<i>Paramecium</i> Polycomb Repressive Complex 2 physically interacts with the small RNA binding PIWI protein to repress transposable elements

Pina, Miro; Kawaguchi, Takayuki; Charmant,; Michaud,; Cohen,; Humbert,; Jaszczyszyn, Yan; Maestro, Del; Holoch,; Ait-Si-Ali,; Arnaiz,; Raphael,; Duharcourt, Sandra

doi:10.1101/2021.08.12.456067

Cited by 4 publications

(2 citation statements)

References 62 publications

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“…To determine whether the retention of TEs can be associated with transcriptional upregulation of these elements, as previously reported upon EZL1 silencing ( 37 ), we performed paired-end mRNA sequencing at late developmental stages (30–40 h after T0) in control, SPT5m and SPT4 -RNAi conditions. Our analysis revealed that expression of TEs is up-regulated during MAC development upon SPT5m -RNAi and the effect was comparable with de-repression observed for EZL1 ( Supplementary Figure S7 ) ( 50 ). On the other hand, SPT4 -RNAi resulted in a very small change in TEs expression.…”

Section: Resultssupporting

confidence: 74%

The transient Spt4-Spt5 complex as an upstream regulator of non-coding RNAs during development

Gruchota

Arnaiz

Nowak

2022

Nucleic Acids Research

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The Spt4-Spt5 complex is conserved and essential RNA polymerase elongation factor. To investigate the role of the Spt4-Spt5 complex in non-coding transcription during development, we used the unicellular model Paramecium tetraurelia. In this organism harboring both germline and somatic nuclei, massive transcription of the entire germline genome takes place during meiosis. This phenomenon starts a series of events mediated by different classes of non-coding RNAs that control developmentally programmed DNA elimination. We focused our study on Spt4, a small zinc-finger protein encoded in P. tetraurelia by two genes expressed constitutively and two genes expressed during meiosis. SPT4 genes are not essential in vegetative growth, but they are indispensable for sexual reproduction, even though genes from both expression families show functional redundancy. Silencing of the SPT4 genes resulted in the absence of double-stranded ncRNAs and reduced levels of scnRNAs – 25 nt-long sRNAs produced from these double-stranded precursors in the germline nucleus. Moreover, we observed that the presence of a germline-specific Spt4-Spt5m complex is necessary for transfer of the scnRNA-binding PIWI protein between the germline and somatic nucleus. Our study establishes that Spt4, together with Spt5m, is essential for expression of the germline genome and necessary for developmental genome rearrangements.

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Section: Resultssupporting

confidence: 74%

The transient Spt4-Spt5 complex as an upstream regulator of non-coding RNAs during development

Gruchota

Arnaiz

Nowak

2022

Nucleic Acids Research

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“…However, only a minor fraction of IESs depend on the scnRNA pathway (Furrer et al, 2017; Lhuillier‐Akakpo et al, 2014). The elimination process in the new developing MAC is initiated either by the interaction of the scnRNA with a nascent transcript or the DNA itself (Pina et al, 2021). In brief, IES targeted by scnRNAs become excised by the domesticated piggyBac transposase called piggyMac.…”

Section: Selective Hybridization Is Used Differently For Genome Scann...mentioning

confidence: 99%

Paramecium epigenetics in development and proliferation

Drews

Boenigk

Simón

2022

J Eukaryotic Microbiology

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CILIATES, particularly Paramecium, served as model organisms in genetics and epigenetics long before the latter term was even used for the first time. From the historical point of view, ciliate genetics had its first's heydays from 1940 to 1960, when many important discoveries were made, resulting in a detailed description of epigenetic phenomena. As a result, most textbooks for undergraduates dedicated individual chapters to ciliate cell biology and genetics in the 1970s, but these chapters disappeared from textbooks in modern times (Preer, 1997).This situation has now changed (Boenigk, 2021). Ciliate epigenetic research experiences a renaissance, although this wording might not be entirely precise as research is not simply making a replica of the former work. We are now able to describe epigenetic phenomena discovered phenotypically in the early 1940s on the molecular level and identify small RNAs, histone modifications, and DNA modifications that are responsible for these phenomena. Still, genetics research is primarily based on yeast, C. elegans, Drosophila, zebrafish, and

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Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics

Zangarelli

Arnaiz

Bourge

et al. 2022

Preprint

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With its nuclear dualism, the ciliate Paramecium constitutes an original model to study how host genomes cope with transposable elements (TEs). P. tetraurelia harbors two germline micronuclei (MIC) and a polyploid somatic macronucleus (MAC) that develops from the MIC at each sexual cycle. Throughout evolution, the MIC genome has been continuously colonized by TEs and related sequences that are removed from the somatic genome during MAC development. Whereas TE elimination is generally imprecise, excision of ~45,000 TE-derived Internal Eliminated Sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with genome amplification. It is guided by non-coding RNAs and repressive chromatin marks. A subset of IESs is excised independently of this epigenetic control, raising the question of how IESs are targeted for elimination. To gain insight into the determinants of IES excision, we established the developmental timing of DNA elimination genome-wide by combining fluorescence-assisted nuclear sorting with next-generation sequencing. Essentially all IESs are excised within only one endoreplication round (32C to 64C), while TEs are eliminated at a later stage. We show that time, rather than replication, controls the progression of DNA elimination. We defined four IES classes according to excision timing. The earliest excised IESs tend to be independent of epigenetic factors, display strong sequence signals at their ends and originate from the most ancient integration events. We conclude that old IESs have been optimized during evolution for early and accurate excision, by acquiring stronger sequence determinants and escaping epigenetic control.

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Paramecium Polycomb Repressive Complex 2 physically interacts with the small RNA binding PIWI protein to repress transposable elements

Cited by 4 publications

References 62 publications

The transient Spt4-Spt5 complex as an upstream regulator of non-coding RNAs during development

The transient Spt4-Spt5 complex as an upstream regulator of non-coding RNAs during development

Paramecium epigenetics in development and proliferation

Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics

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