Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA281363 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1976460.fastq.gz | Fastqsanger.gz | |||
| SRR1976461.fastq.gz | Fastqsanger.gz | |||
| SRR1976462.fastq.gz | Fastqsanger.gz | |||
| SRR1976463.fastq.gz | Fastqsanger.gz | |||
| SRR1976458.fastq.gz | Fastqsanger.gz |
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Project description:Abstract: A network of interactions between functional DNA elements regulates gene expression in a precise spatio-temporal pattern during development. This regulation is implemented through many-to-many looping interactions of DNA elements mediated by specific transcription factors such as Ctcf, Gata1 and Yy1. We carried out RNA polymerase II ChIA-PET and DNase-seq in Mouse Erythroleukemia (MEL) cells to capture genomewide changes in the resulting chromatin interaction graphs (CIGs) during DMSO-induced hemoglobin activation. We found that the change of interactions in CIGs is positively correlated to the change of a corresponding genes’ expression as measured by RNA-seq. DNase footprints and ChIP-seq data indicate that these long-range interactions are controlled through distinct combinations of transcription factors before and after differentiation, with Ctcf or cohesin only mediating half of these interactions, and Gata1 and/or Yy1 interactions accounting for an additional 40% of detected interactions. Strikingly, while Ctcf and Gata1–mediated interactions were enriched in genes involved in erythrocyte differentiation and mitochondrial regulation, Yy1-mediated interactions were enriched for genes involved in RNA processing, translation, and histone remodeling. We further found that about two-thirds of MEL DNA elements with long-range interactions as well 35% of these interactions are conserved in human K562 cells and show similar combinations of factor occupancy. Taken together, our study identifies that a large set of long-range interactions between active enhancers and promoters involving RNA Pol II are mediated by factors other than cohesin and Ctcf in both human and mouse.
2019-04-30 | GSE67955 | GEO
Project description:The landscape of global long-range interactions in human erythroid cells mediated by GATA1 and CTCF during differentiation
| PRJNA433533 | ENA
Project description:A network of long-range interactions between functional DNA elements regulates gene expression in a precise spatio-temporal pattern during development. We carried out anti-RNA polymerase II and cohesin ChIA-PET and DNase-seq in Mouse Erythroleukemia (MEL) cells to capture genome-wide changes between open chromatin elements in chromatin interaction graphs (CIGs) during DMSO-induced hemoglobin activation. We found that the change of interaction strength in CIGs is positively correlated to expression changes in corresponding genes as measured by RNA-seq. DNaseI footprints and ChIP-seq data indicate that these long-range interactions are controlled through distinct combinations of transcription factors before and after differentiation, with CTCF or cohesin only mediating half of these interactions, with GATA1, PU.1 and/or other transcription factorsYY1 interactions accounting for an additional 40% of detected interactions. Strikingly, while CTCF and GATA1–mediated interactions were enriched in genes involved in erythrocyte differentiation and mitochondrial regulation, PU.1YY1-mediated interactions were enriched for genes involved in RNA processing, cell cycletranslation, and chromatin organizationhistone remodeling. We further found that two-thirds of MEL DNA elements with long-range interactions as well as 35% of their interactions are conserved in human K562 cells and they show similar combinations of factor occupancy in both species. Our study highlights the importance of quantitative analysis of changes in long-range interaction strengths in quantifying changes in gene expression.
