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Nucleosome mapping in 20 kb upstream regions of microRNAs

ABSTRACT: We mapped the nucleosome locations in upstream regions of all known microRNAs in 3 cell lines using the method described in Nature Biotechnology 2007 Feb;25(2):244-8. Keywords: Nucleosome Mapping Study 20 kb upstream regions of microRNAs were tiled at 10 bp spacing using mostly 50-mer probes. Duplicate experiments were performed in MCF7, MALME, and UACC62 cell lines.

ORGANISM(S): Homo sapiens

SUBMITTER: Jun Song

PROVIDER: E-GEOD-9029 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chromatin structure analyses identify miRNA promoters.

Ozsolak Fatih F Poling Laura L LL Wang Zhengxin Z Liu Hui H Liu X Shirley XS Roeder Robert G RG Zhang Xinmin X Song Jun S JS Fisher David E DE

Genes & development 20081101 22

Although microRNAs (miRNAs) are key regulators of gene expression in normal human physiology and disease, transcriptional regulation of miRNAs is poorly understood, because most miRNA promoters have not yet been characterized. We identified the proximal promoters of 175 human miRNAs by combining nucleosome mapping with chromatin signatures for promoters. We observe that one-third of intronic miRNAs have transcription initiation regions independent from their host promoters and present a list of ...[more]

PMID: 19056895

Similar Datasets

Nucleosome mapping in 20 kb upstream regions of microRNAs

Project description:We mapped the nucleosome locations in upstream regions of all known microRNAs in 3 cell lines using the method described in Nature Biotechnology 2007 Feb;25(2):244-8. Keywords: Nucleosome Mapping Study

2008-11-16 | GSE9029 | GEO

Nucleosome Mapping in S. pombe Centromeres

Project description:A key element for defining the centromere identity is the incorporation of a specific histone H3, CENP-A, known as Cnp1p in S. pombe. Previous studies have suggested that functional S. pombe centromeres lack nucleosome arrays and may involve chromatin remodeling as a key step of kinetochore assembly. We used tiling microarrays to show that nucleosomes are in fact positioned in regular intervals in the core of centromere 2, providing the first high resolution map of regional centromere chromatin. Nucleosome locations are not disrupted by mutations in kinetochore proteins cnp1, mis18, mis12, nuf2, mal2, overexpression of Cnp1p, or deletion of ams2. Bioinformatic analysis of the centromere sequence indicates certain enriched motifs in linker regions between nucleosomes and reveals a sequence-bias in nucleosome positioning. We conclude that centromeric nucleosome positions are stable and may be derived from the underlying DNA sequence. In addition, sequence analysis of nucleosome-free regions identifies novel binding sites for the GATA-like protein Ams2p, which participates in CENP-A incorporation. Keywords: Nucleosome Mapping Study Entire cnt regions and histone-related genes were tiled at 1-5 bp spacing using 60-mer probes.

2008-05-30 | E-GEOD-10742 | biostudies-arrayexpress

Homo sapiens

Project description:Nucleosome mapping in 20 kb upstream regions of microRNAs

| PRJNA102529 | ENA

GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes. [MNase-seq]

Project description:Promoter-proximal pausing of RNA polymerase II (RNA-Pol) is a rate-limiting step primed for rapid and synchronous induction of genes involved in critical physiological processes. Its underlying mechanisms are not fully understood. Using cytogenetic, genomic and genetic approaches, we provide evidence to support a direct role of a prevalent upstream GAGA binding factor (GAF) in transcriptional pausing of Hsp70 and many developmental regulators in Drosophila. For GAF target genes, the abundance of paused RNA-Pol and GAF is closely correlated. Promoters with higher GAF occupancy show stronger reduction of paused RNA-Pol in Gaf mutants. In addition, nucleosome organization is preferentially affected in the upstream region by GAF in a dosage-dependent manner. Genetic assays using a dominant eye phenotype caused by GAF overexpression suggests that GAF cooperates with nucleosome remodeler NURF, pausing factor NELF and an upstream binding factor BAB1. Thus, GAF plays a critical role in a regulatory network to facilitate transcriptional pausing through modulation of upstream nucleosomes.

2016-07-19 | GSE70633 | GEO

GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes.[ChIP-seq]

2016-07-19 | GSE70632 | GEO

A role for Snf2 related nucleosome spacing enzymes in genome-wide nucleosome organization

Project description:The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleosome spacing enzymes is required to maintain this organization. In the absence of these enzymes regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicated that ATP-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome. Examination of nucleosome positioning in mutants of snf2-related enzymes Other data used in this study are provided in GEO Series GSE31301 and GSE31833.

2011-09-16 | E-GEOD-31015 | biostudies-arrayexpress

Chromatin architectures at fission yeast transcriptional promoters and replication origins

Project description:We have used micrococcal nuclease (MNase) digestion followed by deep sequencing in order to obtain a higher-resolution map than previously available of nucleosome positions in the fission yeast, Schizosaccharomyces pombe. Our data confirm an unusually short average nucleosome repeat length, ~152 bp, in fission yeast and that transcriptional start sites (TSSs) are associated with nucleosome-depleted regions (NDRs), ordered nucleosome arrays downstream and less regularly spaced upstream nucleosomes. In addition, we found enrichments for associated function in four of eight groups of genes clustered according to chromatin configurations near TSSs. At replication origins, our data revealed asymmetric localization of Pre-Replication Complex (pre-RC) proteins within large NDRsM-bM-^@M-^Ta feature that is conserved in fission and budding yeast and is therefore likely to be conserved in other eukaryotic organisms. Examination of nucleosome positioning in Schizosaccharomyces pombe

2012-04-23 | E-GEOD-28071 | biostudies-arrayexpress

Novel Upstream Regulators of YAP/TAZ Activation

Project description:Novel Upstream Regulators of YAP/TAZ Activation

| PRJNA489430 | ENA

TBX2 a novel upstream regulator of labor

Project description:TBX2 a novel upstream regulator of labor

| PRJNA555139 | ENA

Sex reversal following the deletion of a single far upstream enhancer of Sox9.

Project description:Purpose: In this study we employed unbiased, genome wide techniques to identify novel enhancers of Sox9 that may cause Disorders of Sex Development (DSDs) when disrupted in the mouse. Methods: We performed ATAC-seq on 60K FACS-purified gonadal cells before and after sex determination to map nucleosome depleted regions (NDRs) indicative of regulatory elements. We then selected 16 putative enhancers present in Sertoli cells. To determine whether these are active enhancers, we performed ChIP-seq for H3K27ac, a histone modification that marks active enhancers. Transient transgenics was performed on select enhancers to determine whether they drive Sertoli-specific expression in vivo. Finally, we selected a single active Sertoli-specific enhancer to delete with CRISPR. Results: We identified a single enhancer upstream of Sox9 that causes complete male-to-female sex reversal in mice when deleted. Conclusions: Our study is the first to identify a single enhacer supstream of Sox9 which drives Sertoli-specific expression in vivo and causes complete male-to-female sex reversal when deleted in the mouse. Furthermore, this enhancer overlaps a region in humans (XY SR) associated to DSDs.

2018-04-12 | GSE99320 | GEO

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