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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Single nucleotide polymorphisms with Cis-regulatory effects on long non-coding transcripts in human primary monocytes
PLoS ONE, Volume 9, No. 7, Article e102612, Year 2014
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Description
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. © 2014 Carlsson Almlöf et al.
Authors & Co-Authors
Almlöf, Jonas Carlsson
Sweden, Uppsala
Uppsala Universitet
Lundmark, Per E.
Sweden, Uppsala
Uppsala Universitet
Lundmark, Anders
Sweden, Uppsala
Uppsala Universitet
Ge, Bing
Canada, Montreal
Université Mcgill
Pastinen, Tomi M.
Canada, Montreal
Université Mcgill
Goodal, Alison H.
United Kingdom, Leicester
University of Leicester
United Kingdom, Leicester
Glenfield Hospital
Cambien, François A.
France, Paris
Inserm
Deloukas, Panos
United Kingdom, London
Barts and the London School of Medicine and Dentistry
United Kingdom, Hinxton
Wellcome Sanger Institute
Saudi Arabia, Jeddah
King Abdulaziz University
Ouwehand, Willem Hendrik
United Kingdom, Hinxton
Wellcome Sanger Institute
United Kingdom, Bristol
Nhs Blood and Transplant
Syvänen, Ann Christine
Sweden, Uppsala
Uppsala Universitet
Schunkert, Heribert
Germany, Lubeck
Universität zu Lübeck
Attwood, Tony
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Belz, Stephanie
Germany, Lubeck
Universität zu Lübeck
Braund, Peter S.
United Kingdom, Leicester
University of Leicester
Brocheton, Jessy
France, Paris
Inserm
Cooper, Jason D.
United Kingdom, Cambridge
Cambridge Institute for Medical Research
Crisp-Hihn, Abigail
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Diemert, Patrick
Germany, Lubeck
Universität zu Lübeck
Erdmann, Jeanette
Germany, Lubeck
Universität zu Lübeck
Foad, Nicola S.
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Godefroy, Tiphaine
France, Paris
Inserm
Gracey, Jay
United Kingdom, Leicester
University of Leicester
Gray, Emma K.
United Kingdom, Hinxton
Wellcome Sanger Institute
Gwilliams, Rhian
United Kingdom, Hinxton
Wellcome Sanger Institute
Heimerl, Susanne
Germany, Regensburg
Klinikum Der Universität Regensburg Und Medizinische Fakultät
Hengstenberg, Christian
Germany, Regensburg
Klinikum Der Universität Regensburg Und Medizinische Fakultät
Jolley, Jennifer D.M.
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Krishnan, Unni
United Kingdom, Leicester
University of Leicester
Lloyd-Jones, Heather
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Liljedahl, Ulrika
Sweden, Uppsala
Uppsala Universitet
Lugauer, Ingrid
Germany, Regensburg
Klinikum Der Universität Regensburg Und Medizinische Fakultät
Maouche, Seraya
Germany, Lubeck
Universität zu Lübeck
France, Paris
Inserm
Moore, Jasbir S.
United Kingdom, Leicester
University of Leicester
Montalescot, Gilles
France, Paris
Inserm
Muir, David
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Murray, Elizabeth
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Nelson, Christopher P.
United Kingdom, Leicester
University of Leicester
Neudert, Jessica
Germany, Munich
Analysis Online Gmbh
Niblett, David
United Kingdom, Hinxton
Wellcome Sanger Institute
O'Leary, Karen
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Pollard, Helen
United Kingdom, Leicester
University of Leicester
Proust, Carole
France, Paris
Inserm
Rankin, Angela
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Rendon, Augusto
United Kingdom, Hinxton
Embl’s European Bioinformatics Institute
Rice, Catherine M.
United Kingdom, Hinxton
Wellcome Sanger Institute
Sager, Hendrik B.
Germany, Lubeck
Universität zu Lübeck
Samani, Nilesh J.
United Kingdom, Leicester
University of Leicester
United Kingdom, Leicester
Glenfield Hospital
Sambrook, Jennifer G.
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Schmitz, Gerd
Germany, Regensburg
Universität Regensburg
Scholz, Michael
Germany, Munich
Analysis Online Gmbh
Schroeder, Laura
Germany, Lubeck
Universität zu Lübeck
Stephens, Jonathan Claiborne
United Kingdom, Cambridge
University of Cambridge
United Kingdom, Bristol
Nhs Blood and Transplant
Tennstedt, Stephanie
Germany, Lubeck
Universität zu Lübeck
Wallace, Chris
United Kingdom, Cambridge
Cambridge Institute for Medical Research
Statistics
Citations: 54
Authors: 54
Affiliations: 16
Identifiers
Doi:
10.1371/journal.pone.0102612
e-ISSN:
19326203
Research Areas
Genetics And Genomics