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HD2B and HD2C interact with Argonaute 4 to promote tolerance and heterochromatin stabilization during heat stress [ncRNA-Seq]

ABSTRACT: In this study, we show that HD2B/C work with AGO4 to promote heat tolerance

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE212021 | GEO | 2023/08/12

REPOSITORIES: GEO

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HD2B and HD2C interact with Argonaute 4 to promote tolerance and heterochromatin stabilization during heat stress [RNA-Seq]

Project description:In this study, we show that HD2B/C work with AGO4 to promote heat tolerance

2023-08-12 | GSE212019 | GEO

HD2B and HD2C interact with Argonaute 4 to promote tolerance and heterochromatin stabilization during heat stress [ChIP-Seq]

Project description:In this study, we show that HD2B/C work with AGO4 to promote heat tolerance

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HD2B and HD2C interact with Argonaute 4 to promote tolerance and heterochromatin stabilization during heat stress [BS-Seq]

Project description:In this study, we show that HD2B/C work with AGO4 to promote heat tolerance

2023-08-12 | GSE212020 | GEO

HD2B and HD2C interact with Argonaute 4 to promote tolerance and heterochromatin stabilization during heat stress

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-08-12 | GSE212022 | GEO

Functional analysis of HD2C in Arabidopsis

Project description:Ribosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis histone deacetylase HD2C in pre-rRNA processing via both canonical and non-canonical manners. HD2C interacts with HD2B and forms homo- and/or hetero-oligomers in the nucleolus. Depletion of HD2C and HD2B induces a ribosome biogenesis deficiency morphological phenotype and aberrant accumulation of 18S pre-rRNA intermediates. Our genome-wide analysis revealed that HD2C binds and represses the expression of key genes involved in ribosome biogenesis. Using RNA immunoprecipitation and sequencing, we further uncovered a non-canonical mechanism of HD2C directly associating with pre-rRNA and small nucleolar RNAs to regulate rRNA methylation. Together, this study reveals a multifaceted role of HD2C in ribosome biogenesis and provides mechanistic insights into how histone deacetylases modulate rRNA maturation at both transcriptional and post-transcriptional levels.

2018-03-01 | GSE107883 | GEO

Long non-coding RNA produced by RNA polymerase V determines boundaries of heterochromatin

Project description:We report genome-wide detection of long noncoding RNA (lncRNA) generate by Pol V in transcriptional gene silencing in Arabidopsis thaliana. We further show that most of these transcripts are bound by AGO4. RNA immunoprecipitation followed by high-throughput sequencing (RIP-seq) RNA immunoprecipitation with an anti-AGO4 antibody was performed in one biological replicate and included Col-0, nrpe1, and ago4-1; RNA immunoprecipitation with an anti-NRPE1 (largest subunit of Pol V) was performed in two replicates; replicate 1 included Col-0 and nrpe1, replicated two included Col-0, nrpe1, ago4-1, and idn2-1

2016-10-24 | E-GEOD-70290 | biostudies-arrayexpress

Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation [ncRNA-seq 2]

Project description:Ago1 can mediate transcriptional gene silencing without slicing nascent RNA target

2016-12-19 | GSE81733 | GEO

Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation [ncRNA-seq 1]

Project description:Ago1 can mediate transcriptional gene silencing without slicing nascent RNA target

2016-12-19 | GSE81732 | GEO

Ser7 of RNAPII-CTD facilitates heterochromatin formation by linking ncRNA to RNAi.

Project description:Some long noncoding RNAs (ncRNAs) transcribed by RNA polymerase II (RNAPII) are retained on chromatin, where they regulate RNAi and chromatin structure. The molecular basis of this retention remains unknown. We show that in fission yeast serine 7 (Ser7) of the C-terminal domain (CTD) of RNAPII is required for efficient siRNA generation for RNAi-dependent heterochromatin formation. Surprisingly, Ser7 facilitates chromatin retention of nascent heterochromatic RNAs (hRNAs). Chromatin retention of hRNAs and siRNA generation requires both Ser7 and an RNA-binding activity of the chromodomain of Chp1, a subunit of the RNA-induced transcriptional silencing (RITS) complex. Furthermore, RITS associates with RNAPII in a Ser7-dependent manner. We propose that Ser7 promotes cotranscriptional chromatin retention of hRNA by recruiting the RNA-chromatin connector protein Chp1, which facilitates RNAi-dependent heterochromatin formation. Our findings reveal a function of the CTD code: linking ncRNA transcription to RNAi for heterochromatin formation.

| S-EPMC5748204 | biostudies-literature

Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation.

Project description:Small-RNA (sRNA)-guided transcriptional gene silencing by Argonaute (Ago)-containing complexes is fundamental to genome integrity and epigenetic inheritance. The RNA cleavage ("Slicer") activity of Argonaute has been implicated in both sRNA maturation and target RNA cleavage. Typically, Argonaute slices and releases the passenger strand of duplex sRNA to generate active silencing complexes, but it remains unclear whether slicing of target nascent RNAs, or other RNAi components, also contributes to downstream transcriptional silencing. Here, we develop a strategy for loading the fission yeast Ago1 with a single-stranded sRNA guide, which bypasses the requirement for slicer activity in generation of active silencing complexes. We show that slicer-defective Ago1 can mediate secondary sRNA generation, H3K9 methylation, and silencing similar to or better than wild-type and associates with chromatin more efficiently. The results define an ancient and minimal sRNA-mediated chromatin silencing mechanism, which resembles the germline-specific sRNA-dependent transcriptional silencing pathways in Drosophila and mammals.

| S-EPMC5576859 | biostudies-literature

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