mavii

Subsequently the chromatin architecture must be restored to reclaim genomic stability and possibly to preserve epigenetic landscape or to leave an imprint ... Buenrostro J.D., Chakrabarti A., Chu L., Hansen A.S., et al. Advances in chromatin and chromosome research: perspectives from multiple fields. Mol. Cell. 2020;79:881–901. doi: 10.1016/j ...

This special issue of Stem Cell Reports, dedicated to chromatin and nuclear architecture in stem cells, features both original research papers and several review articles, the latter covering chromatin and epigenetic regulation in early mammalian embryogenesis (Xia and Xie, 2020), three-dimensional organization of the pluripotent genome (Pelham ...

Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, 92093-0653, California, USA ... Selvaraj, S. et al. Chromatin architecture reorganization during stem cell differentiation ...

To train a diffusion model that predicts chromatin structures, we collect data samples as single-cell chromatin structures throughout the human genome. We further represented chromatin conformations by their pairwise distance maps, which are square matrices that can directly interface with the U-Net architecture used by many state-of-the-art ...

The structure of chromatin is associated with its function, but precisely how is unclear. New data show that the higher-order architecture of the genome is similar among cell types with widely ...

At the level of transcription, these models all face a formidable challenge: Dichotomizing the genome into two distinct groups simply does not account for the patterns in expression that are observed when chromatin is induced to transform from one state to the other (6, 7, 17–19).Specifically, inhibiting heterochromatin enzymes does not result purely in transcriptional activation (17–19).

Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis Nature Communications 10.1038/s41467-021-27800-9

Background Chromatin loops are critical for the three-dimensional organization of the genome and gene regulation. Accurate identification of chromatin loops is essential for understanding the regulatory mechanisms in disease. However, current mainstream detection methods rely primarily on single-source data, such as Hi-C, which limits these methods’ ability to capture the diverse features of ...

The precleared chromatin was then incubated with the corresponding antibodies at 4°C overnight. Antibody-chromatin complexes were washed and eluted. The purified immunoprecipitated DNA and input DNA were analyzed by qPCR using primers targeting AP-1 binding sites in the CD44 promoter or related enhancers, as listed in Supplemental Table 5.

Connecting the molecular structure and function of chromatin across length and timescales remains a grand challenge to understanding and engineering cellular behaviors. Across five orders of magnitude, dynamic processes constantly reshape chromatin structures, driving spaciotemporal patterns of gene expression and cell fate. Through the interplay of structure and function, the genome operates ...

Cohesin, bromodomain-containing protein BRD4, and Mediator exert critical and distinct functions in transcriptional regulation. The cohesin complex plays a key role in three-dimensional (3D) chromatin architecture by facilitating the formation of topologically associating domains through loop extrusion (48–50), which is halted by CTCF (51, 52).

Academia.edu is a platform for academics to share research papers. Editorial: Probing the Chromatin Architecture ... Chromatin architecture is based on the interaction between DNA and histones as well as the post-translational modifications (PTMs) of non-histone-associated proteins. Among the main proteins responsible for maintaining the 3D ...

The first paper to report Hi-C interaction maps at the resolution of individual restriction fragments in mammals. ... J. R. et al. Chromatin architecture reorganization during stem cell ...

Previous chromatin tracing efforts relied on denaturing FISH protocols, during which the double-stranded DNA is opened up using acid and heat treatment. 15, 16 This method leads to pervasive macro- and microstructural rearrangements of DNA, which likely prevents faithful high-resolution tracing of chromatin. 17, 18 Using enzymatic non ...

Overall, this article motivates the study of 3D chromatin architecture in cancer, which allows for a better understanding of its pathogenesis and develop novel approaches for diagnosis and treatment of cancer. ... In addition, these are great reference regulome maps for cancer research because chromatin accessibility mapping has also been done ...

Many lncRNAs are involved in chromatin regulation by recruiting chromatin-modifying proteins [7], and possess distinct properties that make them potential architectural elements in chromatin organization. For instance, they can form secondary structures, creating unique domains for interacting with specific proteins and other RNA molecules.

This special issue of Stem Cell Reports, dedicated to chromatin and nuclear architecture in stem cells, features both original research papers and several review articles, the latter covering chromatin and epigenetic regulation in early mammalian embryogenesis (Xia and Xie, 2020), three-dimensional organization of the pluripotent genome (Pelham-Webb et al., 2020), nucleolar function and ...

Chromatin architecture is a flexible foundation for gene expression Nat Genet. 2021 Apr 1. doi: 10.1038/s41588-021-00813-2. Online ahead of print. Authors Tom Misteli 1 , Elizabeth H Finn 2 Affiliations 1 National Cancer Institute, National Institutes of ...

This Research Topic aims to highlight the significance of understanding chromatin architecture in unraveling the complexities of gene regulation and its implications for human health and disease. Insights into the genome organization. Chromatin architecture influences gene regulation by regulating the accessibility of DNA to transcriptional ...

A complete understanding of the structure-function relationships of chromatin requires extending primarily one dimensional information, obtained from molecular genetic techniques and based on the underlying linear DNA sequence, to the three dimensional conformation. Recent progress in this endeavor …