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Recruitment of RNA Polymerase II by the pioneer transcription factor PHA-4

ABSTRACT: Using staged embryos, we find many more genes with poised RNA polymerase than had been observed previously in C. elegans embryos, suggesting that early embryos accumulate poised PolII, and that poising is dynamic.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE68280 | GEO | 2015/07/01

SECONDARY ACCESSION(S): PRJNA282374

REPOSITORIES: GEO

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Recruitment of RNA Polymerase II by the pioneer transcription factor PHA-4

Project description:Using staged embryos, we find many more genes with poised RNA polymerase than had been observed previously in C. elegans embryos, suggesting that early embryos accumulate poised PolII, and that poising is dynamic. Embryos were staged at the 8E and Bean stages of development prior to ChIP-seq

2015-07-01 | E-GEOD-68280 | biostudies-arrayexpress

TRANSCRIPTION. Recruitment of RNA polymerase II by the pioneer transcription factor PHA-4.

Project description:Pioneer transcription factors initiate cell-fate changes by binding to silent target genes. They are among the first factors to bind key regulatory sites and facilitate chromatin opening. Here, we identify an additional role for pioneer factors. In early Caenorhabditis elegans foregut development, the pioneer factor PHA-4/FoxA binds promoters and recruits RNA polymerase II (Pol II), often in a poised configuration in which Pol II accumulates near transcription start sites. At a later developmental stage, PHA-4 promotes chromatin opening. We found many more genes with poised RNA polymerase than had been observed previously in unstaged embryos, revealing that early embryos accumulate poised Pol II and that poising is dynamic. Our results suggest that Pol II recruitment, in addition to chromatin opening, is an important feature of PHA-4 pioneer factor activity.

| S-EPMC4861314 | biostudies-literature

Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [ATAC-seq]

Project description:Vertebrate embryos achieve developmental competency during zygotic genome activation (ZGA) by establishing chromatin states that silence yet poise developmental genes for subsequent lineage-specific activation. Here, we reveal how developmental gene poising is established de novo in preZGA zebrafish embryos. Poising is established at promoters and enhancers that initially contain open/permissive chromatin with ‘Placeholder’ nucleosomes (bearing H2A.Z, H3K4me1, and H3K27ac), and DNA hypomethylation. Silencing is initiated by the recruitment of Polycomb Repressive Complex 1 (PRC1), and H2Aub1 deposition by catalytic Rnf2 during preZGA and ZGA stages. During postZGA, H2Aub1 enables Aebp2-containing PRC2 recruitment and H3K27me3 deposition. Notably, preventing H2Aub1 (via Rnf2 inhibition) eliminates recruitment of Aebp2-PRC2 and H3K27me3, and elicits transcriptional upregulation of certain developmental genes during ZGA. However, upregulation is independent of H3K27me3 – establishing H2Aub1 as the critical silencing modification at ZGA. Taken together, we reveal the logic and mechanism for establishing poised/silent developmental genes in early vertebrate embryos.

2022-01-04 | GSE168361 | GEO

Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [ChIP-seq]

2022-01-04 | GSE168360 | GEO

Establishment of Developmental Gene Silencing by Ordered Polycomb Complex Recruitment in Early Zebrafish Embryos [RNA-seq]

2022-01-04 | GSE168359 | GEO

Poised RNA polymerase II co-localises with Polycomb repression at multi-lineage developmental regulator genes in differentiated neurons

Project description:Polycomb repression is tightly associated with promoter co-occupancy of poised RNA polymerase II (RNAPII) in mouse Embryonic Stem Cells (ESCs). However, it remains unclear whether poising is a specific feature of ESCs or also associated with Polycomb during cell differentiation. Here, we show that RNAPII poising at Polycomb repressed genes is found in five stages of ESC differentiation to dopaminergic neurons. We find that key transcription factor genes of non-neuronal lineages are kept silent in the neuronal lineage through Polycomb repression in co-association with poised RNAPII in the absence of DNA methylation within DNA Methylation Valleys (DMVs). This group of poised transcription factors are preferential candidate master regulators for trans-differentiation of neurons into different lineages. We conclude that RNAPII poising is a general feature of Polycomb repression and cell plasticity in pluripotent stem cells and terminally differentiated neurons.

2017-09-29 | GSE94364 | GEO

CDK13 cooperates with CDK12 to control global RNA polymerase II processivity

Project description:The RNA polymerase II (POLII) driven transcription cycle is tightly regulated at distinct checkpoints through cyclin dependent kinases (CDKs) and their cognate Cyclins. The molecular events underpinning transcriptional elongation and processivity and CDK-Cyclins involved remain poorly understood. Using CRISPR-CAS9 homology-directed-repair we generated analog-sensitive-kinase variants of CDK12 and CDK13 to probe their individual and shared biological and molecular roles. Single inhibition of CDK12 or CDK13 induced transcriptional responses associated with DNA-damage and cellular growth signaling pathways respectively, with minimal effects on cell viability. In contrast, dual-kinase inhibition potently induced cell death, which was associated with extensive genome-wide transcriptional changes including wide-spread use of alternative 3’ polyadenylation sites. At the molecular level dual-kinase inhibition resulted in the loss of POLII CTD phosphorylation and greatly reduced POLII elongation rates and processivity. These data define significant redundancy between CDK12 and CDK13, and identify both as fundamental regulators of global POLII processivity and transcription elongation.

2020-04-30 | PXD015453 | Pride

RNA-seq of staged embryos

Project description:RNA-seq of staged embryos

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Poised RNA Polymerase II changes over developmental time and prepares genes for future expression (ChIP-seq data)

Project description:Poised RNA polymerase II is predominantly found at developmental control genes and is thought to allow their rapid and synchronous induction in response to extracellular signals. How the recruitment of poised RNA Pol II is regulated during development is not known. By isolating muscle tissue from Drosophila embryos at five stages of differentiation, we show that the recruitment of poised Pol II occurs at many genes de novo and this makes them permissive for future gene expression. When compared to other tissues, these changes are stage-specific and not tissue-specific. In contrast, Polycomb group repression is tissue-specific and in combination with Pol II (the balanced state) marks genes with highly dynamic expression. This suggests that poised Pol II is temporally regulated and is held in check in a tissue-specific fashion. We compare our data to mammalian embryonic stem cells and discuss a framework for predicting developmental programs based on chromatin state. ChIP-seq for Pol II, H3K4me3 and H3K27me3 in various Drosophila embryos and tissues

2012-12-20 | E-GEOD-34301 | biostudies-arrayexpress

ChIP-seq of ZGA staged embryos

Project description:ChIP-seq of ZGA staged embryos

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