mavii

ChromaFold uses pseudobulk chromatin accessibility, co-accessibility across metacells, and a CTCF motif track as inputs and employs a lightweight architecture to train on standard GPUs.

The primary role of CTCF is thought to be in regulating the 3D structure of chromatin. [8] CTCF binds together strands of DNA, thus forming chromatin loops, and anchors DNA to cellular structures like the nuclear lamina. [10] It also defines the boundaries between active and heterochromatic DNA. Since the 3D structure of DNA influences the regulation of genes, CTCF's activity influences the ...

On the basis of the available evidence CTCF is regarded as an essential, pleiotropic genome organizer that links higher-order chromatin structure with complex biological phenomena (Phillips and Corces, 2009).

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 ...

This review discusses how CTCF shapes the 3D chromatin structure and chromatin domains, how CTCF binding and architectural functions are regulated, and how CTCF controls gene expression in development and disease by acting as an insulator and a facilitator for regulatory element interaction in the nuclear space.

Here, we show evolutionary divergence in CTCF-mediated chromatin topology at the domain and loop scales during primate evolution, elucidating distinct mechanisms for shaping regulatory landscapes.

Here, we used ChIP-seq to map the genome-wide binding sites of CTCF in three cell types and identified significant binding of CTCF to the boundaries of repressive chromatin domains marked by H3K27me3.

Individually, ZFs increase overall binding and chromatin residence time. Unexpectedly, we also uncovered a conserved downstream DNA motif that destabilizes CTCF occupancy. Thus, CTCF associates with a wide array of DNA modules via combinatorial clustering of its 11 ZFs.

Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced ChIA-PET strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CTCF and ...

This suggests multiple ways in which CTCF may impact gene expression. At promoters, CTCF can directly affect transcription. At more distal sites, CTCF may orchestrate interactions between regulatory elements and help separate eu- and heterochromatic areas in the genome, exerting a chromatin barrier function.

CTCF (CCCTC-binding factor) is a key architectural protein that binds specific DNA sites, halts cohesin-mediated loop extrusion, and enables long-range chromatin interactions. There are hundreds of thousands of annotated CTCF-binding sites in mammalian genomes; disruptions of some result in distinct phenotypes, while others have no visible effect.

On the basis of the available evidence CTCF is regarded as an essential, pleiotropic genome organizer that links higher-order chromatin structure with complex biological phenomena (Phillips and Corces, 2009).

All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations ...

Systematic chromatin immunoprecipitation experiments combined with high-throughput sequencing (ChIP-seq) have been performed to map CTCF binding events across the genome in many tissues of different species [8 – 10]. They show that the genome is covered with a myriad of CTCF binding sites.

All known vertebrate chromatin insulators interact with the highly conserved, multivalent 11-zinc finger nuclear factor CTCF to demarcate expression domains by blocking enhancer or silencer signals in a position-dependent manner. Recent observations document that the properties of CTCF include readi …

Our study reveals a novel role of CTCF in regulating erythroid differentiation by maintaining its proper chromatin openness and gene expression network, which extends our understanding of CTCF biology.

CTCF/cohesin mediated chromatin boundary and principle of genome organization The theory of chromosomal territory was proposed as early as 1982, using traditional light microscopic techniques 6 ‘ 7. Later, these findings were confirmed by DNA fluorescence in-situ hybridization (FISH) analysis, notably at the mouse beta-globin gene cluster 8.

CTCF plays key roles in gene regulation, chromatin insulation and organizing the higher-order chromatin architecture of mammalian genomes. Here the authors investigate the function an alternatively spliced shorter CTCF isoform, finding that this isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis.