Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion

Swart, Estienne Carl; Wilkes, Cyril Denby; Sandoval, Pamela Yohanna de Lourdes; Arambasic, Miroslav; Sperling, Linda; Nowacki, Mariusz (2014). Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion. Nucleic acids research, 42(14), pp. 8970-8983. Oxford University Press 10.1093/nar/gku619

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During the development of the somatic genome from the Paramecium germline genome the bulk of the copies of ∼45 000 unique, internal eliminated sequences (IESs) are deleted. IES targeting is facilitated by two small RNA (sRNA) classes: scnRNAs, which relay epigenetic information from the parental nucleus to the developing nucleus, and iesRNAs, which are produced and used in the developing nucleus. Why only certain IESs require sRNAs for their removal has been enigmatic. By analyzing the silencing effects of three genes: PGM (responsible for DNA excision), DCL2/3 (scnRNA production) and DCL5 (iesRNA production), we identify key properties required for IES elimination. Based on these results, we propose that, depending on the exact combination of their lengths and end bases, some IESs are less efficiently recognized or excised and have a greater requirement for targeting by scnRNAs and iesRNAs. We suggest that the variation in IES retention following silencing of DCL2/3 is not primarily due to scnRNA density, which is comparatively uniform relative to IES retention, but rather the genetic properties of IESs. Taken together, our analyses demonstrate that in Paramecium the underlying genetic properties of developmentally deleted DNA sequences are essential in determining the sensitivity of these sequences to epigenetic control.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Biology > Institute of Cell Biology
08 Faculty of Science > Other Institutions > Teaching Staff, Faculty of Science
08 Faculty of Science > Department of Biology > Institute of Cell Biology > Ciliate

UniBE Contributor:

Swart, Estienne Carl; Sandoval, Pamela Yohanna de Lourdes; Arambasic, Miroslav and Nowacki, Mariusz

Subjects:

500 Science > 570 Life sciences; biology

ISSN:

0305-1048

Publisher:

Oxford University Press

Funders:

[4] Swiss National Science Foundation
[18] European Research Council

Language:

English

Submitter:

Mariusz Nowacki

Date Deposited:

01 Sep 2014 14:39

Last Modified:

27 Apr 2018 09:59

Publisher DOI:

10.1093/nar/gku619

PubMed ID:

25016527

BORIS DOI:

10.7892/boris.54637

URI:

https://boris.unibe.ch/id/eprint/54637

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