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Comparison of SUMOylated proteins between wild-type and EMA2 KO Tetrahymena cells

ABSTRACT: Small RNAs target their complementary chromatin regions for gene silencing through nascent long non-coding RNAs (lncRNAs). In programmed DNA elimination of the ciliated protozoan Tetrahymena, the interaction between Piwi-associated small RNA (scnRNAs) and the lncRNA transcripts from the somatic genome has been proposed to induce target-directed scnRNA degradation (TDSD) and scnRNAs not targeted for TDSD later target the germline-limited sequences for DNA elimination. In this study, we show that the SUMO E3 ligase Ema2 is required for the accumulation of lncRNAs from somatic genome, and thus for TDSD and completing DNA elimination to make viable sexual progeny. Ema2 interacts with the SUMO E2 conjugating enzyme Ubc9 and enhances SUMOylation of the transcription regulator Spt6. We further show that Ema2 promotes the association of Spt6 and RNA polymerase II to chromatin. These results suggest that Ema2-directed SUMOylation actively promotes the lncRNA transcription that is a prerequisite for communication between the genome and small RNAs.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Tetrahymena Thermophila (ncbitaxon:5911)

SUBMITTER: Kazufumi MOCHIZUKI

PROVIDER: MSV000092977 | MassIVE |

SECONDARY ACCESSION(S): PXD045728

REPOSITORIES: MassIVE

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EMA2 is required for target-directed scnRNA degradation.

Project description:Piwi-associated small RNAs of the ciliated protozoan Tetrahymena uses such mechanism to induce heterochromatin formation followed by programmed DNA elimination. In this process, target-directed small RNA degradation (TDSD) of small RNAs complementary to the somatic genome enables small RNAs to specifically target the germline-limited sequences for DNA elimination. The data here indicate that the SUMO E3 ligase Ema2 is required for the accumulation of long non-coding RNAs (lncRNAs) from the somatic genome and thus for TDSD.

2023-09-18 | GSE243435 | GEO

Investigation of the timing of secondary small RNA biogenesis during programmed DNA elimination in Tetrahymena

Project description:Signal amplification of the initial small RNA trigger is important to ensure the silencing of repetitive transposable elements (TEs). Curiously, secondary small RNA biogenesis occurs by various mechanisms that are coupled with distinct steps of TE silencing in different eukaryotes, such as nucleolytic cleavage of TE transcripts, recruitment of RNA-dependent RNA polymerase, and heterochromatin-directed transcription. How such a variety of small RNA amplification mechanisms has evolved has not been thoroughly elucidated to date. Ciliated protozoa perform small RNA-directed programmed DNA elimination of thousands of TE-related internal eliminated sequences (IESs) in the newly developed somatic nucleus. In the ciliate Paramecium, secondary small RNAs are produced after primary small RNAs induce the excision of IESs. To examine whether such post-excision production of secondary small RNAs is conserved, we investigate the causality between the excision of IESs and the biogenesis of secondary small RNAs in another ciliate, Tetrahymena. We show that secondary small RNAs accumulate at least a few hours before their derived IESs are excised and that DNA excision is dispensable for their biogenesis in this ciliate. Therefore, unlike the situation in Paramecium, small RNA amplification occurs prior to IES excision in Tetrahymena. This study reveals remarkable mechanistic diversity of secondary small RNA biogenesis mechanisms, even among ciliates showing similar DNA elimination processes, and thus raises the possibility that the evolution of TE-targeting small RNA amplification can be traced by investigating the DNA elimination mechanisms of ciliates.

