Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

61 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1

ABSTRACT: By analysis of ChIP-exo of FOXA1 in LNCaP, we find that an astonishing genome-wide "well-positioned" configuration prevalently occurs between FOXA1 motif and the dyad of nucleosome. Here we performed ChIP-seq data of eight chromatin remodelers and found a higher occupancy of these remodelers on these well-positioned FOXA1 motif sites. Together, our results support a positional-nucleosome-oriented accessing model, in which FOXA1 can examine each underlying DNA nucleotide and be able to sense all potential motifs regardless if they face inward or outward to histone octamers along the DNA helix axis. We have performed ChIP-seq of eight chromatin remodeler factors.

ORGANISM(S): Homo sapiens

SUBMITTER: Zhenqing Ye

PROVIDER: E-GEOD-72690 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.

Ye Zhenqing Z Chen Zhong Z Sunkel Benjamin B Frietze Seth S Huang Tim H-M TH Wang Qianben Q Jin Victor X VX

Nucleic acids research 20160725 16

The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis-regulatory elements. Pioneer factors (PFs) such as FOXA1 are able to directly access these cis-targets within compact chromatin. However, how these PFs interplay with nucleosomes remains to be elucidated, and is critical for us to understand the underlying mechanism of gene regulation. Here, we have conducted a computational analysis on a strand-specific paired-end C ...[more]

PMID: 27458208

Similar Datasets

ChIP-Seq of yeast H3K37me1 in a time-course experiment after release from the G1 cell-cycle phase

Project description:This experiment measured the mono-methylation of lysine 37 of histone H3 in yeast cells at various phases of the cell cycle (G1, G1/S and S).

2021-04-28 | E-MTAB-9058 | biostudies-arrayexpress

ChIP-Seq of yeast MCM2 in a time-course experiment after release from the G1 cell-cycle phase

Project description:ChIP-Seq experiment of MCM2 binding to chromatin in a time-course experiment after release from the G1 cell-cycle phase

2021-04-28 | E-MTAB-9071 | biostudies-arrayexpress

ChIP-Seq experiment of Mcm2-HA in wild type and H3K37R yeast cells

Project description:This ChIP-Seq experiment profiles Mcm2 binding to chromatin in wild type yeast cells and in cells with the K37R mutation in histone H3

2021-04-28 | E-MTAB-9070 | biostudies-arrayexpress

Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1

Project description:By analysis of ChIP-exo of FOXA1 in LNCaP, we find that an astonishing genome-wide "well-positioned" configuration prevalently occurs between FOXA1 motif and the dyad of nucleosome. Here we performed ChIP-seq data of eight chromatin remodelers and found a higher occupancy of these remodelers on these well-positioned FOXA1 motif sites. Together, our results support a positional-nucleosome-oriented accessing model, in which FOXA1 can examine each underlying DNA nucleotide and be able to sense all potential motifs regardless if they face inward or outward to histone octamers along the DNA helix axis.

2016-08-01 | GSE72690 | GEO

Functional enhancers at the gene-poor 8q24 cancer-linked locus

Project description:Multiple discrete regions at 8q24 were recently shown to contain alleles that predispose to many cancers including prostate, breast, and colon. These regions are far from any annotated gene and their biological activities have been unknown. Here we profiled a 5-megabase chromatin segment encompassing all the risk regions for RNA expression, histone modifications, and locations occupied by RNA polymerase II and androgen receptor (AR). This led to the identification of several transcriptional enhancers, which were verified using reporter assays. Two enhancers in one risk region were occupied by AR and responded to androgen treatment; one contained a single nucleotide polymorphism (rs11986220) that resides within a FoxA1 binding site, with the prostate cancer risk allele facilitating both stronger FoxA1 binding and stronger androgen responsiveness. The study reported here exemplifies an approach that may be applied to any risk-associated allele in non-protein coding regions as it emerges from genome-wide association studies to better understand the genetic predisposition of complex diseases. 20 Normal Prostate cDNA samples (no replicates), 4 cell line cDNA samples (each cell line in duplicate), 4 cell line Acetylated H3 ChIP (each line in duplicate), 2 cell line various histone modification and protein ChIPs (6 Abs LNCaP, 5 Abs PC3, each in duplicate). All samples were hybridized with matching genomic DNA as reference.

2009-12-18 | E-GEOD-19561 | biostudies-arrayexpress

Investigating the requirement of H3K14 and H3P16 for optimal H3K4me3

Project description:ChIP-seq experiment for histone H3 and H3K4me3 from wild-type Saccharomyces cerevisiae (WT) and strains in which H3K14 has been substituted for alanine (K14A) or H3P16 has been substituted with valine (P16V).

2014-07-22 | E-MTAB-2717 | biostudies-arrayexpress

RSC and ISW1 Chromatin Remodelers Display Functional and Chromatin-based Promoter Antagonism [ChIP-seq]

Project description:ISWI-family chromatin remodelers organize nucleosome arrays, while SWI/SNF-family remodelers (RSC) disorganize and eject nucleosomes, implying an antagonism that is largely unexplored in vivo. Here, we describe two independent genetic screens for rsc suppressors that yielded mutations in the promoter-focused ISW1a complex, or mutations in the ‘basic patch’ of histone H4 (an epitope that regulates ISWI activity), strongly supporting RSC-ISW1a antagonism in vivo. RSC and ISW1a largely co-localize, and genomic nucleosome studies using rsc isw1 mutant combinations revealed opposing functions: promoters classified with a nucleosome-deficient region (NDR) gain nucleosome occupancy in rsc mutants, but this gain is attenuated in rsc isw1 double mutants. Furthermore, promoters lacking NDRs have the highest occupancy of both remodelers, consistent with regulation by nucleosome occupancy, and decreased transcription in rsc mutants. Taken together, we provide the first genetic and genomic evidence for RSC-ISW1a antagonism, and reveal different mechanisms at two different promoter architectures. Genomic localization of RSC, ISW1a, and SWI/SNF complexes were measured by chromatin immunoprecipitation followed by Illumina paired-end sequencing. Four strains were analyzed, including Rsc8-9xMyc (YBC2882), Sth1-2xFlag (YBC601 p3018), Ioc3-13xMyc (YBC2883), and Snf2-13xMyc (YBC3010). Each sample consists of one chromatin immunoprecipitate and one input chromatin control.

2015-04-01 | E-GEOD-65592 | biostudies-arrayexpress

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [NimbleGen ChIP-chip]

Project description:This study was designed to investigate DNA supercoiling across the human genome and to understand how supercoiling domains impact on higher levels of genome organisation. DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, M-bM-^@M-^\openM-bM-^@M-^] chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes. The binding of bTMP, as a reporter for DNA supercoiling, was investigated in RPE1 cells. Experiments were biological replicates

2013-02-17 | E-GEOD-43448 | biostudies-arrayexpress

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures

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

2013-02-17 | E-GEOD-43451 | biostudies-arrayexpress

Transcription forms and remodels supercoiling domains unfolding large scale chromatin structures [Agilent ChIP-chip]

2013-02-17 | E-GEOD-43450 | biostudies-arrayexpress