Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.ORCID iD: 0000-0002-5035-1736
2017 (English)In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 5, p. 1266-1279Article in journal (Refereed) Published
Abstract [en]

Polymorphism in cis-regulatory sequences can lead to different levels of expression for the two alleles of a gene, providing a starting point for the evolution of gene expression. Little is known about the genome-wide abundance of genetic variation in gene regulation in natural populations but analysis of allele-specific expression (ASE) provides a means for investigating such variation. We performed RNA-seq of multiple tissues from population samples of two closely related flycatcher species and developed a Bayesian algorithm that maximizes data usage by borrowing information from the whole data set and combines several SNPs per transcript to detect ASE. Of 2,576 transcripts analyzed in collared flycatcher, ASE was detected in 185 (7.2%) and a similar frequency was seen in the pied flycatcher. Transcripts with statistically significant ASE commonly showed the major allele in > 90% of the reads, reflecting that power was highest when expression was heavily biased toward one of the alleles. This would suggest that the observed frequencies of ASE likely are underestimates. The proportion of ASE transcripts varied among tissues, being lowest in testis and highest in muscle. Individuals often showed ASE of particular transcripts in more than one tissue (73.4%), consistent with a genetic basis for regulation of gene expression. The results suggest that genetic variation in regulatory sequences commonly affects gene expression in natural populations and that it provides a seedbed for phenotypic evolution via divergence in gene expression.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2017. Vol. 9, no 5, p. 1266-1279
Keyword [en]
ASE, gene expression evolution, regulatory sequences, RNA-seq
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-333414DOI: 10.1093/gbe/evx080ISI: 000406760400013PubMedID: 28453623OAI: oai:DiVA.org:uu-333414DiVA, id: diva2:1157160
Funder
Swedish Research Council, 2010-5650, 2013-8271EU, European Research Council, AdG 249976Knut and Alice Wallenberg Foundation
Available from: 2017-11-15 Created: 2017-11-15 Last updated: 2018-02-22Bibliographically approved

Open Access in DiVA

fulltext(797 kB)8 downloads
File information
File name FULLTEXT01.pdfFile size 797 kBChecksum SHA-512
2e686b6e494286dca9835e27ba9822dc157c46cac55cfc344f0bbf2126c732eedfa1aebf5e252a76241c2d36e0aecf9931183aad0360a7c57a24c33c440c4b4b
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Wang, MiEllegren, Hans
By organisation
Evolutionary Biology
In the same journal
Genome Biology and Evolution
Biological Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 8 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 153 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
v. 2.34-SNAPSHOT
|