mavii

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.

CTCF is a key regulator of chromatin organization. Using a series of CTCF mutations, Do et al. investigate the interplay between CTCF, chromatin accessibility, and cohesin. They show that the impaired properties of each mutant uniquely affect cohesin-mediated loop extrusion and the transcriptomes of cells in a predominantly indirect manner.

Considering that cohesin protein complex is highly associated with CTCF in chromatin biology ... Top right: zoom-in merged image. Bottom right: 3D reconstruction of co-localization with the depth of the scanned volume. Bar chart: statistics of Spearman’s correlation values between CTCF and RNAPII signals from 21 cell nuclei. Control (Ctrl) is ...

CTCF mainly promotes chromatin accessibility and frequently inhibits expression of these direct binding targets, which are enriched for binding motifs of transcription repressors. These findings provide different and sometimes opposite conclusions from previous studies, emphasizing the need to consider cellular heterogeneity and cell-type ...

During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. We exploited the M- to G1-phase progression to interrogate the contributions of the architectural factor CTCF and the process of transcription to genome re-sculpting in newborn nuclei. Deple …

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 ...

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.

Here, we interrogated the contributions of CTCF and the process of active transcription to the establishment of post-mitotic chromatin architecture by acutely depleting CTCF through the auxin-inducible degron (AID) system alone or jointly with chemical inhibition of transcription during the mitosis to G1-phase transition 1,11,26. We demonstrate ...

CTCF plays key roles in gene regulation, chromatin insulation, imprinting, X chromosome inactivation and organizing the higher-order chromatin architecture of mammalian genomes. Previous studies ...

The regulatory functions of these co-factors in CTCF-mediated chromatin insulation and long-range chromatin interactions need to be further investigated in detail. Limitation of the study. As Ctcf is ubiquitously expressed in a manner similar to a housekeeping gene, and CTCF is essential for cell survival, it is therefore not possible to ...

Background CTCF is considered as the most essential transcription factor regulating chromatin architecture and gene expression. However, genome-wide impact of CTCF on erythropoiesis has not been extensively investigated. Results Using a state-of-the-art human erythroid progenitor cell model (HUDEP-2 and HEL cell lines), we systematically investigate the effects of acute CTCF loss by an auxin ...

Summary. 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 RNAPII with haplotype specificity and nucleotide resolution in different human cell lineages.

It will be interesting to assess how Snf2h loss impacts the dynamics of CTCF binding to chromatin in real time. CTCF can promote chromatin opening and incorporation of a histone variant H3.3 (Weth et al, 2014) suggesting that it can act upstream of the establishment of

CTCF barriers: CTCF sites act as bidirectional barriers. Upon encountering a CTCF barrier, LEFs have a 90% capture probability. Captured LEFs remained at CTCF barriers until unbinding from chromatin. The CTCF barriers were located at the following positions on each of the three lattices:

During mitosis, transcription is globally attenuated and chromatin architecture is dramatically reconfigured. Here we exploited the M- to G1-phase progression to interrogate the contributions of the architectural factor CTCF and the process of transcription to re-sculpting the genome in newborn nuclei. Depletion of CTCF specifically during the M- to G1-phase transition altered the re ...

Allele-specific CTCF occupancy on chromatin is generally rare (6.5% of all CTCF peaks), and mostly occurs inside TADs, suggesting that haplotype-specific TAD border formation is not simply based on haplotype-specific CTCF occupancy. We found that TAD organization is related to ASE gene clustering, with ASE genes being present in only half of ...

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 ...

Three decades of research have established the CCCTC-binding factor (CTCF) as a ubiquitously expressed chromatin organizing factor and master regulator of gene expression. A new role for CTCF as a regulator of alternative splicing (AS) has now emerged. CTCF has been directly and indirectly linked to …

CTCF is crucial to the organization of mammalian genomes into loop structures. According to recent studies, the transcription apparatus is compartmentalized and concentrated at super-enhancers to form phase-separated condensates and drive the expression of cell-identity genes. ... CTCF-mediated chromatin looping provides a topological framework ...