title: Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion.
abstract: 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.
authors.affiliation: Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
authors.forename: Estienne C
authors.initials: EC
authors.lastname: Swart
authors.affiliation: CNRS UPR3404 Centre de Génétique Moléculaire, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198 cedex, France Université Paris-Sud, Département de Biologie, Orsay, F-91405, France.
authors.forename: Cyril Denby
authors.initials: CD
authors.lastname: Wilkes
authors.affiliation: Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
authors.forename: Pamela Y
authors.initials: PY
authors.lastname: Sandoval
authors.affiliation: Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland.
authors.forename: Miroslav
authors.initials: M
authors.lastname: Arambasic
authors.affiliation: CNRS UPR3404 Centre de Génétique Moléculaire, 1 avenue de la Terrasse, Gif-sur-Yvette F-91198 cedex, France Université Paris-Sud, Département de Biologie, Orsay, F-91405, France.
authors.forename: Linda
authors.initials: L
authors.lastname: Sperling
authors.affiliation: Institute of Cell Biology, University of Bern, Baltzerstrasse 4, 3012 Bern, Switzerland mariusz.nowacki@izb.unibe.ch.
authors.forename: Mariusz
authors.initials: M
authors.lastname: Nowacki
mesh_terms: D001483:Base Sequence; D016054:DNA, Protozoan / Q000737:chemistry / Q000378:metabolism*; D044127:Epigenesis, Genetic; D020868:Gene Silencing; D018503:Genome, Protozoan; D010247:Paramecium / Q000235:genetics; D034741:RNA, Small Interfering / Q000032:analysis; D058727:RNA, Small Untranslated / Q000032:analysis; D043244:Ribonuclease III / Q000037:antagonists & inhibitors / Q000235:genetics; D017384:Sequence Deletion
chemical_list: D016054:DNA, Protozoan; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated; D043244:Ribonuclease III