Universität zu Köln

Steige, Kim A., Laenen, Benjamin, Reimegard, Johan, Scofield, Douglas G. and Slotte, Tanja ORCID: 0000-0001-6020-5102 (2017). Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora. Proc. Natl. Acad. Sci. U. S. A., 114 (5). S. 1087 - 1093. WASHINGTON: NATL ACAD SCIENCES. ISSN 0027-8424

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Abstract

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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Steige, Kim A. UNSPECIFIED UNSPECIFIED UNSPECIFIED Laenen, Benjamin UNSPECIFIED UNSPECIFIED UNSPECIFIED Reimegard, Johan UNSPECIFIED UNSPECIFIED UNSPECIFIED Scofield, Douglas G. UNSPECIFIED UNSPECIFIED UNSPECIFIED Slotte, Tanja UNSPECIFIED orcid.org/0000-0001-6020-5102 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-242047
DOI:	10.1073/pnas.1612561114
Journal or Publication Title:	Proc. Natl. Acad. Sci. U. S. A.
Volume:	114
Number:	5
Page Range:	S. 1087 - 1093
Date:	2017
Publisher:	NATL ACAD SCIENCES
Place of Publication:	WASHINGTON
ISSN:	0027-8424
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language DNA-SEQUENCING DATA; RNA-SEQ; PROTEIN EVOLUTION; GENE-EXPRESSION; DELETERIOUS MUTATIONS; POPULATION-SIZE; SELECTION; METHYLATION; FRAMEWORK; CONSEQUENCES Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/24204