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Expression of small RNAs during epigenetic disturbances of Tetrahymena DNA elimination

Project description:Epigenetic inheritance of acquired traits is widespread among eukaryotes but how and to what extent such information is trans-generationally inherited is still unclear. The patterns of programmed DNA elimination in ciliates are epigenetically and trans-generationally inherited, and it has been proposed that small RNAs, which shuttle between the germline and the soma, regulate this epigenetic inheritance. In this study, we test the existence of such small RNA-mediated communication by epigenetically disturbing the pattern of DNA elimination in Tetrahymena. We show that the pattern of DNA elimination is indeed determined by the selective turnover of small RNAs, which is induced by the interaction between germline-derived small RNAs and the somatic genome. In addition, we show that DNA elimination of an element is regulated by small RNA-mediated communication with other eliminated elements. By contrast, no evidence obtained thus far supports the notion that transfer of epigenetic information from the soma to the germline, if any, regulates DNA elimination. Our results indicate that small RNA-mediated trans-nuclear and trans-element communication, in addition to unknown information in the germline genome, contributes to determining the pattern of DNA elimination.

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Chromatin-Associated SUMOylation Controls the Transcriptional Switch between Plant Development and Heat Stress Responses

Project description:The post-translational protein modiﬁcation known as SUMOylation has conserved roles in the heat stress responses of various species. The functional connection between the global regulation of gene expression and chromatin-associated SUMOylation in plant cells isunknown. Here, we uncovereda genome-wide relationship between chromatin-associated SUMOylation and transcriptional switches in Arabidopsis thaliana grown at room temperature, exposed to heat stress, and exposed to heat stress followed by recovery. The small ubiquitin-like modiﬁer (SUMO)-associated chromatin sites, characterized by whole-genome ChIP-seq, were generally associated with active chromatin markers. In response to heat stress, chromatin-associated SUMO signals increased at promoter-transcriptional start site regions and decreased in gene bodies. RNAseqanalysissupportedthe role ofchromatin-associatedSUMOylationin transcriptionalactivation duringrapid responses to high temperature. Changes inSUMO signals on chromatinwere associated with the upregulation ofheat-responsivegenesandthedownregulationofgrowth-relatedgenes.DisruptionoftheSUMOligasegene SIZ1 abolished SUMO signals on chromatin and attenuated rapid transcriptional responses to heat stress. The SUMO signal peaks were enriched in DNA elements recognized by distinct groups of transcription factors under different temperature conditions. These observations provide evidence that chromatin-associated SUMOylation regulates the transcriptional switch between development and heat stress response in plant cells.

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SUMOylation on plant chromatin controls transcription switches between development and heat response [RNA-Seq]

Project description:SUMOylation, a post-translational protein modification, is dramatically upregulated and critically involved in heat stress response conservatively among species. Previous studies in Arabidopsis indicated that numerous chromatin associated proteins are SUMOylation substrates and most of heat-enhancing SUMOylation reactions occur in nucleus. However, the global functional connection between gene expression regulation and SUMOylation on chromatin is completely unknown in plant cells. Here we show a genome-wide relationship of chromatin-associated SUMOylation and transcription switches under room temperature, heat stress, and recovering conditions in Arabidopsis. The SUMO-associated chromatin sites, characterized via whole-genome ChIP-seq assays, are generally correlated with active chromatin markers. In response to heat stress, we found chromatin-associated SUMO signals increased at promoter-transcriptional start site regions and decreased in the gene bodies. Further RNA-seq analysis supported the role of chromatin-associated SUMOylation in activation of transcription during rapid responses to high temperature. Changing of SUMO signals on chromatin is correlated with upregulation of heat-responsive genes and downregulation of growth-related genes. Disruption of the SUMO ligase gene SIZ1 abolishes SUMO signals on chromatin and attenuates the rapid transcriptional responses to heat stress. Interestingly, the SUMO signal peaks are enriched in DNA elements recognized by distinguished groups of transcription factors under different temperature conditions. Collectively, our data provide evidence that SUMOylation on chromatin regulates transcription switches during development and heat stress response, improving our understanding on the precise roles of SUMOylation in plant cells.

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SUMOylation on plant chromatin controls transcription switches between development and heat response [ChIP-Seq]

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SUMOylation inhibition overcomes dexamethasone resistance in multiple myeloma

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2016-08-01 | E-GEOD-80681 | biostudies-arrayexpress

Identification of new regulators of the three dimensional Polycomb organization by a microscopy-based genome-wide RNAi screen

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Gene expression profiles in wild-type and SUMO knockdown mice after forebrain ischemia

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