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Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE247539 | GEO | 2024/04/22

REPOSITORIES: GEO

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Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (ChIP)

Project description:Enhancer as a cis-regulatory element (CRE), plays a critical role in gene regulation at many stages of cell growth. Meanwhile, enhancers in cancer cells also act as a regulator controlling oncogene transcription. In this study, we did a comprehensive analysis of long-range chromatin interactions, histone modifications, chromatin status, and expressions of two gastric cancer (GC) cell lines, compared with a human normal epithelial cell line. We found that GC-specific enhancers marked by histone modifications in gastric cancer can activate a population of genes including some oncogenes by enhancer-promoter (E-P) interactions. In addition, motif analysis of E-P interacted enhancers showed that three GC-specific TF sequences may regulate enhancer-interacting gene activation. We found MYB which is crucial for GC cellular growth and is activated by TCF7 regulated E-P loop. To validate this mechanism, we applied CRISPRi (dCas9-KRAB) induced transcriptional regulatory element inactivation in our target enhancer, the growth assay resulted in significant inhibition of cell growth in two GC cell lines. In conclusion, we found oncogene activation by aberrant loop formation that contributes to tumorigenesis in GC.

2024-04-22 | GSE247537 | GEO

Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (HiChIP)

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Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (4C)

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Integrated Enhancer Regulatory Network by Enhancer-Promoter Looping in Gastric Cancer (RNA-seq)

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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-03-29 | E-GEOD-46598 | biostudies-arrayexpress

Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:This SuperSeries is composed of the SubSeries listed below.

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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer.

Project description: Not available

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ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-12-21 | GSE248737 | GEO

ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry

Project description:This SuperSeries is composed of the SubSeries listed below.

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Integrated epigenomic analyses of enhancer as well as promoter regions in gastric cancer

Project description:To understand epigenetic changes in the distal regulatory as well as proximal regions, we performed RNA-seq, MBD-seq, and H3K27ac ChIP-seq on gastric tissues and cell lines MBD sequencing of normal tissue (n), purified gastric cancer (sc), and cultured gastric cancer cell (dc) were generated by deep sequencing, in five samples from three patients (csc1, csc2, csc3) and two replicates (csc1_sc2, csc1_sc3), using Illumina GAIIx.

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