Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

Zhao, Jing; Ohsumi, Toshiro K.; Kung, Johnny T.; Ogawa, Yasushi; Grau, Daniel J.; Sarma, Kavitha; Song, Ji-Joon; Kingston, Robert E.; Borowsky, Mark; Lee, Jeannie T.

doi:10.1016/j.molcel.2010.12.011

Cited by 919 publications

(882 citation statements)

References 59 publications

(106 reference statements)

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“…Many different types of noncoding transcripts have been reported to be associated with promoter regions or to be derived from sequences close to the transcription start site of genes (Davis and Ares, 2006;Parkhomchuk et al, 2009;Zhao et al, 2010). Theoretically, TUs for some of these transcripts may also appear in the intergenic regions.…”

Section: Design Of An Identifier System Of Arabidopsis Lincrnasmentioning

confidence: 99%

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

et al. 2012

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Long intergenic noncoding RNAs (lincRNAs) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. Yet, plant lincRNAs remain poorly characterized and how lincRNA biogenesis is regulated is unclear. Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs. Expression of 2708 lincRNAs was detected by RNA sequencing experiments. Transcriptome profiling by custom microarrays revealed that the majority of these lincRNAs are expressed at a level between those of mRNAs and precursors of miRNAs. A subset of lincRNA genes shows organ-specific expression, whereas others are responsive to biotic and/or abiotic stresses. Further analysis of transcriptome data in 11 mutants uncovered SERRATE, CAP BINDING PROTEIN20 (CBP20), and CBP80 as regulators of lincRNA expression and biogenesis. RT-PCR experiments confirmed these three proteins are also needed for splicing of a small group of introncontaining lincRNAs.

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Section: Design Of An Identifier System Of Arabidopsis Lincrnasmentioning

confidence: 99%

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

et al. 2012

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“…Recent work has suggested various functions and molecular mechanisms for lincRNAs (Mercer et al 2009;Ponting et al 2009), including the regulation of epigenetic marks and gene expression (Rinn et al 2007;Nagano et al 2008;Pandey et al 2008;Zhao et al 2008Zhao et al , 2010Khalil et al 2009;Koziol and Rinn 2010). Other studies have inferred and tested the functional role of lincRNAs in processes such as pluripotency and p53 response pathways by associating the expression of lincRNAs with those of protein-coding genes (Guttman et al 2009;Huarte et al 2010;Loewer et al 2010;Hung et al 2011).…”

mentioning

confidence: 99%

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Cabili¹,

Trapnell²,

Goff³

et al. 2011

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Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalog of >8000 human lincRNAs. Our catalog unifies previously existing annotation sources with transcripts we assembled from RNA-seq data collected from~4 billion RNA-seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of >30 properties, including sequence, structural, transcriptional, and orthology features. We found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that lincRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes. We distinguish an additional subset of transcripts that have high evolutionary conservation but may include short ORFs and may serve as either lincRNAs or small peptides. Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes.

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“…While miRNAs (microRNAs), the best-studied class of sRNAs, regulate their mRNA targets posttranscriptionally (Bartel 2009), mRNA-like lncRNAs act by a range of mechanisms (for reviews, see Koziol 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 2008Zhao et al , 2010Khalil et al 2009;Huarte et al 2010;Tian et al 2010;Tsai et al 2010;Guttman 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).…”

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confidence: 99%

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

Pauli¹,

Valen²,

Lin³

et al. 2011

Genome Res.

739

830

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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.

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Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

Cited by 919 publications

References 59 publications

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

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

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

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