Extent, causes, and consequences of small RNA expression variation in human adipose tissue

Parts, Leopold; Hedman, Åsa K; Keildson, Sarah; Knights, Andrew J; Abreu-Goodger, Cei; van de Bunt, Martijn; Guerra-Assunção, José Afonso; Bartonicek, Nenad; van Dongen, Stijn; Mägi, Reedik; Nisbet, James; Barrett, Amy; Rantalainen, Mattias; Nica, Alexandra; Quail, Michael A; Small, Kerrin S; Glass, Daniel; Enright, Anton J; Winn, John; Deloukas, Panos; Dermitzakis, Emmanouil; McCarthy, Mark I; Spector, Timothy D; Durbin, Richard; Lindgren, Cecilia M

doi:10.1371/journal.pgen.1002704

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Title		Extent, causes, and consequences of small RNA expression variation in human adipose tissue
Authors		Parts, Leopold Hedman, Åsa K Keildson, Sarah Knights, Andrew J Abreu-Goodger, Cei van de Bunt, Martijn Guerra-Assunção, José Afonso Bartonicek, Nenad van Dongen, Stijn Mägi, Reedik Nisbet, James Barrett, Amy Rantalainen, Mattias Nica, Alexandra Quail, Michael A Small, Kerrin S Glass, Daniel Enright, Anton J Winn, John Deloukas, Panos Dermitzakis, Emmanouil McCarthy, Mark I Spector, Timothy D Durbin, Richard Lindgren, Cecilia M show all authors [1 - 25]
Published in		PLOS genetics. 2012, vol. 8, no. 5, e1002704
Abstract		Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expression of 15 to 30 base pair RNA molecules in subcutaneous adipose tissue from 131 individuals using high-throughput sequencing, and quantified levels of 591 microRNAs and small nucleolar RNAs. We identified three genetic variants and three RNA editing events. Highly expressed small RNAs are more conserved within mammals than average, as are those with highly variable expression. We identified 14 genetic loci significantly associated with nearby small RNA expression levels, seven of which also regulate an mRNA transcript level in the same region. In addition, these loci are enriched for variants significant in genome-wide association studies for body mass index. Contrary to expectation, we found no evidence for negative correlation between expression level of a microRNA and its target mRNAs. Trunk fat mass, body mass index, and fasting insulin were associated with more than twenty small RNA expression levels each, while fasting glucose had no significant associations. This study highlights the similar genetic complexity and shared genetic control of small RNA and mRNA transcripts, and gives a quantitative picture of small RNA expression variation in the human population.
Keywords		Animals — Blood Glucose — Body Fat Distribution — Body Mass Index — Fasting — Female — Gene Expression Regulation — Genetic Variation — Genome-Wide Association Study — Genotype — High-Throughput Nucleotide Sequencing — Humans — Insulin/blood — MicroRNAs/genetics/metabolism — Middle Aged — Polymorphism, Single Nucleotide — RNA, Messenger/genetics/metabolism — RNA, Small Nucleolar/genetics/metabolism — RNA, Small Untranslated/genetics/metabolism — Subcutaneous Fat/metabolism
Identifiers		DOI: 10.1371/journal.pgen.1002704 PMID: 22589741
Full text		Article (Published version) (960 Kb) - Free access
Structures		Faculté de médecine / Section de médecine fondamentale / Département de médecine génétique et développement
Research group		Population Genomics and Genetics of Complex Traits (892)
Project		Autre: Jeantet
Citation (ISO format)		PARTS, Leopold et al. Extent, causes, and consequences of small RNA expression variation in human adipose tissue. In: PLOS genetics, 2012, vol. 8, n° 5, p. e1002704. doi: 10.1371/journal.pgen.1002704 https://archive-ouverte.unige.ch/unige:32160