Results 11 to 20 of about 39,377 (243)

Mapping chromatin loops in single cells [PDF]

Trends in Genetics, 2022
Recent advances in high-throughput chromatin conformation capture (Hi-C) technologies at the single-cell level enable the identification of cell type-specific chromatin loops directly from complex tissues. This may help to interpret noncoding variants identified by genome-wide association studies (GWAS) in disease-relevant cell types. We briefly review
, Ming Hu, Miao Yu
exaly   +4 more sources

Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes [PDF]

Communications Biology
Chromosome Conformation Capture (3 C) methods, including Hi-C (a high-throughput variation of 3 C), detect pairwise interactions between DNA regions, enabling the reconstruction of chromatin architecture in the nucleus. HiChIP is a modification of the Hi-
Karolina Buka, Zofia Parteka-Tojek, Abhishek Agarwal, Michał Denkiewicz, Sevastianos Korsak, Mateusz Chiliński, Krzysztof H. Banecki, Dariusz Plewczynski   +7 more
doaj   +2 more sources

DconnLoop: a deep learning model for predicting chromatin loops based on multi-source data integration [PDF]

BMC Bioinformatics
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.
Junfeng Wang, Kuikui Cheng, Chaokun Yan, Huimin Luo, Junwei Luo   +4 more
doaj   +2 more sources

Comprehensive Predictions of Mef2-Mediated Chromatin Loops, Which May Inhibit Ubx Binding by Blocking Low-Affinity Binding Sites [PDF]

Journal of Developmental Biology
Gene regulation depends on the interaction between chromatin-associated factors, such as transcription factors (TFs), which promote chromatin loops to ensure tight contact between enhancer and promoter regions.
Katrin Domsch
doaj   +2 more sources

Transcriptionally active chromatin loops contain both ‘active’ and ‘inactive’ histone modifications that exhibit exclusivity at the level of nucleosome clusters [PDF]

Epigenetics & Chromatin
Chromatin state is thought to impart regulatory function to the underlying DNA sequence. This can be established through histone modifications and chromatin organisation, but exactly how these factors relate to one another to regulate gene expression is ...
Stefan A. Koestler, Madeleine L. Ball, Leila Muresan, Vineet Dinakaran, Robert White   +4 more
doaj   +2 more sources

CD-Loop: a chromatin loop detection method based on the diffusion model

Frontiers in Genetics
MotivationIn recent years, there have been significant advances in various chromatin conformation capture techniques, and annotating the topological structure from Hi-C contact maps has become crucial for studying the three-dimensional structure of ...
Jiquan Shen, Yang Wang, Junwei Luo
doaj   +3 more sources

Extrusion of chromatin loops by a composite loop extrusion factor. [PDF]

Phys Rev E, 2021
12 pages, 7 ...
Yan H, Surovtsev I, Williams JF, Bailey MLP, King MC, Mochrie SGJ.   +5 more
europepmc   +5 more sources

SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data [PDF]

Nature Methods, 2021
Guoqiang Li, Yuchen Yang, Yanxiao Zhang   +2 more
exaly   +2 more sources

Landscape of cohesin-mediated chromatin loops in the human genome [PDF]

Nature, 2020
Marlene Rabinovitch, Judith B Zaugg, Rohith Srivas   +2 more
exaly   +2 more sources

Chromatin Loop Extrusion and Chromatin Unknotting [PDF]

Polymers, 2018
It has been a puzzle how decondensed interphase chromosomes remain essentially unknotted. The natural expectation is that in the presence of type II DNA topoisomerases that permit passages of double-stranded DNA regions through each other, all chromosomes should reach the state of topological equilibrium.
Racko, Dusan, Benedetti, Fabrizio, Goundaroulis, Dimos, Stasiak, Andrzej   +3 more
openaire   +4 more sources