Results 21 to 30 of about 5,528,770 (310)

3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing

Acta Pharmaceutica Sinica B, 2021
The three-dimensional (3D) conformation of chromatin is integral to the precise regulation of gene expression. The 3D genome and genomic variations in non-alcoholic fatty liver disease (NAFLD) are largely unknown, despite their key roles in cellular ...
Lina Xu, Lianhong Yin, Yan Qi, Xuemei Tan, Meng Gao, Jinyong Peng   +5 more
doaj   +1 more source

Computational methods for analyzing multiscale 3D genome organization

Nature reviews genetics, 2023
In this Review, Zhang et al. discuss how recent advances in computational methods are helping to reveal the multiscale features involved in genome folding within the nucleus and how the resulting 3D genome organization relates to genome function.
Yang Zhang, Lorenzo Boninsegna, Mu-Yu Yang, Tom Misteli, Frank Alber, Jian-xing Ma   +5 more
semanticscholar   +1 more source

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Cell, 2015
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 ...
Zhonghui Tang, O. Luo, Xing-Wang Li, Meizhen Zheng, J. J. Zhu, Przemyslaw Szalaj, Paweł Trzaskoma, Adriana Magalska, J. Włodarczyk, B. Ruszczycki, Paul J. Michalski, Emaly Piecuch, Ping Wang, Danjuan Wang, S. Tian, M. Penrad‐Mobayed, L. Sachs, Xiaoan Ruan, Chia-Lin Wei, E. Liu, G. Wilczynski, Dariusz M Plewczynski, Guoliang Li, Y. Ruan   +23 more
semanticscholar   +1 more source

Mechanical determinants of chromatin topology and gene expression

Nucleus, 2022
The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin.
Rajiv Kumar Jha, David Levens, Fedor Kouzine   +2 more
doaj   +1 more source

Single Cell DNA Methylation and 3D Genome Architecture in the Human Brain

Science, 2023
Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chromatin ...
Wei Tian, Jing-Tian Zhou, Anna Bartlett, Qiurui Zeng, Han-Qing Liu, R. Castanon, M. Kenworthy, Jordan Altshul, Cynthia Valadon, Andrew I. Aldridge, J. Nery, H. Chen, Jiaying Xu, Nicholas D. Johnson, J. Lucero, Julia K. Osteen, N. Emerson, Jon Rink, Jasper Lee, Y. Li, K. Siletti, Michelle Liem, Naomi Claffey, Caz O'Connor, A. Yanny, J. Nyhus, Nick Dee, Tamara Casper, N. Shapovalova, Daniel Hirschstein, Song-Lin Ding, R. Hodge, Boaz P. Levi, C. Keene, S. Linnarsson, E. Lein, Bing-Jie Ren, M. Behrens, J. Ecker   +38 more
semanticscholar   +1 more source

3DIV update for 2021: a comprehensive resource of 3D genome and 3D cancer genome

, 2021
Three-dimensional (3D) genome organization is tightly coupled with gene regulation in various biological processes and diseases. In cancer, various types of large-scale genomic rearrangements can disrupt the 3D genome, leading to oncogenic gene ...
M Kim, M S Kim, I Jung, Insu Jang, K Kim, J Choi, Byungwook Lee   +6 more
core   +1 more source

From association to mechanism in complex disease genetics: the role of the 3D genome

Arthritis Research & Therapy, 2018
Genome-wide association studies (GWAS) and fine mapping studies in autoimmune diseases have identified thousands of genetic variants, the majority of which are located in non-protein-coding enhancer regions.
Yao Fu, Kandice L Tessneer, Chuang Li, Patrick M Gaffney   +3 more
doaj   +1 more source

Life-long Restructuring of 3D Genome Architecture in Cerebellar Granule Cells

Science, 2023
The cerebellum contains most of the neurons in the human brain and exhibits distinctive modes of development and aging. In this work, by developing our single-cell three-dimensional (3D) genome assay—diploid chromosome conformation capture, or Dip-C—into
Long-Zhi Tan, Jenny Shi, Siavash Moghadami, B. Parasar, Cydney P. Wright, Yunji Seo, Kristen Vallejo, Inma Cobos, Laramie E. Duncan, Ritchie Chen, K. Deisseroth   +10 more
semanticscholar   +1 more source

DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency

Cell Reports, 2019
Summary: The DNA hypomethylation that occurs when embryonic stem cells (ESCs) are directed to the ground state of naive pluripotency by culturing in two small molecule inhibitors (2i) results in redistribution of polycomb (H3K27me3) away from its target ...
Katy McLaughlin, Ilya M. Flyamer, John P. Thomson, Heidi K. Mjoseng, Ruchi Shukla, Iain Williamson, Graeme R. Grimes, Robert S. Illingworth, Ian R. Adams, Sari Pennings, Richard R. Meehan, Wendy A. Bickmore   +11 more
doaj   +1 more source

High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding

Nature Communications, 2023
Here the authors establish a high throughput Pore-C (HiPore-C) method increasing the sequencing output of multi-way chromatin contacts and reveal single-allele topology diversity and cell type-specificity of 3D genome folding. Canonical three-dimensional
Jia-Yong Zhong, Long-Jian Niu, Zhuo-Bin Lin, Xin Bai, Ying Chen, F. Luo, Chunhui Hou, Chuan-Le Xiao   +7 more
semanticscholar   +1 more source