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Single nucleotide p...
Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes
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- Almlöf, Jonas (författare)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Lundmark, Per (författare)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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- Lundmark, Anders (författare)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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Ge, Bing (författare)
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Pastinen, Tomi (författare)
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Goodall, Alison H (författare)
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Cambien, François (författare)
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Deloukas, Panos (författare)
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Ouwehand, Willem H (författare)
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- Syvänen, Ann-Christine (författare)
- Uppsala universitet,Molekylär medicin,Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2014-07-15
- 2014
- Engelska.
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:7, s. e102612-
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://journals.plo...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
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- 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
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Almlöf, Jonas
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Lundmark, Per
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Lundmark, Anders
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Ge, Bing
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Pastinen, Tomi
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Goodall, Alison ...
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visa fler...
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Cambien, Françoi ...
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Deloukas, Panos
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Ouwehand, Willem ...
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Syvänen, Ann-Chr ...
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visa färre...
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Uppsala universitet