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SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [next-generation sequencing]

ABSTRACT: SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [next-generation sequencing]

PROVIDER: PRJNA288531 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2082690.fastq.gz	Fastqsanger.gz
	SRR2082700.fastq.gz	Fastqsanger.gz
	SRR2082710.fastq.gz	Fastqsanger.gz
	SRR2082691.fastq.gz	Fastqsanger.gz
	SRR2082701.fastq.gz	Fastqsanger.gz

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SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [array]

Project description:Development of an alternative method to ChIP for the identification of DNA bound by transcriptional complexes assayed using Nimblegen arrays Nimblegen promoter arrays allowing identification of sites bound by different Notch complexes using SpDamID

2015-08-01 | E-GEOD-70388 | biostudies-arrayexpress

SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [next-generation sequencing]

Project description:Development of an alternative method to ChIP for the identification of DNA bound by transcriptional complexes assayed using next-generation sequencing Next-generation sequencing data from sites identified by different Notch complexes using SpDamID-seq and compared against FAIRE and ChIP data

2015-08-01 | E-GEOD-70387 | biostudies-arrayexpress

SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [array]

Project description:Development of an alternative method to ChIP for the identification of DNA bound by transcriptional complexes assayed using Nimblegen arrays

2015-08-01 | GSE70388 | GEO

SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers.

Project description:We developed Split DamID (SpDamID), a protein complementation version of DamID, to mark genomic DNA bound in vivo by interacting or juxtapositioned transcription factors. Inactive halves of DAM (DNA adenine methyltransferase) were fused to protein pairs to be queried. Either direct interaction between proteins or proximity enabled DAM reconstitution and methylation of adenine in GATC. Inducible SpDamID was used to analyze Notch-mediated transcriptional activation. We demonstrate that Notch complexes label RBP sites broadly across the genome and show that a subset of these complexes that recruit MAML and p300 undergo changes in chromatin accessibility in response to Notch signaling. SpDamID differentiates between monomeric and dimeric binding, thereby allowing for identification of half-site motifs used by Notch dimers. Motif enrichment of Notch enhancers coupled with SpDamID reveals co-targeting of regulatory sequences by Notch and Runx1. SpDamID represents a sensitive and powerful tool that enables dynamic analysis of combinatorial protein-DNA transactions at a genome-wide level.

| S-EPMC4553207 | biostudies-literature

SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [next-generation sequencing]

Project description:Development of an alternative method to ChIP for the identification of DNA bound by transcriptional complexes assayed using next-generation sequencing

2015-08-01 | GSE70387 | GEO

SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers

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

2015-08-01 | GSE70402 | GEO

Epigenetic landscapes in wild-type and dimer-mutant Notch regulated T-LL cells

Project description:NOTCH/RBPJ/MAML ternary transcriptional complex binds to regulatory element and drives gene expression. The complex can function as monomer and dimer. How dimeric complexes regulate gene expression in human cancer is not well studied. Here, we integrate genomic data sets and analyze Notch dimeric complexes-regulated transcriptome and cis-regulatory elements. A subset of coding and non-coding RNA is Notch dimeric complexes-associated. Dimeric complexes recognition sequence enriched in functional dynamic Notch sites and majority of dimer recognition sequence located in (super-)enhancers. Using CRISPR-Cas9-mediated genome editing, we evaluated the function of one dimer-responsive element located in the promoter region of a noncoding RNA NDANR1 and 5' end 16kb away from HES5. Mutation of SPS in this element reduced expression of HES5 and NDANR1. This finding indicates that dimer-responsive elements can function as enhancer for HES5 and at the same time can function as promoter for noncoding RNA NDANR1. Our study reveals the pervasive role of Notch dimeric complexes in transcriptional regulation in human cancer genome.

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Sequence dependency and regulatory function of dimeric NOTCH1/RBPJ complexes on coding and non-coding transcription in T-lymphoblastic leukemia

2017-08-23 | GSE72482 | GEO

Project description:SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers

| PRJNA288533 | ENA

Mus musculus

Project description:SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [array]

| PRJNA288532 | ENA