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SRX10973777: GSM5333662: MBT Flav input DNA; Danio rerio; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 45.1M spots, 2.3G bases, 1.1Gb downloads

Submitted by: NCBI (GEO)
Study: Distinctive roles for the chromatin remodeling ATPases Brg1 and Brm in early zebrafish embryos [ChIP-seq]
show Abstracthide Abstract
Brg1 and Brm function as alternative core enzymatic ATPases of SWI/SNF complex in vertebrates, with clear homologs in zebrafish. Brg1 (but not Brm) is required for early cleavage-stage transcription in mice, but where and how Brg1 or Brm impact chromatin in early embryos remains unexplored. Here, we utilize zebrafish embryos to provide the first simultaneous genome-wide profiling of Brg1 and Brm occupancy in any organism/cell type, alongside our profiling of open chromatin and RNA polymerase II. We reveal shared and unique loci for Brg1 and Brm, their shared occupancy of open chromatin and particular developmental promoters, and higher transcription at co-occupied genes. Interestingly, only Brg1 is strongly associated with active histone modifications. Strikingly, only Brm commonly occupies gene bodies, overlapping precisely with Pol II. Functional experiments involving Pol II elongation inhibition alongside bioinformatic analyses suggest that Brm travels with Pol II into gene bodies, primarily at short, very highly-transcribed genes with few introns. Taken together, our results support roles for Brg1 primarily at promoters and enhancers, and for Brm in association with Pol II in elongation through chromatin within gene bodies during genome-wide transcriptional activation Overall design: Examination of Brg1, Brm and PolII at 3 zebrafish developmental stages. In addition, ChIP-seq of Brm, PolII and H3K36me3 were perfromed in embryos treated with flavopiridol.
Sample: MBT Flav input DNA
SAMN19317930 • SRS9051168 • All experiments • All runs
Organism: Danio rerio
Library:
Instrument: Illumina HiSeq 2500
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Nuclei from formaldehyde crosslinked (1%; 10min at room temperature) embryos were isolated and chromatin was fragmented using sonicator (Branson). Lysates were cleared and protein-DNA complexes were isolated using target specific antibodies and Dynabeads. DNA fragments were purified and libraries were prepared by NEBnext DNA Library Prep Kit (NEB, E7370L). Adapter ligated DNA was purified using AMPure XP beads (Beckman Coulter, A63881) and sequenced by illumina HiSeq 2500. NEBnext DNA Library Prep Kit
Experiment attributes:
GEO Accession: GSM5333662
Links:
Runs: 1 run, 45.1M spots, 2.3G bases, 1.1Gb
Run# of Spots# of BasesSizePublished
SRR1463398745,123,3332.3G1.1Gb2024-05-24

ID:
14592157

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