mavii

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. ... Considering that cohesin protein complex is highly associated with CTCF in chromatin biology (Ong and Corces, 2014), we examined the CTCF-anchor sites for co-occupancy by cohesin using ChIP sequencing (ChIP-seq) data of subunits RAD21 and SMC3. The vast ...

Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) with haplotype specificity and ...

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. Here we perform ...

CTCF, which regulates chromatin architecture, was first identified as an insulator protein that prevents gene expression by blocking enhancer-promoter interactions, and subsequent studies revealed the ability of CTCF to facilitate the formation of TADs and intra-TAD loops. 20, 21 CTCF expression is vital for cell survival, ...

The different chromatin architecture and choice between DDR pathways might be a reason why the survival of mESC-AID-CTCF cells upon CTCF depletion does not meet our model predictions and also why the experimental data showed a different sensitivity between tumor and embryonic cells (Figure 3 and Figure 8, respectively). Indeed, stem cells are ...

Chromatin architecture facilitates accurate transcription at a number of loci, but it remains unclear how much chromatin architecture is involved in global transcriptional regulation. Previous work has shown that rapid depletion of the architectural protein CTCF in cell culture alters global chromatin organization but results in surprisingly ...

CTCF-s competes with CTCF to alter the chromatin architecture and loop formation, mainly because CTCF-s is unable to interact with the cohesin ring. Created with BioRender.com (accessed on 23 April 2023). Similarly, CTCF has a paralogous gene called CTCF-Like (CTCFL), which encodes the protein Brother of the Regulator of Imprinted Sites (BORIS).

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. In this review, we outline how CTCF contributes to the regulation of the three-dimensional structure of chromatin and the formation of chromatin domains.

In recent years, it has become evident that the three-dimensional (3D) organization of chromatin is highly regulated and likely to play important roles in gene regulation (Neems et al., 2016; Nora et al., 2012).A key factor for regulating the chromatin architecture is CTCF, a DNA-binding protein known to bring distant genomic elements into close spatial proximity by driving chromatin loop ...

We segmented the chromatin based on CTCF-binding peaks. ... 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 node (vertex) attributes consist 14-dimensional chromatin features. ...

As outgroup species, we studied chromatin architecture in three unicellular holozoans: the ichthyosporean Sphaeroforma arctica 24, ... (CTCF) and other transcription factors 49. ...

Studies have shown that the binding of the chromatin architecture protein CTCF, to its target sites are perturbed in AML. CTCF is a ubiquitously expressed transcription factor shown to play multiple roles in regulating gene expression. CTCF is most widely known for its role in regulating and stabilizing the three-dimensional genome architecture ...

For example, TADs boundaries are usually delimited by CCCTC-binding-factor (CTCF) which stalls cohesin. 13, 75 CTCF forms clusters that couple with cohesin to create complexes, 75 which may facilitate 3D trans-communication. 47 Future studies should investigate the generality and structural origins of these phenomena.

Specifically, CTCF has many roles in regulating gene expression as an insulator and in its functions in chromatin architecture 24,25,26. ... CTCF binding is known to alter chromatin topology, ...

Genome-wide analyses have revealed a strong overlap between chromatin loops and CTCF binding sites . Furthermore, different studies have proven that the alteration of the CTCF binding site – either through its disruption or its inversion – has an impact on chromatin architecture, which disturbs promoter-enhancer interactions [51, 52].

The architectural protein CTCF is a mediator of chromatin conformation, but how CTCF binding to DNA is regulated remains poorly understood. Here the authors find that there is a shared subset of CTCF-bound sites resistant to protein depletion in different cell lines, which are enriched at domain boundaries and chromatin loops constitutive to all cell types.

CCCTC-binding factor (CTCF) is a DNA-binding protein with diverse roles in chromatin architecture and gene regulation. The contextual basis for distinct CTCF functions remains largely unknown. As an architectural protein in chromatin, one role of CTCF involves domain organization.

Binding of CTCF at multiple DNase I hypersensitive sites (DHSs) is also required to maintain a specific chromatin architecture at the murine β-globin locus 56. Similarly, D. melanogaster architectural proteins BEAF-32 and ZW5 were shown to mediate long-range interactions at the hsp70 locus and between copies of the gypsy retrotransposon 57 , 58 .

Chromatin architecture facilitates accurate transcription at a number of loci, but it remains unclear how much chromatin architecture is involved in global transcriptional regulation. Previous work has shown that rapid depletion of the architectural protein CTCF in cell culture strongly alters chromatin organization but results in surprisingly ...