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Sequence-Targeted Nucleosome Sliding in vivo

ABSTRACT: Sequence-Targeted Nucleosome Sliding in vivo

PROVIDER: PRJNA294374 | ENA |

REPOSITORIES: ENA

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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

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 - Transcription Profiling

Project description:RNA sequencing was performed on various W303 variants to determine effects of nucleosome repositioning on transcript abundance RNA sequencing was carried out in multiple backgrounds to determine effects of nucleosome repositioning in various contexts. For engineered chromatin remodeling factors, a catalytically inactive control was included.

2016-03-12 | E-GEOD-72571 | biostudies-arrayexpress

Sequence-Targeted Nucleosome Sliding in vivo - Transcription Profiling

Project description:RNA sequencing was performed on various W303 variants to determine effects of nucleosome repositioning on transcript abundance

2016-03-12 | GSE72571 | GEO

Sequence-Targeted Nucleosome Sliding in vivo

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-12 | E-GEOD-72572 | biostudies-arrayexpress

Sequence-Targeted Nucleosome Sliding in vivo

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

2016-03-12 | GSE72572 | GEO

Saccharomyces cerevisiae

Project description:Sequence-Targeted Nucleosome Sliding in vivo - Nucleosome Mapping

| PRJNA294376 | ENA

Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler.

Project description:ATP-dependent chromatin remodelers regulate chromatin dynamics by modifying nucleosome positions and occupancy. DNA-dependent processes such as replication and transcription rely on chromatin to faithfully regulate DNA accessibility, yet how chromatin remodelers achieve well-defined nucleosome positioning in vivo is poorly understood. Here, we report a simple method for site-specifically altering nucleosome positions in live cells. By fusing the Chd1 remodeler to the DNA binding domain of the Saccharomyces cerevisiae Ume6 repressor, we have engineered a fusion remodeler that selectively positions nucleosomes on top of adjacent Ume6 binding motifs in a highly predictable and reproducible manner. Positioning of nucleosomes by the fusion remodeler recapitulates closed chromatin structure at Ume6-sensitive genes analogous to the endogenous Isw2 remodeler. Strikingly, highly precise positioning of single founder nucleosomes by either chimeric Chd1-Ume6 or endogenous Isw2 shifts phased chromatin arrays in cooperation with endogenous chromatin remodelers. Our results demonstrate feasibility of engineering precise nucleosome rearrangements through sequence-targeted chromatin remodeling and provide insight into targeted action and cooperation of endogenous chromatin remodelers in vivo.

| S-EPMC4864466 | biostudies-literature

Saccharomyces cerevisiae

Project description:Sequence-Targeted Nucleosome Sliding in vivo - Transcription Profiling

| PRJNA294375 | ENA

Nucleosome sliding by the Chd1 chromatin remodeler relies on the integrity of the DNA duplex

Project description:The experiments are done with three libraries by introducing base-pair perturbations on Widom 601: (1) poly(dA:dT) tract library (2) mismatch library (3) insertion library. And additional two more libraries based on native yeast genomic sequences: (4) Park97 mismatch library (5) Park97 insertion library. And we measured the nucleosome positioining in the base-pair resolution for before and after sliding by Chd1 chromatin remodeler.

2022-05-12 | GSE198440 | GEO

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