Results 81 to 90 of about 303,776 (147)

CTCF Binding Polarity Determines Chromatin Looping

Molecular Cell, 2015
CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding
de Wit, Elzo, Vos, Erica S M, Holwerda, Sjoerd J B, Valdes-Quezada, Christian, Verstegen, Marjon J A M, Teunissen, Hans, Splinter, Erik, Wijchers, Patrick J, Krijger, Peter H L, de Laat, Wouter   +9 more
openaire   +4 more sources

Topological Spectra and Entropy of Chromatin Loop Networks

Physical Review Letters
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites,
Bonato, Andrea, Chiang, Michael, Corbett, Dom, Kitaev, Sergey, Marenduzzo, Davide, Morozov, Alexander, Orlandini, Enzo   +6 more
openaire   +5 more sources

Cohesin residency determines chromatin loop patterns

eLife, 2020
The organization of chromatin into higher order structures is essential for chromosome segregation, the repair of DNA-damage, and the regulation of gene expression. Using Micro-C XL to detect chromosomal interactions, we observed the pervasive presence of cohesin-dependent loops with defined positions throughout the genome of budding yeast, as seen in ...
Lorenzo Costantino, Tsung-Han S Hsieh, Rebecca Lamothe, Xavier Darzacq, Douglas Koshland   +4 more
openaire   +5 more sources

Cross–cell-line conservation-resolved interactions reveal conservation-dependent relationships among CTCF loops

BMC Genomics
The three-dimensional organization of the genome is shaped by CTCF-mediated chromatin loops, which vary widely in strength, conservation, and cell-type specificity. A longstanding model proposes that highly conserved loops form autonomously and establish
Maryam Mirabolghasemi, Mohammad Hossein Karimi-Jafari, Ali Mohammad Banaei-Moghaddam   +2 more
doaj   +1 more source

Thermodynamic pathways to genome spatial organization in the cell nucleus [PDF]

, 2009
The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to their state of activity and, yet, displace their genes to interact with remote sites in complex ...
A. Prisco, Prisco, Antonella, Nicodemi, Mario, Nicodemi M, Prisco A   +4 more
core   +1 more source

Recent evidence that TADs and chromatin loops are dynamic structures [PDF]

, 2017
Mammalian genomes are folded into spatial domains, which regulate gene expression by modulating enhancer-promoter contacts. Here, we review recent studies on the structure and function of Topologically Associating Domains (TADs) and chromatin loops.
Robert Tjian, Hansen, Anders S, Cattoglio, Claudia, Claudia Cattoglio, Anders S. Hansen, Xavier Darzacq, Darzacq, Xavier, Tjian, Robert   +7 more
core   +1 more source

Additional file 5 of Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution

, 2022
Additional file 5: Table S6 The interchromosomal open chromatin ...
Jingya Yuan (9668621), Guanghong Jia (3523712), Lulu Li (608444), Haojie Sun (4516129), Yijin Wang (6115649), Junrong Mao (11996516), Xiue Wang (111266), Wu Jiao (9668624), Zhongfu Ni (48118), Shiting Chen (11996513), Longfei Wang (217360), Qingxin Song (11996519)   +11 more
core   +1 more source

Genome-wide absolute quantification of chromatin looping

Nature Structural & Molecular Biology
Three-dimensional genomics methods such as Hi-C and Micro-C have uncovered chromatin loops across the genome and linked these loops to gene regulation. However, these methods only measure three-dimensional interaction probabilities on a relative scale.
James M. Jusuf, Jin H. Yang, Jack Toppen, Simon Grosse-Holz, Michele Gabriele, Pia Mach, Ilya M. Flyamer, Christoph Zechner, Luca Giorgetti, Leonid A. Mirny, Anders S. Hansen   +10 more
openaire   +4 more sources

An extrinsic motor directs chromatin loop formation by cohesin

The EMBO Journal
The ring-shaped cohesin complex topologically entraps two DNA molecules to establish sister chromatid cohesion. Cohesin also shapes the interphase chromatin landscape with wide-ranging implications for gene regulation, and cohesin is thought to achieve ...
Thomas M Guérin, Christopher Barrington, Georgii Pobegalov, Maxim I Molodtsov, Frank Uhlmann   +4 more
doaj   +1 more source

Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF [PDF]

, 2019
Mammalian genomes are folded into topologically associating domains (TADs), consisting of chromatin loops anchored by CTCF and cohesin. Some loops are cell-type specific.
Hansen, Anders S, Hsieh, Tsung-Han S., Cattoglio, Claudia, Reinberg, Danny, Pustova, Iryna, Saldaña-Meyer, Ricardo, Hansen, Anders S., Hsieh, Tsung-Han S, Darzacq, Xavier, Tjian, Robert   +9 more
core   +1 more source