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The plant POLYMERASE ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome-wide [RNA-seq]

ABSTRACT: The transcriptome of WT, elf7-3 and hub1-4 seedlings was obtained by RNA-seq in order to determine the effect of mutations on transcript levels and to correlate them with chromatin features determined by ChIP-seq.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE244848 | GEO | 2024/03/07

REPOSITORIES: GEO

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The plant POLYMERASE-ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome wide [ChIP-seq]

Project description:We have determined the distribution of two subunits of Paf1C, namely ELF7 and VIP3. We have investigated the contribution of the Paf1 complex to the monoubiquitination of H2B genome-wide by ChIP-seq. Finally, we have investigated the effect of defective Paf1C on the distribution of total RNAPII.

2024-03-07 | GSE244846 | GEO

The plant POLYMERASE-ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome wide

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

2024-03-07 | GSE244850 | GEO

Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis

Project description:In eukaryotes, chromatin-based mechanisms superimpose with DNA sequence information to determine the transcriptional output of the genome. Therefore, evaluating the role of chromatin modifications in the regulation of gene expression is key to understand the contribution of chromatin state variations to development. Recent studies identified several transcriptional coactivators that contribute to selectively regulate cellular pathways by coordinating histone H2B monoubiquitination (H2Bub) with other histone modifications. Although H2Bub is present on a large number of genes, loss of H2B monoubiquitination activity was shown to affect RNA steady levels for a small subset of genes and therefore its influence on gene expression is not well understood. In this study we assessed the impact of H2Bub on dynamic expression changes during a rapid developmental tranistion that initiates only when exposing plants to light. This revealed that H2Bub deposition is highly dynamic in a genomic context. Furthermore, plants lacking histone H2B monoubiquitination activity were impaired for rapid changes of RNA levels for a large repertoire of genes, indicating that H2Bub is important for attaining appropriate expression levels /in fine/. Finally, the detection power of the genomic approach has allowed us to define a set of genes impacted by H2Bub dynamics for rapid changes in RNA levels. The purpose of this study was to integrate the genome-wide distribution of H2Bub chromatin mark together with transcriptome profiles of wild-type and /hub1 /mutant plants (accession GSE21922) at three time points during early photomorphogenesis H2Bub epigenome in 5-day-old dark-grown seedlings, H2Bub epigenome in 5-day-old dark-grown seedlings +1h light, and H2Bub epigenome in 5-day-old dark-grown seedlings +6h light 2 biological replicates for each time point in dye-swap - ChIP-chip

2013-03-13 | E-GEOD-36515 | biostudies-arrayexpress

Cap-binding complex assists RNA Polymerase II transcription in plant salt stress response

Project description:Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in mRNA production is crucial for maximized plant survival. Transcription and pre-mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap-binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II-associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 co-regulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt-activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance.

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Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination.

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RNA sequencing of polymerase II-associated factor 1 complex (PAF1c) mutants at 10°C and 23°C under LD conditions

Project description:We sequenced mRNA of WT (Col-0) and PAF1c single mutants (php, elf7, vip3, vip4, vip5, and vip6) grown at 10°C and 23°C under LD conditions. RNA was extracted from seedlings of 1.02 developmental stage at both temperatures and proceeded for library preparation

2022-03-02 | GSE171778 | GEO

GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data]

Project description:We have found that histone H2B is GlcNAcylated at residue S112 by O-GlcNAc transferase and that H2B S112 GlcNAcylation fluctuates in response to extracellular glucose level. We have also found that H2B S112 GlcAcylation promotes H2B K120 ubiquitination. To investigate whether these histone modification correlate to transcriptional activation, we performed comprehensive gene expression analysis using Affymetrix GeneChip in HeLa cell cultured with different conditions, i.e. without glucose, with glucose and with FBS.

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