Results 41 to 50 of about 392,690 (299)

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

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. [PDF]

, 2015
Spatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and ...
Liu, Edison, Zhu, Jacqueline Jufen, Ruan, Yijun, Luo, Oscar Junhong, Zhu, Jacqueline,, Wang, Danjuan, Piecuch, Emaly, Tang, Zhonghui, Sachs, Laurent, Jufen Zhu, Jacqueline, Wei, Chia-Lin, Plewczynski, Dariusz, Luo, Oscar,, Zhongyuan Tian, Simon, Zheng, Meizhen, Michalski, Paul, Wilczynski, Grzegorz M, Wilczynski, Grzegorz M., Wilczynski, Grzegorz,, Liu, Edison T., Liu, Edison T, Tian, Simon,, Wlodarczyk, Jakub, Szala, Przemyslaw, Wang, Ping, Sachs, Laurent M, Trzaskoma, Pawel, Tian, Simon Zhongyuan, Ruan, Xiaoan, Sachs, Laurent M., Ruszczycki, Blazej, We, Chia-Lin, Szalaj, Przemyslaw, Li, Xingwang, Li, Guoliang, Magalska, Adriana, Penrad-Mobayed, May   +36 more
core   +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

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

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

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

Optoepigenetics for 3D genome engineering [PDF]

Nature Reviews Genetics, 2019
A study in Nature Methods describes a light-activated dynamic looping (LADL) system, which consists of a synthetic architectural protein that rapidly induces long-range chromatin interactions in response to blue light.
openaire   +2 more sources

Integrating Transposable Elements in the 3D Genome [PDF]

Mobile DNA, 2019
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling.
Bousios, Alexandros, Nuetzmann, Hans-Wilhelm, Buck, Dorothy, Michieletto, Davide   +3 more
openaire   +6 more sources

Automatic generation of 3D motifs for classification of protein binding sites

, 2007
BACKGROUND: Since many of the new protein structures delivered by high-throughput processes do not have any known function, there is a need for structure-based prediction of protein function. Protein 3D structures can be clustered according to their fold
Herzyk, P, Herzyk, Pawel, Gilbert, D, Nebel, J, Gilbert, David R., Jean-Christophe Nebel, Herzyk, P., Gilbert, D.R., Nebel Jean-Christophe, Nebel, J.C., David R Gilbert, Gilbert David R, Nebel, Jean-Christophe, Pawel Herzyk, Herzyk Pawel   +14 more
core   +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