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Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1 [SLAM-seq]

ABSTRACT: Using SLAM-seq to capture de novo synthesized polyadenylated RNAs, we quantitated changes in nascent RNA expression, as well as in total RNA expression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE171133 | GEO | 2021/11/11

REPOSITORIES: GEO

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Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1 [SLAM-seq]

Project description:Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1 [SLAM-seq]

| PRJNA718531 | ENA

Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1

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

2021-11-11 | GSE171134 | GEO

Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1 [ChIP-seq]

Project description:By following chromatin occupancy of RNAPII and TOP1 using ChIP-seq throughout mitosis, we found that TOP1 is required for RNAPII translocation along genes. The stimulation of TOP1 activity through its interaction with RNAPII during elongation, allowed RNAPII clearance from genes in prometaphase and enabled proper chromosomal segregation. Interference with the TOP1-RNAPII interaction or acute depletion of TOP1 at the onset of mitosis impaired RNAPII spiking at promoters, which is necessary for the first pioneering round of transcription during mitotic exit, and triggered defects in the transcriptional program of the post-mitotic cells.

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Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1

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Topoisomerase 1 activity during mitotic transcription favors the transition from mitosis to G1 [ChIP-seq]

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SLAM-seq ML-792

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SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis [SLAM-seq]

Project description:Defining direct targets of transcription factors and regulatory pathways is key to understanding their role in physiology and disease. Here we combine SLAM-seq, a novel method for direct quantification of newly synthesized mRNAs, with pharmacological and rapid chemical-genetic perturbation to interrogate primary transcriptional targets of BRD4 and MYC and define the response to BET bromodomain inhibitors (BETi). While BRD4 acts as a global co-activator of Pol2-dependent transcription in a BET bromodomain-dependent manner, therapeutic BETi doses deregulate a small set of hypersensitive target genes. In contrast to BRD4, MYC primarily acts as a selective transcriptional activator that controls basic metabolic processes such as ribosome biogenesis and de-novo purine synthesis across diverse cancer contexts. Beyond defining primary regulatory functions of BRD4 and MYC in cancer, our study establishes a simple, robust and scalable approach to dissect direct transcriptional targets of any gene or pathway.

2018-04-05 | GSE100708 | GEO

Transcriptome-wide survey of binding partner of slam protein in early Drosophila embryos

Project description:Purpose: Slam protein and RNA co-localize in early drosophila embryos. slam RNA specifically co-immunoprecipitates with its own protein from embryonic lysate as shown by RNA-IP and QRT-PCR. The goal of this study is to survey transcriptome wide (RNA-seq) targets of slam protein and validate the data from qRT–PCR analysis. Methods: RNA-ip was performed for staged embryos (1.5 – 3 h after egg laying) Using slam antibody or GFP binder. RNA profiles in immune-predicates were generated by deep sequencing. Results: Slam RNA specifically co-predicates with slam protein as shown by both next generation sequencing and RT-QPCR. No mRNA of other genes was detected in all independent experiments or showed the averaged enrichment in the same range.

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PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - SLAM - seq

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PHF3 binds RNA polymerase II via the SPOC domain and regulates transcription of neuronal genes - Targeted SLAM-seq

Project description:Tergeted SLAM seq of WT, PHF3 KO and dSPOC, HEK293 cells

2021-09-07 | E-MTAB-7899 | biostudies-arrayexpress