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RPASE: Individual-based allele-specific expression detection without prior knowledge of haplotype phase
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. Yale Sch Med, Dept Genet, New Haven, CT USA.ORCID iD: 0000-0003-2439-6946
Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden.ORCID iD: 0000-0003-0324-7052
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.ORCID iD: 0000-0001-5235-6461
2018 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, no 6, p. 1247-1262Article in journal (Refereed) Published
Abstract [en]

Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele-specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel method called RPASE (Read-backed Phasing-based ASE detection) to test for genes that show ASE. With mapped RNA-seq data from a single individual and a list of SNPs from the same individual as the only input, RPASE is capable of aggregating information across multiple dependent SNPs and producing individual-based gene-level tests for ASE. RPASE performs well in simulations and comparisons. We applied RPASE to multiple bird species and found a potentially rich landscape of ASE.

Place, publisher, year, edition, pages
2018. Vol. 18, no 6, p. 1247-1262
Keywords [en]
allele-specific expression, gene expression evolution, regulatory variation, RNA-seq
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-369587DOI: 10.1111/1755-0998.12909ISI: 000449535600007PubMedID: 29858523OAI: oai:DiVA.org:uu-369587DiVA, id: diva2:1272602
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationAvailable from: 2018-12-19 Created: 2018-12-19 Last updated: 2019-06-11Bibliographically approved
In thesis
1. Gene regulatory evolution in flycatchers: statistical approaches for the analysis of allele-specific expression
Open this publication in new window or tab >>Gene regulatory evolution in flycatchers: statistical approaches for the analysis of allele-specific expression
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Understanding the molecular mechanisms underlying evolutionary changes in gene expression is a major research topic in biology. While a powerful approach to study this is the analysis of allele-specific expression (ASE), most of previously published methods can only be applied to lab organisms. In this thesis, to enable the analysis of ASE in natural organisms, I developed two methods for ASE detection. The first one was Bayesian negative binomial approach, and the second one was Read-backed Phasing-based ASE approach. Both methods performed well in simulations and comparisons. By applying those methods, I found that ASE was prevalent in natural flycatcher species. Combining the analyses of differential gene expression and ASE, I found a widespread cis-trans compensation and a critical role of tissue-specific regulatory mechanism during gene expression evolution. Moreover, for cis-regulatory sequences, there was a larger proportion of slightly deleterious mutations and weaker signatures of positive selection for genes with ASE than genes without ASE. For coding sequence, no such difference was observed. These results indicated that the evolution of gene expression and coding sequences could be uncoupled and occurred independently.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2019. p. 46
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1823
Keywords
ASE, gene expression evolution, bayesian, RPASE, flycatcher.
National Category
Evolutionary Biology
Research subject
Biology with specialization in Evolutionary Genetics
Identifiers
urn:nbn:se:uu:diva-384493 (URN)978-91-513-0686-5 (ISBN)
Public defence
2019-09-04, Lindahlsalen, Norbyvägen 14, Uppsala, 13:00 (English)
Opponent
Supervisors
Available from: 2019-08-13 Created: 2019-06-05 Last updated: 2019-08-13

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Wang, MiUebbing, SeverinScofield, Douglas G.

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