Systematic Identification of Protein Combinations Mediating Chromatin Looping

Overview

Journal Nat Commun

Specialty Biology

Date 2016 Jul 28

PMID 27461729

Citations 23

Authors

Kai Zhang

Nan Li

Richard I Ainsworth

Wei Wang

Affiliations

Soon will be listed here.

Abstract

Chromatin looping plays a pivotal role in gene expression and other biological processes through bringing distal regulatory elements into spatial proximity. The formation of chromatin loops is mainly mediated by DNA-binding proteins (DBPs) that bind to the interacting sites and form complexes in three-dimensional (3D) space. Previously, identification of DBP cooperation has been limited to those binding to neighbouring regions in the proximal linear genome (1D cooperation). Here we present the first study that integrates protein ChIP-seq and Hi-C data to systematically identify both the 1D- and 3D-cooperation between DBPs. We develop a new network model that allows identification of cooperation between multiple DBPs and reveals cell-type-specific and -independent regulations. Using this framework, we retrieve many known and previously unknown 3D-cooperations between DBPs in chromosomal loops that may be a key factor in influencing the 3D organization of chromatin.

Citing Articles

Footprint-C reveals transcription factor modes in local clusters and long-range chromatin interactions.

Liu X, Wei H, Zhang Q, Zhang N, Wu Q, Xu C Nat Commun. 2024; 15(1):10922.

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ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.

Magnitov M, Maresca M, Alonso Saiz N, Teunissen H, Dong J, Sathyan K Mol Cell. 2024; 85(1):24-41.e11.

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ZNF143 binds DNA and stimulates transcription initiation to activate and repress direct target genes.

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Chromatin insulator mechanisms ensure accurate gene expression by controlling overall 3D genome organization.

Bhattacharya M, Lyda S, Lei E Curr Opin Genet Dev. 2024; 87:102208.

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ZNF143 binds DNA and stimulates transcripstion initiation to activate and repress direct target genes.

Dong J, Scott T, Mukherjee R, Guertin M bioRxiv. 2024; .

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