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Isw2 and Ume6 ChIP-chip in transcription factor deletion (Δume6, Δnrg1, Δcin5, and Δsok2) and DNA-looping deficient (sua7-1) cells

ABSTRACT: The sequence-specific transcription factors Ume6, Nrg1, Cin5, and Sok2 and the general transcription factor TFIIB mediate the genome-wide targeting of the ATP-dependent chromatin remodeling enzyme Isw2.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE39542 | GEO | 2013/03/14

SECONDARY ACCESSION(S): PRJNA171092

REPOSITORIES: GEO

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Isw2 and Ume6 ChIP-chip in transcription factor deletion (M-NM-^Tume6, M-NM-^Tnrg1, M-NM-^Tcin5, and M-NM-^Tsok2) and DNA-looping deficient (sua7-1) cells

Project description:The sequence-specific transcription factors Ume6, Nrg1, Cin5, and Sok2 and the general transcription factor TFIIB mediate the genome-wide targeting of the ATP-dependent chromatin remodeling enzyme Isw2. At least two biological replicates comparing Isw2-ChIP (Isw2-K215R ChIP DNA competitively hybridized against WT Isw2 ChIP DNA) in WT and M-NM-^Tume6, M-NM-^Tnrg1, M-NM-^Tcin5, M-NM-^Tsok2, and sua7-1 strains or Ume6-ChIP (ChIP DNA competitively hybridized again Input DNA) in WT and sua7-1 strains

2013-03-14 | E-GEOD-39542 | biostudies-arrayexpress

Isw2 ChIP in S cerevisiae

Project description:Study to detect to genome wide localization of the ATP dependent chromatin remodelling factor Isw2 using ChIP. Keywords: ChIP chip

2007-09-10 | GSE8815 | GEO

Determination of ncRNAs repressed by Isw2

Project description:It has previously been shown that Isw2 represses cryptic antisense transcripts from the 3’-end of three genes. However, whether Isw2 generally functions to repress cryptic RNA transcription is currently unknown. We thus sought to determine the loci at which Isw2 is required to repress cryptic non-coding RNA (ncRNA) expression and to map their transcription start sites relative to nucleosome positions on a global scale.

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Histone octamer structure is altered early in ISW2 ATP-dependent remodeling of nucleosomes

Project description:Histone octamers are thought to be a rigid part of nucleosomes that shape chromatin and block cellular machinery from accessing DNA. ATP-dependent chromatin remodelers like ISW2 mobilize nucleosomes to provide DNA access. We find evidence for histone octamer distortion preceding DNA being moved into nucleosomes and processive movement of the ATPase motor of ISW2 on nucleosomal DNA. DNA entering nucleosome is uncoupled from the ATPase activity of ISW2 and alterations of the histone octamer structure mediated by ISW2 by deletion of the SANT domain from the C-terminus of the Isw2 catalytic subunit. We also find that restricting histone movement by chemical crosslinking traps remodeling intermediates resembling those seen by loss of the SANT domain, further supporting the importance of changes in histone octamer structure early in ISW2 remodeling. Transient octamer distortions are stabilized by H3-H4 tetramer disulfide crosslinking, thereby linking intrinsic histone octamer flexibility to chromatin remodeling.

2020-05-27 | PXD013967 | Pride

Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping

Project description:Nucleosome positions were determined in wild type cells, cells lacking Isw2 or Ume6, and cells containing a hybrid Chd1-Ume6 chimeric remodeler

2016-03-12 | GSE72570 | GEO

Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping

Project description:Nucleosome positions were determined in wild type cells, cells lacking Isw2 or Ume6, and cells containing a hybrid Chd1-Ume6 chimeric remodeler Matched MNase digests from W303 strain variants during log growth (OD600=0.4-0.6) were subject to paired-end sequencing for nucleosome mapping. For effects of the engineered fusion remodeling protein, a catalytically inactive (ATPase dead D513N) variant was included as a control.

2016-03-12 | E-GEOD-72570 | biostudies-arrayexpress

Yeast replication in the presence of MMS: WT and isw2 nhp10 strains

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2007-11-30 | GSE9122 | GEO

Genome-wide maps of chromatin remodeling factors Isw2 and Ino80 in asynchronously growing yeast cells

Project description:ChIP-seq of Isw2 (subunit of Isw2 complex) and Nhp10 (subunit of Ino80 complex) was performed on two independent isolates of FLAG-tagged Isw2 or Nhp10 Sample naming convention: <ChIP target>_<growth condition>_<genotype-replicate>_<strain name>

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Mapping Nucleosome positions in WT and delta isw2 cells

Project description:To map nucleosome positions in WT and delta isw2 cells Keywords: Nucleosomal DNA hybridization

2007-09-10 | GSE8814 | GEO

Effect of Tup1, Xbp1, Isw2, and Sds3 on transcription in diauxic shift and stationary phase.

Project description:To investigate the effect of Tup1, Xbp1, Isw2, and Sds3 on transcription we generated knockout strains and measured their transcript abundance compared to wild type during diauxic shift and stationary phase.

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