Collectively, these results reveal that several embryonic lncRNAs are expressed not only in specific tissues but also in specific subcellular domains

On By msisig

Collectively, these results reveal that several embryonic lncRNAs are expressed not only in specific tissues but also in specific subcellular domains. == Conversation == We have generated a systematic annotation of the zebrafish embryonic transcriptome, focusing specifically around the identification and characterization of lncRNAs. during embryogenesis. These include long intergenic ncRNAs (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs (sRNAs). Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length, low exon number, low expression, and conservation levels comparable to that of introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than are protein-coding genes and PD 150606 are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and unique subcellular PD 150606 localization PD 150606 patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions, ranging from cell cycle regulation to morphogenesis. Our study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies. Large-scale genomic studies have identified a significant quantity of transcripts that do not code for proteins (Kapranov et al. 2002,2007;Bertone 2004;Carninci et al. 2005;ENCODE Project Consortium et al. 2007;Ponjavic et al. 2007;Fejes-Toth et al. 2009;Guttman et al. 2009,2010;Cabili et al. 2011). Such noncoding RNAs (ncRNAs) can be broadly classified as either small (<200 nucleotides [nt]; sRNAs) or large (>200 nt; lncRNAs) based on the size of their mature transcripts. While miRNAs (microRNAs), the best-studied class of sRNAs, regulate their mRNA targets post-transcriptionally (Bartel 2009), mRNA-like lncRNAs take action by a range of mechanisms (for reviews, seeKoziol and Rinn 2010;Pauli et al. 2011;Wang and Chang 2011). For example, several lncRNAs have been shown to interact with and modulate the activity of the chromatin modifying machinery (Rinn et al. 2007;Nagano et al. 2008;Pandey et al. 2008;Zhao et al. 2008,2010;Khalil et al. 2009;Huarte et al. 2010;Tian et al. 2010;Tsai et al. 2010;Guttman et al. 2011;Wang et al. 2011). Other lncRNAs may act as decoys in the sequestration of miRNAs (Poliseno et al. 2010), transcription factors (Hung et al. 2011), or other proteins (Tripathi et al. 2010). Yet others may serve as precursors for the generation of sRNAs (Kapranov et al. 2007;Wilusz et al. 2008;Fejes-Toth et al. 2009). Although most lncRNAs have not been functionally characterized, an emerging theme is usually their role in the regulation of gene expression in eithercisortrans. Severaltrans-acting lncRNAs have been recognized, includingHOTAIR(Rinn et al. 2007),TP53COR1(also known aslincRNA-p21) (Huarte et al. 2010), andPANDA(Hung et al. 2011). Moreover, knockdown of more than 100 individual long intergenic ncRNAs (lincRNAs) in mouse embryonic stem cells led PD 150606 to widespread changes in gene expression that could not be explained by acis-acting mechanism (Guttman et al. 2011). Other well-described lncRNAs take action incis. For example, mammalian X chromosome inactivation and allelic imprinting depend on lncRNAs that mediate the silencing of neighboring genes by recruiting repressive chromatin modifiers (Sleutels et al. 2002;Mancini-Dinardo et al. 2006;Nagano et al. 2008;Pandey et al. 2008;Zhao et al. 2008). Additional recently identifiedcis-acting RNAs activate the expression of neighboring genes (Kim et al. 2010;rom et al. 2010;Wang et al. 2011). Collectively, these studies have exhibited that lncRNAs can have a profound impact on gene regulation in bothcisandtrans. Existing annotations of mammalian lncRNAs are derived from large-scale studies of cultured cells (Kapranov et al. 2002;Rinn et al. 2003;Carninci et al. 2005;ENCODE Project Consortium et al. 2007; Dinger et al. 2008;Guttman et al. 2009,2010) or adult tissue samples (Ponjavic et al. 2009;Cabili et al. 2011). Such relatively homogenous and abundant samples have facilitated the identification of low large quantity, cell typespecific transcripts. However, this strategy is likely to miss lncRNAs that are only expressed during thin developmental time windows. To fully characterize vertebrate lncRNAs, it is therefore necessary to systematically search for lncRNAs that are expressed during specific developmental stages. Here, we statement the systematic identification and characterization of developmental lncRNAs. NS1 We leveraged the ability to obtain large numbers of developmentally synchronous zebrafish embryos in order to perform a time-series of eight RNA-seq experiments (200300 million reads per stage) from shortly after fertilization to early larval stages. As a measure of quality of our data set, we were able to reconstruct the vast majority of annotated zebrafish RefSeq genes and a large portion of Ensembl gene models (Flicek et al. 2011). In contrast to recent smaller-scale.