Feb 4, 2016

Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs

Genome Biology
Jenny ChenManuel Garber

Abstract

Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. We present slncky, a lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-sequencing data and further uses evolutionary constraint to prioritize lncRNAs that are likely to be functionally important. Our automated filtering pipeline is comparable to manual curation efforts and more sensitive than previously published computational approaches. Furthermore, we developed a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for analyzing sequence and transcript evolution. Our analysis reveals that evolutionary selection acts in several distinct patterns, and uncovers two notable classes of ...Continue Reading

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  • Citations20

Citations

Mentioned in this Paper

TNS3
Patterns
RNA, Untranslated
Regulation of Biological Process
Sequence Determinations, RNA
Computer Programs and Programming
Sequencing
Long Intergenic Non-Protein Coding RNA
RNA, Long Untranslated
Toxic Epidermal Necrolysis

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