Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (ATAC-seq)

ABSTRACT: Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (ATAC-seq)

PROVIDER: PRJNA480448 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7504540_1.fastq.gz	Fastqsanger.gz
	SRR7504540_2.fastq.gz	Fastqsanger.gz
	SRR7504541_1.fastq.gz	Fastqsanger.gz
	SRR7504541_2.fastq.gz	Fastqsanger.gz
	SRR7504542_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo

Project description:Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo

| PRJNA480443 | ENA

Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (Hi-C)

Project description:Mechanisms by which the mammalian gametes encode epigenetic information that can be transmitted to the progeny are relatively unknown. We find that many sperm promoters in mouse sperm are occupied by phosphorylated forms of RNA polymerase II and the Mediator complex. Analysis of ATAC-seq data suggest that the same promoters are occupied by components of the transcription complex in GV and MII oocytes and preimplantation embryos. Furthermore, distal ATAC-seq sites containing transcription factor motifs are conserved in monkeys and humans. ChIP-seq analyses confirm that transcription factors, including FoxA1 and the androgen and estrogen receptors, occupy distal enhancers. These sites and their interactions with promoters in the gametes are maintained in the early embryo. Additionally, sperm- or oocyte-specific interactions mediated by CTCF/cohesin are only present in the paternal or maternal chromosome, respectively in the zygote and 2-cell stages. These interactions converge in both chromosomes by the 8-cell stage. These results suggest that the mammalian gametes contain a large repertoire of transcription factors that organize a complex pattern of 3D interactions and can be transmitted to the zygote after fertilization.

2019-02-28 | GSE116856 | GEO

Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (ChIP-seq)

2019-02-28 | GSE116855 | GEO

Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (ATAC-seq)

2019-02-28 | GSE116854 | GEO

Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (Hi-C)

Project description:Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (Hi-C)

| PRJNA480450 | ENA

Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (ChIP-seq)

Project description:Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo (ChIP-seq)

| PRJNA480447 | ENA

Maintenance of CTCF- and Transcription Factor-Mediated Interactions from the Gametes to the Early Mouse Embryo.

Project description:The epigenetic information present in mammalian gametes and whether it is transmitted to the progeny are relatively unknown. We find that many promoters in mouse sperm are occupied by RNA polymerase II (Pol II) and Mediator. The same promoters are accessible in GV and MII oocytes and preimplantation embryos. Sperm distal ATAC-seq sites containing motifs for various transcription factors are conserved in monkeys and humans. ChIP-seq analyses confirm that Foxa1, ERα, and AR occupy distal enhancers in sperm. Accessible sperm enhancers containing H3.3 and H2A.Z are also accessible in oocytes and preimplantation embryos. Furthermore, their interactions with promoters in the gametes persist during early development. Sperm- or oocyte-specific interactions mediated by CTCF and cohesin are only present in the paternal or maternal chromosomes, respectively, in the zygote and 2-cell stages. These interactions converge in both chromosomes by the 8-cell stage. Thus, mammalian gametes contain complex patterns of 3D interactions that can be transmitted to the zygote after fertilization.

| S-EPMC6625867 | biostudies-literature

Maintenance of CTCF and transcription factor-mediated interactions from gametes to the early mouse embryo

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

2019-02-28 | GSE116857 | GEO

RNA interactions are essential for proper CTCF function

Project description:The function of the CCCTC-binding factor (CTCF) in the organization of the genome has become an important area of investigation, but the mechanisms by which CTCF dynamically contributes to genome organization are not clear. We previously discovered that CTCF binds to large numbers of endogenous RNAs, promoting its self-association. In this regard, we now report two independent features that disrupt CTCF association with chromatin: inhibition of transcription and disruption of CTCF-RNA interactions through mutations of two of its 11 zinc fingers which are not required for CTCF binding to its cognate DNA site: zinc finger-1 (ZF1) or -10 (ZF10). These mutations alter gene expression profiles as CTCF mutants lose their ability to form chromatin loops and thus, the ability to insulate chromatin domains as well as mediate CTCF long-range genomic interactions. Our results point to the importance of CTCF-mediated RNA interactions as a structural component of genome organization.

2019-09-12 | GSE125595 | GEO

Cohesin and CTCF Differentially Affect the Chromatin Architecture and Gene Expression in Human Cells

Project description:Recent studies of genome-wide chromatin interactions have revealed that the human genome is partitioned into many self-associating topological domains. The boundary sequences are enriched for binding sites of CTCF and the cohesin complex, implicating these two factors in the establishment or maintenance of topological domains. To determine the role of cohesin and CTCF in higher order chromatin architecture in human cells, we proteolytically cleaved the cohesin complex from interphase chromatin and examined changes in chromosomal organization as well as transcriptome. We observed a general loss of local chromosomal interactions upon disruption of cohesin complex, but the topological domains remain intact. However, we found that depletion of CTCF by RNA interference in these cells not only reduced intra-domain interactions but also increased inter-domain interactions. Further more, distinct groups of genes become mis-regulated upon depletion of cohesin and CTCF. Taken together, these observations suggest that CTCF and cohesin contribute in different ways to chromatin organization and gene regulation. Hi-C and mRNA-seq experiments in Cohesin and CTCF depleted HEK293 cells

2013-12-16 | E-GEOD-44267 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data