Single nucleotide polymorphisms with Cis-regulatory effects on long non-coding transcripts in human primary monocytes

Jonas Carlsson Almlöf, Per Lundmark, Anders Lundmark, Bing Ge, Tomi Pastinen, Alison H. Goodal, François Cambien, Panos Deloukas, Willem H. Ouwehand, Ann Christine Syvänen, Heribert Schunkert, Tony Attwood, Stephanie Belz, Peter Braund, Jessy Brocheton, Jason Cooper, Abi Crisp-Hihn, Patrick Diemert, Jeanette Erdmann, Nicola FoadTiphaine Godefroy, Jay Gracey, Emma Gray, Rhian Gwilliams, Susanne Heimerl, Christian Hengstenberg, Jennifer Jolley, Unni Krishnan, Heather Lloyd-Jones, Ulrika Liljedahl, Ingrid Lugauer, Seraya Maouche, Jasbir S. Moore, Gilles Montalescot, David Muir, Elizabeth Murray, Chris P. Nelson, Jessica Neudert, David Niblett, Karen O'Leary, Helen Pollard, Carole Proust, Angela Rankin, Augusto Rendon, Catherine M. Rice, Hendrik Sager, Nilesh J. Samani, Jennifer Sambrook, Gerd Schmitz, Michael Scholz, Laura Schroeder, Jonathan Stephens, Stefanie Tennstedt, Chris Wallace

7 Citations (Scopus)


We applied genome-wide allele-specific expression analysis of monocytes from 188 samples. Monocytes were purified from white blood cells of healthy blood donors to detect cis-acting genetic variation that regulates the expression of long non-coding RNAs. We analysed 8929 regions harboring genes for potential long non-coding RNA that were retrieved from data from the ENCODE project. Of these regions, 60% were annotated as intergenic, which implies that they do not overlap with protein-coding genes. Focusing on the intergenic regions, and using stringent analysis of the allele-specific expression data, we detected robust cis-regulatory SNPs in 258 out of 489 informative intergenic regions included in the analysis. The cis-regulatory SNPs that were significantly associated with allele-specific expression of long non-coding RNAs were enriched to enhancer regions marked for active or bivalent, poised chromatin by histone modifications. Out of the lncRNA regions regulated by cis- acting regulatory SNPs, 20% (n = 52) were co-regulated with the closest protein coding gene. We compared the identified cis-regulatory SNPs with those in the catalog of SNPs identified by genome-wide association studies of human diseases and traits. This comparison identified 32 SNPs in loci from genome-wide association studies that displayed a strong association signal with allele-specific expression of non-coding RNAs in monocytes, with p-values ranging from 6.7×10-7 to 9.5×10-89. The identified cis-regulatory SNPs are associated with diseases of the immune system, like multiple sclerosis and rheumatoid arthritis.

Original languageEnglish
Article numbere102612
JournalPLoS ONE
Issue number7
Publication statusPublished - 15.07.2014

Research Areas and Centers

  • Research Area: Medical Genetics


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