Chromatin conformation identification by Cut-C
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ABSTRACT:
PROVIDER: PRJNA518761 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Understanding of the 3D structure of the genome is essential to decipher the detailed regulatory mechanisms of gene expression. Here we present CUT-C, a method that combines the antibody mediated cleavage by tethered nuclease with the chromosome conformation capture technique to identify chromatin interactions mediated by a protein of interest. CUT-C identifies protein-centric chromatin conformation along with the genome wide distribution of target proteins.
2019-07-18 | GSE125988 | GEO
Project description:Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag
| PRJNA738523 | ENA
Project description:Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag
| PRJNA739658 | ENA
Project description:Cut regulates the programmed death of neural stem cells by altering cohesin levels and promoting a more open chromatin conformation to allow cell death gene expression.
2019-04-17 | GSE124998 | GEO
Project description:Background: Although genetic or epigenetic alterations have shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. Results: Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. Conclusions: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes. Examination of CTCF and RAD21 binding sites in THP-1 cell.
2014-02-27 | E-GEOD-55407 | biostudies-arrayexpress
Project description:Background: Although genetic or epigenetic alterations have shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. Results: Here, we explore whether chromatin conformation can be used to classify human leukemia. We map the conformation of the HOXA gene cluster in a panel of cell lines with 5C chromosome conformation capture technology, and use the data to train and test a support vector machine classifier named 3D-SP. We show that 3D-SP is able to accurately distinguish leukemias expressing MLL-fusion proteins from those expressing only wild-type MLL, and that it can also classify leukemia subtypes according to MLL fusion partner, based solely on 5C data. Conclusions: Our study provides the first proof-of-principle demonstration that chromatin conformation contains the information value necessary for classification of leukemia subtypes. Analysis of 38 samples using 5C technology. All data normalized using a 'master' BAC consisting of 5C data from 6 samples.
2014-02-27 | E-GEOD-55406 | biostudies-arrayexpress
Project description:Here we describe successful implementation of CUT&Tag for profiling protein-DNA interactions in zebrafish embryos. We optimized CUT&Tag protocol to generate high resolution maps of enrichment for the histone variant H2A.Z during zebrafish development. We were able to establish dynamics of H2A.Z genomic patterning from shield stage to 24hpf embryos. Our work demonstrates the power of combining CUT&Tag with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.
2022-02-15 | GSE178559 | GEO
Project description:Here we describe successful implementation of CUT&RUN for profiling protein-DNA interactions in zebrafish embryos. We apply modified a CUT&RUN method to generate high resolution maps of enrichment for H3K4me3, H3K27me3, H3K9me3, and RNA polymerase II during zebrafish gastrulation. Using this data, we identify a conserved subset of developmental genes that are enriched in both H3K4me3 and H3K27me3 during gastrulation, and we demonstrate the increased effectiveness of CUT&RUN for detecting protein enrichment at repetitive sequences with reduced mappability. Our work demonstrates the power of combining CUT&RUN with the strengths of the zebrafish system to better understand the changing embryonic chromatin landscape and its roles in shaping development.
2021-06-17 | GSE178343 | GEO
Project description:Emerging evidence suggests that chromatin adopts a non-random three-dimensional (3D) topology and that the organization of genes into structural hubs and domains affects their transcriptional status. How chromatin conformation changes in diseases such as cancer is poorly understood. Moreover, how oncogenic transcription factors, which bind to thousands of sites across the genome, influence gene regulation by globally altering the topology of chromatin requires further investigation. To address these questions, we performed unbiased high-resolution mapping of intra- and inter-chromosome interactions upon over-expression of ERG, an oncogenic transcription factor frequently over-expressed in prostate cancer as a result of a gene fusion. By integrating data from genome-wide chromosome conformation capture (Hi-C), ERG binding and gene expression, we demonstrate that oncogenic transcription factor over-expression is associated with global, reproducible and functionally coherent changes in chromatin organization. The results presented here have broader implications, as genomic alterations in other cancer types frequently give rise to aberrant transcription factor expression e.g., EWS-FLI1, c-Myc, n-Myc, PML-RARα. We used stable isogenic, normal benign prostate epithelial cell lines (RWPE1) that differ with respect to ERG3 over-expression. To test whether ERG over-expression is associated with global changes in chromatin structure, we performed unbiased chromatin interaction mapping using the Hi-C technique from both RWPE1-ERG and RWPE1-GFP cells, with biological replicates. Successful fill-in and ligation were determined as previously reported by testing for a known interaction between two distant genomic loci located on chromosome 6. The Hi-C libraries were paired-end sequenced using an Illumina GAIIx platform. Following alignment to the human genome (hg18) and filtering to remove un-ligated and self-ligated DNA, we identified intra-chromosomal (or cis-) and inter-chromosomal (or trans-) interactions in both RWPE1 cell lines. To characterize ERG binding and ERG-mediated gene expression changes in these cells, we performed chromatin-immunoprecipitation combined with high-throughput sequencing (ChIP-seq) and RNA sequencing (RNA-seq). ERG was bound to 6,398 sites in RPWE1-ERG cells. Based on paired-end RNA-seq data from both cell lines, 1,266 genes were differentially expressed between RWPE1-ERG and RWPE1-GFP cell lines.
2012-05-23 | E-GEOD-37752 | biostudies-arrayexpress
Project description:Recent advances in the development of single cell epigenomic assays have facilitated the analysis of the gene regulatory landscapes in complex biological systems. Single-cell variations of methods such as DNA methylation-sequencing and ATAC-seq hold tremendous promise for delineating distinct cell types and identifying their critical cis-regulatory sequences. Emerging evidence in recent years has shown that in addition to cis-regulatory sequences, dynamic regulation of 3D chromatin conformation is a critical mechanism for the modulation of gene expressions during development and disease. While assays for the investigation of single-cell 3D chromatin structure have been developed, cell-type specific chromatin conformation in primary human tissues has not been extensively explored. It remains unclear whether single-cell Chromatin Conformation Capture (3C) or Hi-C profiles are suitable for cell type identification and allow the reconstruction of cell-type specific chromatin conformation maps. To address these challenges, we have developed a multi-omic method single-nucleus methyl-3C sequencing (sn-m3C) to profile chromatin conformation and DNA methylation from the same cell. We have shown that bulk m3C and sn-m3C accurately capture chromatin organization information and robustly separate mouse cell types. We have developed a fluorescent-activated nuclei sorting strategy based on DNA content that eliminates nuclei multiplets caused by crosslinking. The sn-m3C-seq method allows high-resolution cell-type classification using two orthogonal types of epigenomic information and the reconstruction of cell-type specific chromatin conformation maps.
2018-12-26 | GSE124391 | GEO