Journal Article

CTCF-mediated functional chromatin interactome in pluripotent cells

Bourque, Guillaume, Mulawadi, Fabianus, Xu, Han, Lee, Charlie Wah Heng, Sung, Wing-Kin, Poh, Thompson, Ruan, Yijun, Shahab, Atif, Ngan, Chew Yee, Sheng, Jianpeng, Ye, Chaopeng, Cacheux-Rataboul, Valere, Wong, Eleanor, Chew, Elaine, Wei, Chia-Lin, Zhang, Yubo, Chan, Chee Seng, Li, Guoliang, Ping, Joanne Lim Hui, Kunarso, Galih, Handoko, Lusy, Schnapp, Marie

2011

Overview

Chia-Lin Wei, Yijun Ruan and colleagues used chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) to determine the CTCF-chromatin interactome in mouse embryonic stem cells. Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. However, little is known about CTCF-associated higher-order chromatin structures at a global scale. Here we applied chromatin interaction analysis by paired-end tag (ChIA-PET) sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, we identified 1,480 cis - and 336 trans -interacting loci with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive cross-talk between promoters and regulatory elements. This highly complex nuclear organization offers insights toward the unifying principles that govern genome plasticity and function.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 631/208/176 / 631/208/191 / 631/532/2064 / Agriculture / Analysis / Animal Genetics and Genomics / Animals / Binding proteins / Binding sites / Biological and medical sciences / Biomedical and Life Sciences / Biomedicine / Cancer Research / CCCTC-Binding Factor / Cells, Cultured / Chromatin / Chromatin - chemistry / Chromatin - genetics / Chromatin - metabolism / Chromatin Immunoprecipitation / Chromatin. Chromosome / Chromosomes / Data processing / DNA-Binding Proteins - genetics / DNA-Binding Proteins - metabolism / Embryo, Mammalian - cytology / Embryo, Mammalian - metabolism / Epigenetics / Epigenomics / Experiments / Fundamental and applied biological sciences. Psychology / Gene Expression Regulation / Gene Function / Genes, Regulator / Genetic aspects / Genetics / Genetics of eukaryotes. Biological and molecular evolution / Genomes / Human Genetics / In Situ Hybridization, Fluorescence / Mice / Molecular and cellular biology / Molecular genetics / Physiological aspects / Pluripotent Stem Cells - metabolism / Promoter Regions, Genetic - genetics / Repressor Proteins - antagonists & inhibitors / Repressor Proteins - genetics / Repressor Proteins - metabolism / RNA polymerase / RNA, Small Interfering - genetics / Stem cells / Transcription, Genetic