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The dynamics of chromatin accessibility during EMT

ABSTRACT: The power of our genome-wide survey lies in that we were able to query chromatin accessibility changes concurrently with those in DNA methylation. We identified both opening and closing events, predominantly independent of DNA methylation, in both systems. Our results have powerful implications for future basic and clinical research on this developmental process and its resurfacing during cancer cell metastasis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE63366 | GEO | 2015/12/31

SECONDARY ACCESSION(S): PRJNA267574

REPOSITORIES: GEO

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The dynamics of chromatin accessibility during EMT

Project description:The power of our genome-wide survey lies in that we were able to query chromatin accessibility changes concurrently with those in DNA methylation. We identified both opening and closing events, predominantly independent of DNA methylation, in both systems. Our results have powerful implications for future basic and clinical research on this developmental process and its resurfacing during cancer cell metastasis. To address epigenetic changes that mediate EMT, we used two models in the human system: EMT induced by the transcriptional repressor Twist as well as EMT induced by TGF-beta. We performed AcceSssIble on these cells at several time points through the course of the transition and identified genes that need to be repressed to allow for the process.

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Project description:We performed open chromatin analysis and genome-wide analysis for RAR-DNA association, on the hiPSC-derived cells in the 2C protocol. The purposes were to analyze sequential opening and closing of chromatin elements, and to elucidate the molecular roles of RAR, in each differentiation stage of the 2C protocol.

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Chromatin Accessibility Dynamics during Chemical Induction of Pluripotency [ATAC-Seq]

Project description:Chemical induction of pluripotency (CIP) is an ideal way to reprogram cell fate, but remains poorly understood. Here we report the development of an efficient CIP protocol and the chromatin accessibility dynamics (CAD) during CIP by ATAC-seq. CIP first reorganizes the somatic genome to an intermediate state that must be resolved by primarily closing loci opened earlier before reaching a pluripotent state with gradual opening of loci enriched with motifs for the OCT/SOX/KLF families. Bromodeoxyuridine, a critical ingredient of CIP, is responsible for both closing and opening critical loci, at least in part by preventing the opening of loci enriched with motifs for the AP1 family and facilitating the opening of loci enriched with SOX/KLF/GATA motifs. Our studies provide the first link between small molecules and nuclear architecture in the context of cell fate decisions.

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Chromatin Accessibility Dynamics during Chemical Induction of Pluripotency [RNA-seq]

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Gene Expression in Arabidopsis thaliana Guard Cells

Project description:Stomata are formed by a pair of specialized guard cells that control the opening and closing of the stomatal pores on the leaf surface. These pores are the main route for microbe penetration into leaves. However, plants show a remarkable ability to close the pore when sensing the presence of microbial invaders; a phenomenon recently described as stomatal immunity. This study was initiated to understand the transcriptional regulation of this early plant defense against pathogens.

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EMT

Project description:three pairs of isogenic human mammary epithelial and fibroblast cells, were used to characterized cell type specific dna methylation using using methyla cytosin immunoprecipitation

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Effect of NKD1, NKD2 and O2 on Chromatin Accessible Regions

Project description:NKD1, 2 and O2 are key transcription factors interactively regulating endosperm development. Their mutation combinations may diversely alter the global gene regulatory landscape. To investigate how interactions between NKD1, 2 and O2 affect endosperm regulatome, which is indicated by accessible regions for regulators on chromatins, Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed for 16 DAP endosperms of all 8 genotype combinations (2 biological replicate per genotype). Among 16 sequenced samples, 20,478 to 49,640 (mean: 34,766) peaks were called, and these peaks represent potential chromatin accessible regions. Distribution of the peaks on chromatins varies among samples: 54.35% - 66.73% peaks are located at distal intergenic region (>3kb upstream and >300 bp downstream of a gene) and 6.7% - 12.1% are located at promoter region (within 3 kb flanking transcription starting site), and 4.62% - 8.88% peaks are located within 1kb flanking transcription starting site. Also, in WT background, nkd1 and nkd2 single mutants have overall greater number of opening regions (upregulated peaks) than closing regions (downregulated peaks), whereas nkd1,2 double mutant has similar number of opening and closing regions. In contrast, in o2-background, all nkd1, nkd2 and nkd1,2 mutants have greater number of closing than opening regions. This indicates that o2 may alter differential accessibility of nkd1, nkd2 single or nkd1,2 double mutants.

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