mavii

Here the authors determine the high-resolution 3D chromatin architecture of mouse male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin dictates the gene expression ...

The architectural protein CTCF is a mediator of chromatin conformation, but how CTCF binding to DNA is orchestrated to maintain long-range gene expression is poorly understood.

Advanced ChIA-PET shows that CTCF/cohesin and RNA polymerase II arrange spatial organization for coordinated transcription. Haplotype variants exhibit allelic effects on chromatin topology and transcription that link disease susceptibility.

Furthermore, we show that haplotype variants and allelic interactions have differential effects on chromosome configuration, influencing gene expression, and may provide mechanistic insights into functions associated with disease susceptibility. 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is ...

The work of Zuin et al. in PNAS explores the 3D architecture of the genome by studying the contributions of two leading players in loop organization: the CCCTC-binding factor (CTCF) and the cohesin complex (7). CTCF is a highly conserved protein with a unique structure that confers a versatile role in genome function (8).

The 3D architectural role of CTCF underlies its multifarious functions, including developmental regulation of gene expression, protocadherin (Pcdh) promoter choice in the nervous system, immunoglobulin (Ig) and T-cell receptor (Tcr) V (D)J recombination in the immune system, homeobox (Hox) gene control during limb development, as well as many ...

CCCTC-binding factor (CTCF) is a multifunctional zinc finger protein that is conserved in metazoan species. CTCF is consistently found to play an important role in many diverse biological processes. CTCF/cohesin-mediated active chromatin ‘loop extrusion’ architects three-dimensional (3D) genome folding. The 3D architectural role of CTCF underlies its multifarious functions, including ...

The architectural protein CTCF plays a complex role in decoding the functional output of the genome. Guo et al. now show that the orientation of a CTCF site restricts its choice of interacting partner, thus creating a code that predicts the ...

In this Journal Club, Julia Horsfield recounts two papers that demonstrated how cohesin and CTCF together organize the genome and regulate gene expression.

Graph representation of 3D-genome and “Chrombus” auto-encoder architecture. Each subgraph consists 128 vertices, and each vertex represents a chromatin segment derived from CTCF binding peaks.

The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development.

To comprehensively characterize the 3D topology of chromatin interactions between functional elements and higher-order organization in the human genome, we applied ChIA-PET, targeting on two protein factors, CTCF (CCCTC-binding zinc finger protein) and RNAPII (RNA polymerase II) in a number of human cell lines.

In this review, we outline how CTCF contributes to the regulation of the three‐dimensional structure of chromatin and the formation of chromatin domains. We discuss how CTCF binding and architectural functions are regulated.

Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high ...

Here we determine the high-resolution three-dimensional (3D) chromatin architecture of mouse male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin dictates the gene expression program required for spermatogenesis.

Given the outsized role that DNA methylation plays on CTCF-mediated gene control at imprinted loci, it is attractive to expand such regulation to the genome-wide scale.

Mediated by architectural proteins such as CTCF and cohesin complexes, these loops bring enhancers, silencers, and promoters into close spatial proximity, facilitating precise regulation of gene expression [12].

The architectural protein CTCF plays a complex role in decoding the functional output of the genome. Guo et al. now show that the orientation of a CTCF site restricts its choice of interacting partner, thus creating a code that predicts the three-dimensional organization of the genome. We propose a DNA extrusion model to account for orientation-specific loop formation.

Here we determine the high-resolution 3D chromatin architecture of male germ cells during spermatogenesis and show that CTCF-mediated 3D chromatin predetermines the gene expression program required for spermatogenesis.