Results 41 to 50 of about 39,377 (243)

InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop

Briefings in Bioinformatics, 2023
Abstract Deciphering cell-type-specific 3D structures of chromatin is challenging. Here, we present InferLoop, a novel method for inferring the strength of chromatin interaction using single-cell chromatin accessibility data. The workflow of InferLoop is, first, to conduct signal enhancement by grouping nearby cells into bins, and then ...
Feng Zhang 0051, Huiyuan Jiao, Yihao Wang, Chen Yang, Linying Li, Zhiming Wang, Ran Tong, Junmei Zhou, Jianfeng Shen, Lingjie Li   +9 more
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CTCF mediates the cell-type specific spatial organization of the Kcnq5 locus and the local gene regulation. [PDF]

PLoS ONE, 2012
Chromatin loops play important roles in the dynamic spatial organization of genes in the nucleus. Growing evidence has revealed that the multivalent functional zinc finger protein CCCTC-binding factor (CTCF) is a master regulator of genome spatial ...
Licheng Ren, Yang Wang, Minglei Shi, Xiaoning Wang, Zhong Yang, Zhihu Zhao   +5 more
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Diffusion Based Looping of Chromatin [PDF]

Biophysical Journal, 2010
Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order folding still remains elusive. Flourescent in situ hybridization reveals a tight connection between genome folding and function as well as a folding
Heermann, Dieter W., Bohn, Manfred
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R-loops associated with triplet repeat expansions promote gene silencing in Friedreich ataxia and fragile X syndrome.

PLoS Genetics, 2014
Friedreich ataxia (FRDA) and Fragile X syndrome (FXS) are among 40 diseases associated with expansion of repeated sequences (TREDs). Although their molecular pathology is not well understood, formation of repressive chromatin and unusual DNA structures ...
Matthias Groh, Michele M P Lufino, Richard Wade-Martins, Natalia Gromak   +3 more
doaj   +1 more source

Chromatin: A Connection Between Loops and Barriers? [PDF]

Current Biology, 2002
A genetic screen for proteins that can block the spread of silenced heterochromatin has identified components of the nuclear pores with potential barrier activity. These results suggest that formation of loops of chromatin anchored to the pore could be one mechanism of barrier function.
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R-loop: an emerging regulator of chromatin dynamics [PDF]

Acta Biochimica et Biophysica Sinica, 2016
The dynamic structure of chromatin, which exists in two conformational states: heterochromatin and euchromatin, alters the accessibility of the DNA to regulatory factors during transcription, replication, recombination, and DNA damage repair. Chemical modifications of histones and DNA, as well as adenosine triphospahate-dependent nucleosome remodeling,
Qais, Al-Hadid, Yanzhong, Yang
openaire   +2 more sources

LASCA: loop and significant contact annotation pipeline

Scientific Reports, 2021
Chromatin loops represent one of the major levels of hierarchical folding of the genome. Although the situation is evolving, current methods have various difficulties with the accurate mapping of loops even in mammalian Hi-C data, and most of them fail ...
Artem V. Luzhin, Arkadiy K. Golov, Alexey A. Gavrilov, Artem K. Velichko, Sergey V. Ulianov, Sergey V. Razin, Omar L. Kantidze   +6 more
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CRISPR-Mediated Reorganization of Chromatin Loop Structure [PDF]

Journal of Visualized Experiments, 2018
Recent studies have clearly shown that long-range, three-dimensional chromatin looping interactions play a significant role in the regulation of gene expression, but whether looping is responsible for or a result of alterations in gene expression is still unknown.
Morgan, Stefanie L., Chang, Erin Y., Mariano, Natasha C., Bermudez, Abel, Arruda, Nicole L., Wu, Fanting, Luo, Yunhai, Shankar, Gautam, Huynh, Star K., Huang, Chiao-Chain, Pitteri, Sharon J., Wang, Kevin C.   +11 more
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Multi-scale phase separation by explosive percolation with single-chromatin loop resolution

Computational and Structural Biotechnology Journal, 2022
The 2 m-long human DNA is tightly intertwined into the cell nucleus of the size of 10 μm. The DNA packing is explained by folding of chromatin fiber.
Kaustav Sengupta, Michał Denkiewicz, Mateusz Chiliński, Teresa Szczepińska, Ayatullah Faruk Mollah, Sevastianos Korsak, Raissa D'Souza, Yijun Ruan, Dariusz Plewczynski   +8 more
doaj   +1 more source

CGLoop: a neural network framework for chromatin loop prediction

BMC Genomics
Background Chromosomes of species exhibit a variety of high-dimensional organizational features, and chromatin loops, which are fundamental structures in the three-dimensional (3D) structure of the genome. Chromatin loops are visible speckled patterns on
Junfeng Wang, Lili Wu, Jingjing Wei, Chaokun Yan, Huimin Luo, Junwei Luo, Fei Guo   +6 more
doaj   +1 more source