Results 1 to 10 of about 303,776 (147)

SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data [PDF]

Nature Communications, 2023
Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometers and up to several kilobases in resolution in single cells.
Lindsay Lee, Hongyu Yu, Bojing Blair Jia, Adam Jussila, Chenxu Zhu, Jiawen Chen, Liangqi Xie, Antonina Hafner, Shreya Mishra, Duan Dennis Wang, Caterina Strambio-De-Castillia, Alistair Boettiger, Bing Ren, Yun Li, Ming Hu   +14 more
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Back-spliced RNA from retrotransposon binds to centromere and regulates centromeric chromatin loops in maize. [PDF]

PLoS Biology, 2020
In most plants, centromeric DNA contains highly repetitive sequences, including tandem repeats and retrotransposons; however, the roles of these sequences in the structure and function of the centromere are unclear.
Yalin Liu, Handong Su, Jing Zhang, Yang Liu, Chao Feng, Fangpu Han   +5 more
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CapsNetYY1: identifying YY1-mediated chromatin loops based on a capsule network architecture

BMC Genomics, 2023
Background Previous studies have identified that chromosome structure plays a very important role in gene control. The transcription factor Yin Yang 1 (YY1), a multifunctional DNA binding protein, could form a dimer to mediate chromatin loops and active ...
Zhimin Zhang, Fenglin Li, Jianping Zhao, Chunhou Zheng   +3 more
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Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C

Epigenetics & Chromatin, 2022
Background Regulatory elements such as promoters, enhancers, and insulators interact each other to mediate molecular processes. To capture chromatin interactions of regulatory elements, 3C-derived methods such as Hi-C and Micro-C are developed.
Beoung Hun Lee, Zexun Wu, Suhn K. Rhie
doaj   +1 more source

R-loop landscape in mature human sperm: Regulatory and evolutionary implications

Frontiers in Genetics, 2023
R-loops are three-stranded nucleic acid structures consisting of an RNA:DNA hybrid and a displaced DNA strand. While R-loops pose a potential threat to genome integrity, they constitute 5% of the human genome.
Maurice Scheuren, Jonas Möhner, Hans Zischler   +2 more
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Spatial Organization of Chromatin: Transcriptional Control of Adaptive Immune Cell Development

Frontiers in Immunology, 2021
Higher-order spatial organization of the genome into chromatin compartments (permissive and repressive), self-associating domains (TADs), and regulatory loops provides structural integrity and offers diverse gene regulatory controls.
Jagan M. R. Pongubala, Cornelis Murre
doaj   +1 more source

Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops

Nature Communications, 2022
The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to ...
Shuai Liu, Yaqiang Cao, Kairong Cui, Qingsong Tang, Keji Zhao   +4 more
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DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes.

PLoS Computational Biology, 2022
In recent years, major advances have been made in various chromosome conformation capture technologies to further satisfy the needs of researchers for high-quality, high-resolution contact interactions.
Siguo Wang, Qinhu Zhang, Ying He, Zhen Cui, Zhenghao Guo, Kyungsook Han, De-Shuang Huang   +6 more
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A supervised learning framework for chromatin loop detection in genome-wide contact maps

Nature Communications, 2020
Predicting chromatin loops from genome-wide interaction matrices such as Hi-C data provides insight into gene regulation events. Here, the authors present Peakachu, a Random Forest classification framework that predicts chromatin loops from genome-wide ...
Tarik J. Salameh, Xiaotao Wang, Fan Song, Bo Zhang, Sage M. Wright, Chachrit Khunsriraksakul, Yijun Ruan, Feng Yue   +7 more
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Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution

Genome Biology, 2022
Background Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their ...
Jingya Yuan, Haojie Sun, Yijin Wang, Lulu Li, Shiting Chen, Wu Jiao, Guanghong Jia, Longfei Wang, Junrong Mao, Zhongfu Ni, Xiue Wang, Qingxin Song   +11 more
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