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Patterns of variation in cis-regulatory regions: examining evidence of purifying selection
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. (Evolutionär organismbiologi)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. (Evolutionär organismbiologi)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. (Evolutionär organismbiologi)ORCID iD: 0000-0002-8160-9621
Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. (Evolutionär organismbiologi)ORCID iD: 0000-0001-7840-7853
2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 95Article in journal (Refereed) Published
Abstract [en]

Background: With only 2 % of the human genome consisting of protein coding genes, functionality across the rest of the genome has been the subject of much debate. This has gained further impetus in recent years due to a rapidly growing catalogue of genomic elements, based primarily on biochemical signatures (e.g. the ENCODE project). While the assessment of functionality is a complex task, the presence of selection acting on a genomic region is a strong indicator of importance. In this study, we apply population genetic methods to investigate signals overlaying several classes of regulatory elements.

Results: We disentangle signals of purifying selection acting directly on regulatory elements from the confounding factors of demography and purifying selection linked to e.g. nearby protein coding regions. We confirm the importance of regulatory regions proximal to coding sequence, while also finding differential levels of selection at distal regions. We note differences in purifying selection among transcription factor families. Signals of constraint at some genomic classes were also strongly dependent on their physical location relative to coding sequence. In addition, levels of selection efficacy across genomic classes differed between African and non-African populations.

Conclusions: In order to assign a valid signal of selection to a particular class of genomic sequence, we show that it is crucial to isolate the signal by accounting for the effects of demography and linked-purifying selection. Our study highlights the intricate interplay of factors affecting signals of selection on functional elements.

Place, publisher, year, edition, pages
BIOMED CENTRAL LTD , 2018. Vol. 19, article id 95
Keywords [en]
Regulatory regions, Purifying selection, Selection efficacy, Non-coding DNA, Functional elements, Population genetics
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-343792DOI: 10.1186/s12864-017-4422-yISI: 000423443900002PubMedID: 29373957OAI: oai:DiVA.org:uu-343792DiVA, id: diva2:1187552
Funder
Göran Gustafsson Foundation for Research in Natural Sciences and MedicineKnut and Alice Wallenberg FoundationSwedish Research CouncilAvailable from: 2018-03-05 Created: 2018-03-05 Last updated: 2018-03-05Bibliographically approved

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Naidoo, ThijessenSjödin, PerSchlebusch, CarinaJakobsson, Mattias
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