ArticleNucleic acids research2014
Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- A PIWI protein-dependent DNA N6-adenine methylation pathway inbioRxiv : the preprint server for biology · 2026Article
- Two paralogous PHD finger proteins participate in natural genome editing in Paramecium tetraurelia.Journal of cell science · 2024Article
- MITE infestation accommodated by genome editing in the germline genome of the ciliateProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium.The EMBO journal · 2022Article
- Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements.RNA (New York, N.Y.) · 2022Article
- BleTIES: annotation of natural genome editing in ciliates using long read sequencing.Bioinformatics (Oxford, England) · 2021Article
- Evolutionary Plasticity of Mating-Type Determination Mechanisms in Paramecium aurelia Sibling Species.Genome biology and evolution · 2021Article
- Epigenetics as Driver of Adaptation and Diversification in Microbial Eukaryotes.Frontiers in genetics · 2021Article
- Programmed genome rearrangements in ciliates.Cellular and molecular life sciences : CMLS · 2020Review
- Roles of Noncoding RNAs in Ciliate Genome Architecture.Journal of molecular biology · 2020Review
- Evolutionary origins and impacts of genome architecture in ciliates.Annals of the New York Academy of Sciences · 2019Review
- A mating-type mutagenesis screen identifies a zinc-finger protein required for specific DNA excision events in Paramecium.Nucleic acids research · 2018Article
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- Insights into transgenerational epigenetics from studies of ciliates.European journal of protistology · 2017Review
- A meiosis-specific Spt5 homolog involved in non-coding transcription.Nucleic acids research · 2017Article
- Article
- Cis-acting signals modulate the efficiency of programmed DNA elimination in Paramecium tetraurelia.Nucleic acids research · 2015Article
- TFIIS-Dependent Non-coding Transcription Regulates Developmental Genome Rearrangements.PLoS genetics · 2015Article
- Pdsg1 and Pdsg2, novel proteins involved in developmental genome remodelling in Paramecium.PloS one · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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