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High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [ARC-C]

ABSTRACT: High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [ARC-C]

PROVIDER: PRJNA604566 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11004600_1.fastq.gz	Fastqsanger.gz
	SRR11004600_2.fastq.gz	Fastqsanger.gz
	SRR11004601_1.fastq.gz	Fastqsanger.gz
	SRR11004601_2.fastq.gz	Fastqsanger.gz
	SRR11004602_1.fastq.gz	Fastqsanger.gz

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High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [ARC-C]

Project description:Interactions between cis-regulatory elements such as promoters and enhancers are important for transcription but global identification of these interactions remains a major challenge. Leveraging the chromatin accessiblity of regulatory elements, we developed ARC-C (accessible region chromosome conformation capture), which profiles chromatin regulatory interactions genome-wide at high resolution. Applying ARC-C to C. elegans, we identify ~15,000 significant interactions at 500bp resolution. Regions bound by transcription factors and chromatin regulators such as cohesin and condensin II are enriched for interactions, and we use ARC-C to show that the BLMP-1 transcription factor mediates interactions between its targets. Investigating domain level architecture, we find that C. elegans chromatin domains defined by either active or repressive modifications form topologically associating domains (TADs) and that these domains interact to form A/B (active/inactive) compartment structure. ARC-C is a powerful new tool to interrogate genome architecture and regulatory interactions at high resolution.

2021-06-01 | GSE144670 | GEO

High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [RNA-Seq]

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High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [ChIP-Seq]

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High-resolution mapping of regulatory element interactions and genome architecture using ARC-C

Project description:High-resolution mapping of regulatory element interactions and genome architecture using ARC-C

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High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [RNA-Seq]

Project description:High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [RNA-Seq]

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High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [ChIP-Seq]

Project description:High-resolution mapping of regulatory element interactions and genome architecture using ARC-C [ChIP-Seq]

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High-resolution mapping of regulatory element interactions and genome architecture using ARC-C

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

2021-06-01 | GSE144673 | GEO

Endogenous brain ARC complexes

Project description:Arc is an activity regulated neuronal protein yet little is known about its protein interactions, assembly into multiprotein complexes, role in human disease and cognition. We applied an integrated proteomic and genetic strategy using targeted tagging of a Tandem Affinity Purification (TAP) tag and Venus fluorescent protein into the endogenous Arc gene in mice, biochemical and proteomic characterization of native complexes in wild type and knockout mice, and human genetic analyses of disease and intelligence. TAP tagging enabled efficient purification of complexes and identification of many novel Arcinteracting proteins, of which PSD95 was the most abundant. PSD95 was essential for Arc assembly into 1.5 MDa complexes and activity-dependent recruitment to excitatory synapses. Integrating human genetic data with proteomic data showed postsynaptic Arc- PSD95 complexes are enriched in schizophrenia, intellectual disability, autism and epilepsy mutations and normal variants in intelligence. Arc-PSD95 postsynaptic complexes are a molecular substrate for the convergence of normal and pathological genetic variants impacting on human cognitive function.

2017-10-19 | PXD007283 | Pride

Defining genome architecture at base-pair resolution

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Detection of Arc/Arg3.1 oligomers in rat brain: constitutive and synaptic activity-evoked dimer expression in vivo

Project description:The immediate early gene product activity-regulated cytoskeleton-associate protein (Arc or Arg3.1) is a major regulator long-term synaptic plasticity with critical roles in postnatal cortical development and memory formation. However, the molecular basis of Arc function is not defined. Arc is a hub protein with interaction partners in the postsynaptic neuronal compartment and nucleus. In vitro biochemical and biophysical analysis of purified recombinant Arc show formation of low-order oligomers and larger particles including retrovirus-like capsids. Here, we provide evidence for naturally occurring Arc oligomers in mammalian brain. Using in situ protein crosslinking to trap weak Arc-Arc interactions, we identified in various preparations a prominent Arc immunoreactive band on SDS-PAGE of molecular mass corresponding to a dimer. While heavier Arc species or putative trimers and tetramers were detected, they were of lower abundance. In the dentate gyrus (DG) of adult anesthetized rats, induction of long-term potentiation (LTP) by high-frequency stimulation (HFS) of medial perforant synapses or by brief intrahippocampal infusion of BDNF led to a massive increase in Arc dimer expression. Arc immunoprecipitation of crosslinked DG tissue showed enhanced expression of dimer during four hours of LTP maintenance. Mass spectrometric proteomic analysis of immunoprecipitated, gel-excised bands corroborated detection of Arc dimer. Furthermore, Arc dimer was constitutively expressed in naïve cortical, hippocampal and DG tissue, with lowest levels in the DG. Taken together the results implicate Arc dimers as the predominant low-oligomeric form in mammalian brain, exhibiting regional differences in its constitutive expression and pronounced enhanced expression during DG LTP.

2023-07-20 | PXD039612 | Pride

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