Promoter capture GM12878 CD34
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Borbala Mifsud
PROVIDER: E-MTAB-2323 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts mediated by the PRC1 complex we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in a HiC library in Ring1a KO and Ring1a/b dKO mouse ES cells.
2015-08-01 | E-MTAB-3109 | biostudies-arrayexpress
Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in HiC libraries from mouse ESC and E14.5 fetal liver. Please note additional files included. These files were created using the following protocol: Significantly interacting regions were called using the GOTHiC BioConductor package (http://www.bioconductor.org/packages/devel/bioc/html/GOTHiC.html) as described in (Mifsud et al.).<br>Update on December 2015: the original additional file E-MTAB-2414.additional.1.zip contained an earlier iteration of processed data and not the one that was used for the published paper. The file now contains the correct list of interactions.
2015-02-01 | E-MTAB-2414 | biostudies-arrayexpress
Project description:To identify distal chromatin contacts between promoters and their putative regulatory elements in human airway smooth muscle cells (ASMC), we performed Hi-C with a capture step to enrich the library for contacts involving promoters. Promoter capture Hi-C was performed according to PMID: 29988018 The cells were cultured and maintained in 10% FBS in PBS for 24 hours with no additional treatment given. probes-MboI_fragments-hg19.baitmap.bz2 can be used in CHiCAGO to call interactions. Interactions provided correspond to hg19 coordinates.
2025-03-11 | E-MTAB-14295 | biostudies-arrayexpress
Project description:Capture Hi-C (CHi-C) is a state-of-the art method for profiling chromosomal interactions involving targeted regions of interest (such as gene promoters) globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model, and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments, in which many spatially dispersed regions are captured, such as in Promoter CHi-C. We implement these procedures in CHiCAGO (http://regulatorygenomicsgroup.org/chicago), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs.
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Project description:Capture Hi-C (CHi-C) is a state-of-the art method for profiling chromosomal interactions involving targeted regions of interest (such as gene promoters) globally and at high resolution. Signal detection in CHi-C data involves a number of statistical challenges that are not observed when using other Hi-C-like techniques. We present a background model, and algorithms for normalisation and multiple testing that are specifically adapted to CHi-C experiments, in which many spatially dispersed regions are captured, such as in Promoter CHi-C. We implement these procedures in CHiCAGO (http://regulatorygenomicsgroup.org/chicago), an open-source package for robust interaction detection in CHi-C. We validate CHiCAGO by showing that promoter-interacting regions detected with this method are enriched for regulatory features and disease-associated SNPs. Three human CHi-C biological replicates were generated (comprising 1, 2and 3 technical replicates). Two mouse CHi-C biological replicates were generated (both comprising three technical replicates) and a mouse Hi-C dataset. The publicly available HiCUP pipeline (doi: 10.12688/f1000research.7334.1) was used to process the raw sequencing reads. This pipeline was used to map the read pairs against the mouse (mm9) and human (hg19) genomes, to filter experimental artefacts (such as circularized reads and re-ligations), and to remove duplicate reads. For the CHi-C data, the resulting BAM files were processed into CHiCAGO input files, retaining only those read pairs that mapped, at least on one end, to a captured bait. CHiCAGO then identified Hi-C restriction fragments interacting, with statistical significant, to captured baits.
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Project description:Recent advances in high-throughput transcriptomics have revealed extensive gene expression changes during cerebral ischemia. However, the changes in 3D chromatin architecture and long-range chromatin looping between genes and distal regulatory elements that drive these gene expression changes remain virtually unexplored. In this study, we mapped the landscape of altered 3D chromatin looping the in the ischemic cortex and evaluated its contributions to post-stroke transcriptional changes. We used genome-wide chromatin conformation capture (Hi-C) to profile changes in the 3D chromatin architecture in the cerebral cortex of adult mice following a 1 h middle cerebral artery occlusion and 6 h of reperfusion, or sham surgery. We identified a total of 15,592 loops in the stroke group with a mean enrichment core of 6.108, and these included 1973 promoter-promoter contacts, 7857 enhancer-enhancer contacts, and 5762 enhancer-promoter contacts. In the sham group, there were 14,779 chromatin loops with a mean enrichment score of 5.473, including 1714 promoter-promoter contacts, 8597 enhancer-enhancer contacts, and 4468 enhancer-promoter contacts. Together, our study represents the first genome-wide evaluation of 3D chromatin looping following stroke.
2025-05-30 | GSE294767 | GEO
Project description:Genome organisation determines chromosome interactions between regulatory elements, such as promoters and enhancers, influencing gene expression. Despite the fact that it is possible to assess whether a gene is actively transcribed, it has been challenging to point out the genomic regions that are involved in the regulation of a particular gene. We are interested in better understanding the interactions between promoters and their regulatory elements in colorectal cancer in order to unveil novel non-coding regions which might have a role in tumour development. To do so, we utilise the HiC method complemented with promoter capture in combination with NGS to map promoter interactions in two CRC cell lines, representing two distinct CRC subtypes.
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Project description:Genome-wide chromosome conformation capture (Hi-C) and promoter-capture Hi-C (CHi-C) were performed during epidermal differentiation. These data indicate that dynamic and constitutive enhancer-promoter contacts combine to control gene induction during differentiation and that chromosome conformation enables discovery of new TFs with distinct roles in this process.
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