Dataset Information

CRISPR-Mediated Reorganization of Chromatin Loop Structure.

ABSTRACT: Recent studies have clearly shown that long-range, three-dimensional chromatin looping interactions play a significant role in the regulation of gene expression, but whether looping is responsible for or a result of alterations in gene expression is still unknown. Until recently, how chromatin looping affects the regulation of gene activity and cellular function has been relatively ambiguous, and limitations in existing methods to manipulate these structures prevented in-depth exploration of these interactions. To resolve this uncertainty, we engineered a method for selective and reversible chromatin loop re-organization using CRISPR-dCas9 (CLOuD9). The dynamism of the CLOuD9 system has been demonstrated by successful localization of CLOuD9 constructs to target genomic loci to modulate local chromatin conformation. Importantly, the ability to reverse the induced contact and restore the endogenous chromatin conformation has also been confirmed. Modulation of gene expression with this method establishes the capacity to regulate cellular gene expression and underscores the great potential for applications of this technology in creating stable de novo chromatin loops that markedly affect gene expression in the contexts of cancer and development.

SUBMITTER: Morgan SL

PROVIDER: S-EPMC6235177 | biostudies-other | 2018 Sep

REPOSITORIES: biostudies-other

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Publications

CRISPR-Mediated Reorganization of Chromatin Loop Structure.

Morgan Stefanie L SL Chang Erin Y EY Mariano Natasha C NC Bermudez Abel A Arruda Nicole L NL Wu Fanting F Luo Yunhai Y Shankar Gautam G Huynh Star K SK Huang Chiao-Chain CC Pitteri Sharon J SJ Wang Kevin C KC

Journal of visualized experiments : JoVE 20180914 139

Recent studies have clearly shown that long-range, three-dimensional chromatin looping interactions play a significant role in the regulation of gene expression, but whether looping is responsible for or a result of alterations in gene expression is still unknown. Until recently, how chromatin looping affects the regulation of gene activity and cellular function has been relatively ambiguous, and limitations in existing methods to manipulate these structures prevented in-depth exploration of the ...[more]

PMID: 30272647

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Project description:In the cell nucleus, each chromosome is confined to a chromosome territory. This spatial organization of chromosomes plays a crucial role in gene regulation and genome stability. Recently an additional level of organization has been discovered at the chromosome scale: the spatial segregation into open and closed chromatin to form two genome-wide compartments. Although considerable progress has been made in our knowledge of chromatin organization, a fundamental issue remains the understanding of its dynamic, especially in cancer. To address this issue, we performed genome-wide mapping of intra- and interchromosomal interactions (Hi-C) over the time after estrogen (E2) stimulation of breast cancer cells. To biologically interpret these interactions, we integrated with estrogen receptor alpha (ER alpha) binding events, gene expression and multiple epigenetic marks. We show that E2 induces a global reorganization of genome. More specifically, gene-rich chromosomes as well as areas of open and highly transcribed chromatins are moved spatially closer, thus enabling genes to share transcriptional machinery and regulatory elements. At a lower scale, differentially interacting loci are enriched for cancer proliferation and E2 related genes. We also observe that these differentially interacting loci are correlated with higher ER alpha binding events and gene expression. 5 time points: before E2 (0h) and after E2 (0.5h, 1h, 4h and 24h). For each time point, there are two lanes per sample and two biological replicate samples. Please note that a processed data file corresponds to the merging of 2 replicates, and that there are 2 lanes per replicates (4 files in total per processed data file). Information about data merging is provided in the title of the sample. For instance : 0h_replicate_1_lane 1 0h_replicate_1_lane 2 0h_replicate_2_lane_1 0h_replicate_2_lane_2 are merged to generate the processed data hic_0h-all-1M.IC.csv.gz. Several bin sizes are provided for the same processed data: hic_0h-all-1M.IC.csv.gz hic_0h-all-2M.IC.csv.gz hic_0h-all-4M.IC.csv.gz hic_0h-all-500k.IC.csv.gz are the same processed data, but with different bin sizes.

Dataset Information

CRISPR-Mediated Reorganization of Chromatin Loop Structure.

Publications

CRISPR-Mediated Reorganization of Chromatin Loop Structure.

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