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Genomic analysis re...
Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora
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- Steige, Kim A. (författare)
- Uppsala universitet,Stockholms universitet,Institutionen för ekologi, miljö och botanik,Science for Life Laboratory (SciLifeLab),Uppsala University, Sweden,Evolutionsbiologi
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- Laenen, Benjamin (författare)
- Stockholms universitet,Institutionen för ekologi, miljö och botanik,Science for Life Laboratory (SciLifeLab)
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- Reimegård, Johan (författare)
- Uppsala universitet,Molekylär evolution,Science for Life Laboratory, SciLifeLab
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- Scofield, Douglas G. (författare)
- Uppsala universitet,Evolutionsbiologi
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- Slotte, Tanja (författare)
- Uppsala universitet,Stockholms universitet,Institutionen för ekologi, miljö och botanik,Science for Life Laboratory (SciLifeLab),Uppsala University, Sweden,Evolutionsbiologi
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(creator_code:org_t)
- 2017-01-17
- 2017
- Engelska.
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:5, s. 1087-1092
- Relaterad länk:
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https://www.pnas.org...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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https://urn.kb.se/re...
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Abstract
Ämnesord
Stäng
- Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are underweaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Genetik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Genetics (hsv//eng)
Nyckelord
- allele-specific expression
- fitness effects
- purifying selection
- positive selection
- gene body methylation
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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