Long non-coding RNA gene regulation and trait associations across human tissues

Olivia M. de Goede; Nicole M. Ferraro; Daniel C. Nachun; Abhiram S. Rao; François Aguet; Alvaro Barbeira; Stephane E. Castel; Sarah Kim-Hellmuth; Yongjin Park; A. J. Scott; Benjamin J. Strober; Christopher D. Brown; Xiaoquan Wen; Ira M. Hall; Alexis J. Battle; Tuuli Lappalainen; Hae Kyung Im; Kristin Ardlie; Thomas Quertermous; Karla Kirkegaard; Stephen B. Montgomery

doi:10.1101/793091

GeneticsbioRxivOct 4, 2019

Preprint

Long non-coding RNA gene regulation and trait associations across human tissues

Olivia M. de Goede, Nicole M. Ferraro iD, Daniel C. Nachun iD, Abhiram S. Rao, François Aguet iD, Alvaro Barbeira iD, Stephane E. Castel iD, Sarah Kim-Hellmuth iD, Yongjin Park iD, A. J. Scott, Benjamin J. Strober iD, Christopher D. Brown iD, Xiaoquan Wen iD, Ira M. Hall iD, Alexis J. Battle iD, Tuuli Lappalainen iD, Hae Kyung Im iD, Kristin Ardlie iD, Thomas Quertermous iD, Karla Kirkegaard iD, Stephen B. Montgomery iD

Abstract

Long non-coding RNA (lncRNA) genes are known to have diverse impacts on gene regulation. However, it is still a major challenge to distinguish functional lncRNAs from those that are byproducts of surrounding transcriptional activity. To systematically identify hallmarks of biological function, we used the GTEx v8 data to profile the expression, regulation, network relationships and trait associations of lncRNA genes across 49 tissues encompassing 87 distinct traits. In addition to revealing widespread differences in regulatory patterns between lncRNA and protein-coding genes, we identified novel disease-associated lncRNAs, such as C6orf3 for psoriasis and LINC01475/RP11-129J12.1 for ulcerative colitis. This work provides a comprehensive resource to interrogate lncRNA genes of interest and annotate cell type and human trait relevance.\n\nOne Sentence SummarylncRNA genes have distinctive regulatory patterns and unique trait associations compared to protein-coding genes.

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