Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers


Up to 80% of mammalian genomes are actively transcribed, producing large numbers of non-coding RNAs without known functions. One particularly exciting category of such non-coding transcripts are the recently discovered enhancer RNAs (eRNAs) transcribed from distant-acting enhancer elements. Studies in cell-based paradigms suggest a functional requirement for such eRNA in enhancer-mediated gene regulation. In this study, we explored the in vivo expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues via in-depth transcriptome profiling. Our results suggest that enhancers may be a predominant function associated with differentially expressed non-coding loci across developing tissues, and that differential eRNA expression signatures from total RNA-Seq can be used to identify uncharacterized tissue-specific in vivo enhancers independent of known epigenomic marks. Our results highlight the widespread and potentially important role of eRNAs in orchestrating gene expression and the necessity for functional studies in interpreting genome-wide enhancer predictions.


Vyšlo v časopise: Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers. PLoS Genet 10(9): e32767. doi:10.1371/journal.pgen.1004610
Kategorie: Research Article
prolekare.web.journal.doi_sk: 10.1371/journal.pgen.1004610

Souhrn

Up to 80% of mammalian genomes are actively transcribed, producing large numbers of non-coding RNAs without known functions. One particularly exciting category of such non-coding transcripts are the recently discovered enhancer RNAs (eRNAs) transcribed from distant-acting enhancer elements. Studies in cell-based paradigms suggest a functional requirement for such eRNA in enhancer-mediated gene regulation. In this study, we explored the in vivo expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues via in-depth transcriptome profiling. Our results suggest that enhancers may be a predominant function associated with differentially expressed non-coding loci across developing tissues, and that differential eRNA expression signatures from total RNA-Seq can be used to identify uncharacterized tissue-specific in vivo enhancers independent of known epigenomic marks. Our results highlight the widespread and potentially important role of eRNAs in orchestrating gene expression and the necessity for functional studies in interpreting genome-wide enhancer predictions.


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Genetika Reprodukčná medicína

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