Results 31 to 40 of about 5,528,770 (310)

3D genome folding in epigenetic regulation and cellular memory

Trends in Cell Biology
The 3D folding of the genome is tightly linked to its epigenetic state which maintains gene expression programmes. Although the relationship between gene expression and genome organisation is highly context dependent, 3D genome organisation is emerging ...
Flora Paldi, G. Cavalli
semanticscholar   +1 more source

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction. [PDF]

PLoS Computational Biology, 2015
The three-dimensional (3D) structure of the genome is important for orchestration of gene expression and cell differentiation. While mapping genomes in 3D has for a long time been elusive, recent adaptations of high-throughput sequencing to chromosome ...
Jonas Paulsen, Odin Gramstad, Philippe Collas   +2 more
doaj   +1 more source

Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs

Nature Genetics
In animal genomes, regulatory DNA elements called enhancers govern precise spatiotemporal gene expression patterns in specific cell types. However, the spatial organization of enhancers within the nucleus to regulate target genes remains poorly ...
Honggui Wu, Jiankun Zhang, Long-Zhi Tan, X. Xie   +3 more
semanticscholar   +1 more source

Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging

Science Advances, 2023
Little is known about three-dimensional (3D) genome organization in skeletal muscle stem cells [also called satellite cells (SCs)]. Here, we comprehensively map the 3D genome topology reorganization during mouse SC lineage progression.
Yu Zhao, Yingzhe Ding, Liangqiang He, Qin Zhou, Xiaona Chen, Yu-Ying Li, Marianna Alfonsi, Zhen-Guo Wu, Hao Sun, Hua-Ting Wang   +9 more
semanticscholar   +1 more source

Enhancers dysfunction in the 3D genome of cancer cells

Frontiers in Cell and Developmental Biology, 2023
Eukaryotic genomes are spatially organized inside the cell nucleus, forming a threedimensional (3D) architecture that allows for spatial separation of nuclear processes and for controlled expression of genes required for cell identity specification and ...
Giulia Della Chiara, Carlos Jiménez, Mohit Virdi, Nicola Crosetto, Nicola Crosetto, Nicola Crosetto, Magda Bienko, Magda Bienko, Magda Bienko   +8 more
doaj   +1 more source

Perturb-tracing enables high-content screening of multi-scale 3D genome regulators

Nature Methods
Three-dimensional (3D) genome organization becomes altered during development, aging and disease, but the factors regulating chromatin topology are incompletely understood and currently no technology can efficiently screen for new regulators of multi ...
Yu-Bao Cheng, Mengwei Hu, Bing Yang, Tyler B. Jensen, Yuan Zhang, Tian-Qi Yang, Ruihuan Yu, Zhaoxia Ma, Jonathan S. D. Radda, Shengyan Jin, C. Zang, Si-Yuan Wang   +11 more
semanticscholar   +1 more source

Organizational Principles of 3D Genome Architecture

Nature reviews genetics, 2018
Studies of 3D chromatin organization have suggested that chromosomes are hierarchically organized into large compartments composed of smaller domains called topologically associating domains (TADs).
M. Rowley, V. Corces
semanticscholar   +1 more source

A novel neoantigen discovery approach based on chromatin high order conformation

BMC Medical Genomics, 2020
Background High-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify potential neoantigens that ...
Yi Shi, Mingxuan Zhang, Luming Meng, Xianbin Su, Xueying Shang, Zehua Guo, Qingjiao Li, Mengna Lin, Xin Zou, Qing Luo, Yaoliang Yu, Yanting Wu, Lintai Da, Tom Weidong Cai, Guang He, Ze-Guang Han   +15 more
doaj   +1 more source

Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation

bioRxiv
Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multi-omic profiling of 3D genome structure and DNA methylation for 86,689 single nuclei across ...
Jing-Tian Zhou, Yue Wu, Han-Qing Liu, Wei Tian, R. Castanon, Anna Bartlett, Zuolong Zhang, G. Yao, De-Li Shi, Benjamin Clock, Samantha Marcotte, J. Nery, Michelle Liem, Naomi Claffey, Lara Boggeman, Cesar Barragan, R. A. Drigo, Annika K. Weimer, Min-Yi Shi, J. Cooper-Knock, Sai Zhang, Michael P. Snyder, Sebastian Preissl, Bing Ren, Carolyn O'Connor, Shengbo Chen, C. Luo, Jesse R. Dixon, J. Ecker   +28 more
semanticscholar   +1 more source

In vitro reconstitution of chromatin domains shows a role for nucleosome positioning in 3D genome organization

bioRxiv, 2023
The spatial organization of the genome modulates nuclear processes, including transcription, replication, and DNA repair1,2. Eukaryotic genomes are organized into distinct 3D chromatin domains3.
Elisa Oberbeckmann, Kimberly Quililan, P. Cramer, A. M. Oudelaar   +3 more
semanticscholar   +1 more source