2020-02-29 | GSE110361 | GEO
Project description:The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH- rearranged gene segment in the proximal Igh domain. By high-resolution mapping of long-range interactions, we now demonstrate that an array of local interaction domains establishes the three- dimensional structure of the extended Igh locus in lymphoid progenitors and thymocytes. In pro- B cells, these local domains engage in long-range interactions across the entire Igh locus, which depend on the transcription factors Pax5, YY1 and CTCF. The large VH gene cluster thereby undergoes flexible long-range interactions with the more rigidly structured 3M-bM-^@M-^Y proximal domain, which ensures that all VH genes can participate with similar probability in VH-DJH recombination to generate a diverse antibody repertoire. Notably, these long-range interactions appear to be an intrinsic feature of the VH gene cluster, as they are still generated upon mutation of the EM-NM-< enhancer, IGCR1 insulator or 3M-bM-^@M-^Y regulatory region present in the 3M-bM-^@M-^Y proximal Igh domain. 4C sequencing from mutliple celltypes with multiple viewpoints; uneven number of replicates ChIP-Seq
2013-09-30 | E-GEOD-43008 | biostudies-arrayexpress
Project description:CTCF is a master regulator that plays a role in genome architecture and gene expression. A key aspect of CTCF’s mechanism involves bringing together distant genetic elements for intra- and inter-chromosomal interactions. Evidence from epigenetic processes, such as X-chromosome inactivation (XCI), suggests that CTCF may carry out its functions through interacting RNAs. Using genome-wide approaches to investigate the relationship between CTCF’s RNA interactome and its epigenomic landscape, here we report that CTCF interacts with thousands of transcripts in mouse embryonic stem cells (mESC), many in close proximity to CTCF’s genomic binding sites. Biochemical analysis demonstrates that CTCF is a high-affinity RNA binding protein that contacts RNA directly and specifically. In the XCI model, CTCF binds the active and inactive X-chromosomes allele-specifically. At the X-inactivation center, Tsix RNA binds CTCF and targets CTCF to a region associated with X-chromosome pairing. Our work implicates CTCF-RNA interactions in long-range chromosomal interactions in trans and adds a new layer of complexity to CTCF regulation. The genome-wide datasets reported here will provide a useful resource for further study of CTCF-mediated epigenomic regulation. CTCF RNA interactome was identified by UV-crosslinking and immunoprecipitation followed by high-throughput sequencing (CLIP-seq), and was compared to CTCF's epigenomic landscape as obtained by chromatin immunoprecipitation (ChIP-seq).
2015-01-09 | E-GEOD-58242 | biostudies-arrayexpress
Project description:Gene expression is controlled under spatial chromatin structures with short-range in topologically associating domains (TAD) and long-range chromatin interactions between TADs, compartments or chromosomes, and disruption of chromatin structure leads to human diseases. The mechanism of short-range chromatin interactions has been well characterized by loop-extrusion model, but little is known about how long-range chromatin interactions are organized. Here, we demonstrate that CTCF contributes to long-range chromatin interactions via phase separation. Surprisingly, RYBP is required for the phase separation and long-range chromatin organization of CTCF. Artificial CTCF phase seperation restores the long-range chromatin interactions and corresponding gene expression which were eliminated by RYBP depletion, and manipulation of CTCF phase separation also maintains pluripotency and inhibits differentation of embryonic stem cells. These findings support a model that long-range chromatin interactions are organized through phase sepearation of architectural protein, and further reveals the distinct mechanisms of architectural protein in organizing short-range and long-range chromatin interactions.
2022-08-10 | GSE147919 | GEO
Project description:The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH- rearranged gene segment in the proximal Igh domain. By high-resolution mapping of long-range interactions, we now demonstrate that an array of local interaction domains establishes the three- dimensional structure of the extended Igh locus in lymphoid progenitors and thymocytes. In pro- B cells, these local domains engage in long-range interactions across the entire Igh locus, which depend on the transcription factors Pax5, YY1 and CTCF. The large VH gene cluster thereby undergoes flexible long-range interactions with the more rigidly structured 3’ proximal domain, which ensures that all VH genes can participate with similar probability in VH-DJH recombination to generate a diverse antibody repertoire. Notably, these long-range interactions appear to be an intrinsic feature of the VH gene cluster, as they are still generated upon mutation of the Eμ enhancer, IGCR1 insulator or 3’ regulatory region present in the 3’ proximal Igh domain.
2013-09-30 | GSE43008 | GEO
Project description:There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. Here we show that the transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements in all cells examined. YY1 forms dimers that can facilitate DNA interactions. Deletion of YY1 binding sites or depletion of YY1 can disrupt enhancer-promoter looping and normal gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.
2017-11-16 | GSE103574 | GEO
Project description:There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. Here we show that the transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements in all cells examined. YY1 forms dimers that can facilitate DNA interactions. Deletion of YY1 binding sites or depletion of YY1 can disrupt enhancer-promoter looping and normal gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.
2017-11-16 | GSE99515 | GEO
Project description:There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. Here we show that the transcription factor Yin Yang 1 (YY1) contributes to enhancer-promoter structural interactions in a manner analogous to DNA interactions mediated by CTCF. YY1 binds to active enhancers and promoter-proximal elements in all cells examined. YY1 forms dimers that can facilitate DNA interactions. Deletion of YY1 binding sites or depletion of YY1 can disrupt enhancer-promoter looping and normal gene expression. We propose that YY1-mediated enhancer-promoter interactions are a general feature of mammalian gene control.
2017-11-16 | GSE99520 | GEO