental regulators, on appropriate levels of gene expres- of target genes, including important regulators of em- sion and activity. bryonic processes, and thereby fine-tune gene regulato- For decades, deciphering the function of individual ry networks controlling cell fate, lineage balance, and important transcription factors and chromatin organizing organogenesis. Intriguingly, an increase in organ com- proteins has been the major focus of developmental biol- plexity during evolution parallels a rise in lncRNA abun- ogists attempting to understand the control of embryonic dance. The current data suggest that lncRNAs support processes. Despite these efforts, a comprehensive under- the generation of cell diversity and organ complexity standing of the genomic control mechanisms acting in during embryogenesis, and thereby have promoted the individual cells and cell lineages during embryonic devel- evolution of more complex organisms. opment is still lacking. In this review, we provide an overview of recent studies elucidating the function of Genetic control of cell differentiation during lncRNAs in embryonic development and discuss their embryogenesis implications for understanding the role of lncRNAs in The diversity of cell types and organs of multicellular fine-tuning GRNs during development, cell diversification, organisms develops by differentiation of the descendants and the evolution of higher organ complexity. of a single totipotent cell, the fertilized egg. As all cells of the developing organism contain the same genome, the ncRNAs as modulators of gene activity differentiation process requires that the genomes of cells Systematic transcriptome analyses by deep sequencing of taking different fates vary with respect to transcriptionally human cell lines have revealed that close to 75% of the active and inactive regions. This variation in nuclear or- human genome is transcribed into primary transcripts, but ganization involves modifications of chromatin causing less than 3% of the genome accounts for protein coding activation or silencing of genes, and is controlled by differ- transcripts [4]. Thus, the vast majority of the mammalian entially expressed developmental regulators, such as tran- genome encodes non-protein coding RNAs (ncRNAs). Anal- scription factors that are organized in gene regulatory ogous to the functional diversity of proteins, ncRNA tran- networks (GRN). Besides qualitative differences (i.e., scripts are highly heterogeneous with respect to size and cell-type specific expression), quantitative differences such function. Some well investigated classes of ncRNAs, in- as the expression levels of regulators appears to play an cluding rRNAs, small nucleolar RNAs (snoRNAs), and important role in differentiation processes. This is, for tRNAs, have been shown to play important roles in mRNA instance, reflected by the fact that many important tran- translation or splicing. Furthermore, short RNA molecules scription factors display haplo-insufficiency phenotypes. of 21–28 nucleotides in length, such as miRNAs, siRNAs, For example, normal heart development requires that both and PIWI-interacting RNAs (piRNAs), are involved in transcriptional or post-transcriptional RNA silencing, Corresponding authors: Grote, P. ([email protected]); and thus in fine-tuning target gene activity at the tran- Herrmann, B.G. ([email protected]). Keywords: lncRNAs; embryo; development; organ; cell lineage. script level. Finally, numerous circular RNA species 0168-9525/ (circRNAs) [5] that are expressed in a tissue- and develop- ß 2015 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.tig.2015.02.002 mental stage-specific manner [6] have recently been discovered and presumably are also involved in the control Trends in Genetics, June 2015, Vol. 31, No. 6 329 Review Trends in Genetics June 2015, Vol. 31, No. 6 of regulatory networks. Some of these circRNAs may act development, binds thousands of ncRNAs, including nu- as sponges for miRNAs, thereby adding an additional merous lncRNAs [19–21]. This finding sparked the idea regulatory layer [6]. that lncRNAs might be involved in targeting PRC2 to specific gene control elements. Re-emergence of a neglected ncRNA species: the long For instance, Xist (X-inactivation specific transcript) noncoding RNAs binds to PRC2, thereby causing extensive tri-methylation The extraordinary advance in sequencing technology, allow- of histone 3 lysine 27 (H3K27me3) along the X-chromo- ing the detection of low abundance transcripts in genome- some, followed by inactivation of the marked copy, a mech- wide transcriptome analyses via massive parallel sequenc- anism required for dosage compensation in (mammalian) ing, has put a class of ncRNAs in the spotlight that has been females [22]. Several other lncRNAs exerting their func- known but neglected for a long time. These so-called long tion through binding to PRC2 have recently been identi- noncoding RNAs (lncRNAs) are by definition longer than fied. One well-studied example is Hotair (HOX antisense 200 nucleotides and have limited or no protein-coding po- intergenic RNA), which regulates the expression of genes tential. However, many lncRNAs associate with ribosomes in the HoxD cluster and multiple imprinted genes [23]. The and, hence, might have the potential to encode short pep- loss of Hotair in null-mutant mouse embryos results in tides, but to what extent this actually occurs remains to be homeotic transformations and fusions of carpal elements investigated [7,8]. In addition, some lncRNAs might have in the wrist [23]. Another example is Fendrr (fetal-lethal dual roles, acting as both full-length transcripts and as noncoding developmental regulatory RNA). Interaction of precursors of small RNAs [9]. In general, lncRNAs tend to Fendrr with PRC2 is required to adjust the expression be expressed at a lower level than mRNAs [4]. The RNA levels of its target genes that are involved in the control stability of lncRNAs was found to be only slightly decreased of lateral mesoderm development. Remarkably, the two as compared to mRNAs, suggesting that the lower tran- direct target genes of Fendrr identified so far, Foxf1 (Fork- script level is the result of a reduced transcription rate [10]. head-box F1) and Pitx2 (paired-like homeodomain tran- LncRNA genes exist in various genomic contexts. Like scription factor 2), are transcription factors that play mRNA genes they can have their own promoters and pivotal roles in lateral mesoderm differentiation, and show regulatory elements, distant from any known mRNA gene haplo-insufficiency phenotypes in mutants expressing only locus. However, many lncRNAs overlap with mRNA tran- one functional allele. The targeting of PRC2 to the promo- scripts in sense or antisense orientation, or are transcribed ters of these transcription factors by Fendrr thus plays an from introns. A large subset of lncRNAs is transcribed important role in fine-tuning the expression levels of these divergently (antisense) from mRNA coding genes [11], dosage-sensitive regulators. Genetic ablation of the Fendrr sharing promoter and regulatory elements with the latter, transcript results in malformations of the heart and the or lie upstream of neighboring mRNA coding genes and are body wall, which originate from the lateral mesoderm, and transcribed in sense orientation into the promoter of the eventually in embryonic death [24,25]. Another lncRNA neighbor. LncRNAs can also originate from enhancers important for the specification of the early heart cell (eRNAs) as long unspliced or spliced transcripts lineage is Braveheart, which interacts with the PRC2 [12,13]. The number of lncRNA transcripts expressed in component SUZ12 [26]. Braveheart is required for the human and mouse is in the range of tens of thousands, activation of a network of genes that establish the cardiac when summed up over all developmental and adult cell lineage from lateral mesoderm progenitors. Interestingly, types. However, although the number of studies and data- Braveheart acts upstream of Mesp1, a transcriptional