Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes

Alam, Tanvir; Medvedeva, Yulia A.; Jia, Hui; Brown, James B.; Lipovich, Leonard; Bajic, Vladimir B.; Mantovani, Roberto

doi:10.1371/journal.pone.0109443

Title: Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes

Journal Article · Thu Oct 02 00:00:00 EDT 2014 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0109443· OSTI ID:1212466

Alam, Tanvir ^[1]; Medvedeva, Yulia A. ^[1]; Jia, Hui ^[2]; Brown, James B. ^[3]; Lipovich, Leonard ^[4]; Bajic, Vladimir B. ^[1]; Mantovani, Roberto ^[5]

King Abdullah University of Science and Technology (KAUST), Thuwal (Saudi Arabia)
Wayne State Univ., Detroit, MI (United States). Center for Molecular Medicine and Genetics.
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Department of Genome Dynamics, Life Sciences Division.
Wayne State Univ., Detroit, MI (United States). Center for Molecular Medicine and Genetics and Dept. of Neurology.
Universita` degli Studi di Milano (Italy)

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE; National Institute of Health

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1212466

Journal Information:: PLoS ONE, Vol. 9, Issue 10; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 61 works

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