Two Piwis with Ago-like functions silence somatic genes at the chromatin level

Drews, Franziska; Karunanithi, Sivarajan; Götz, Ulrike; Marker, Simone; deWijn, Raphael; Pirritano, Marcello; Rodrigues-Viana, Angela M.; Jung, Martin; Gasparoni, Gilles; Schulz, Marcel H.; Simón, Martín

doi:10.1080/15476286.2021.1991114

Cited by 5 publications

(5 citation statements)

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“…For the antibody against P. tetraurelia RPB1, the peptide SPHYTSHTN SPSPSYRSS-C was used for immunization. Purification and testing of specificity by western blots and immunostaining were performed as described recently (Drews et al 2021). Because there are some amino acid differences in the N-terminal tail of the Paramecium H3P1 to Human H3 (Supplemental Fig.…”

Section: Antibodiesmentioning

confidence: 99%

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

et al. 2022

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The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics, including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin, our study characterizes the functional epigenomic organization necessary for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) reveal no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicate H3K4me3 levels inside ORFs to be the main factor associated with gene expression, and H3K27me3 appears in association with H3K4me3 in plastic genes. Silent and lowly expressed genes show low nucleosome occupancy, suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Because of a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different from that of other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data imply that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. In summary, gene activation and silencing in Paramecium run counter to the current understanding of chromatin biology.

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Section: Antibodiesmentioning

confidence: 99%

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

et al. 2022

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“… 12 Additionally, the closely related paralog of Ptiwi08, Ptiwi14, was shown to bind endo-siRNAs from SRCs, as well as siRNAs from all protein coding genes in the Paramecium genome. 11 Since we found Ptiwi08-bound sRNAs to also map in clusters in the genome, we crossreferenced our clusters with the previously published SRCs. Indeed, the majority of the clusters we identified in our analysis are SRCs (90%, 63 of 70 clusters), yet not all SRCs are Ptiwi08 bound (2.4%, 63 of 2,602 clusters).…”

Section: Resultsmentioning

confidence: 99%

“…All Ptiwi-bound sRNAs in Paramecium that have been investigated so far are produced in a Dicer-dependent manner and map with perfect complementarity to their targets. 9 , 10 , 11 , 15 , 18 Hence, their biogenesis more resembles siRNAs than PIWI-interacting RNAs (piRNAs). The strong strand bias of the Ptiwi08-bound endo-siRNAs may suggest that they derive from single-stranded precursors or that they are generated from double-stranded precursors and undergo strong strand selection after production.…”

Section: Resultsmentioning

confidence: 99%

“…The Ptiwi proteins investigated to date have been shown to perform diverse roles, including both exogenous and endogenous small interfering RNA (siRNA) pathways, as well as two sRNA pathways essential for DNA deletions during development as an extreme form of transposon silencing. 9 , 10 , 11 Hence, Paramecium is an excellent model for investigating the diversity of Argonaute proteins and sRNA pathways, yet the function of most Ptiwis still remains unknown. One of these is Ptiwi08, a protein that is expressed exclusively during development of a new somatic genome concomitant with the start of zygotic transcription.…”

Section: Introductionmentioning

confidence: 99%

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Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium

2023

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“…Their precise role remains to be elaborated: they could be mutually exclusive specific for 1° or 2° siRNAs, which would then be similar to the developmental RNAi pathway. Ptiwi13 has been shown to load siRNAs matching to food bacterial genomes (Drews et al, 2021); thus, it may also be responsible for loading 1° siRNAs in this mechanism here. However, transgene-induced RNAi recently reported that the two Ptiwis involved do not show a mutual exclusive loading of 1° and 2° siRNAs: their function may be in RNA shuttling and transport (Drews et al, 2021;Götz et al, 2016).…”

Section: Primary and Secondary Sirnas Are Involved In Feeding Induced...mentioning

confidence: 92%

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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Two Piwis with Ago-like functions silence somatic genes at the chromatin level

Cited by 5 publications

References 70 publications

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

Broad domains of histone marks in the highly compact Paramecium macronuclear genome

Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium

Paramecium epigenetics in development and proliferation

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