Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

Abstract

Long noncoding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in humans and the mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time-series of RNA-seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1133 noncoding multi-exonic transcripts expressed 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 are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and distinct subcellular localization 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.

Genome-Wide Analysis Uncovers Regulation of Long Intergenic Noncoding RNAs in Arabidopsis

“…However, the total number of lincRNAs (<200) was still far below the number of reported lincRNAs (550 to ;8000) in animals (Guttman et al, 2009(Guttman et al, , 2010Khalil et al, 2009;Cabili et al, 2011;Ulitsky et al, 2011;Pauli et al, 2012). Assuming that a large number of lincRNAs may still remain undiscovered in Arabidopsis, we developed a bioinformatics strategy to identify lincRNAs on a genome-wide basis.…”

“…Average signal values of two independent flower samples are given. Ulitsky et al, 2011;Pauli et al, 2012). We aligned RNA sequences to TAIR9 using Tophat and SAMtools (Trapnell et al, 2009).…”

Characterizing and annotating the genome using RNA-seq data

“…Long noncoding RNAs (lncRNAs) have important regulatory functions and they have become a hot research field in recent years (Cabili et al, 2011;Chen et al, 2011c;Derrien et al, 2012;Fan and Zhang, 2015;Lee and Kikyo, 2012;Pauli et al, 2012). In the past decades, researchers mainly focused on exploring the functions of protein-coding genes, but neglected an important category of genes called lncRNAs.…”

“…RNA-seq provides unprecedented opportunities for exploring those novel lncRNAs. Some studies identified a number of novel lncRNAs based on the RNA-seq data in different organisms including humans (Cabili et al, 2011), mouse (Guttman et al, 2010) and zebrafish (Pauli et al, 2012). A popular way to identify lncRNAs is to conduct transcriptome reconstruction using genome-guided methods (such as Cufflinks (Trapnell et al, 2010)) first (Figure 4).…”

“…These problems raise the urgent need for identifying and characterizing those novel genes/transcripts on or out of the reference genome. Many studies, using RNA-seq, have identified a number of novel protein-coding and noncoding genes/transcripts of interested organisms (Cabili et al, 2011;Chettoor et al, 2014;Guttman et al, 2010;Pauli et al, 2012;Roberts et al, 2011). Because long noncoding RNAs (lncRNAs) were less explored previously, they are a significant portion of those identified novel genes/transcripts.…”