Results 71 to 80 of about 94,335 (243)

CNNKSCEC: a deep learning-based framework for chromatin loop prediction with multi-source feature integration

Frontiers in Genetics
MotivationChromatin in the cell nucleus adopts a complex three-dimensional (3D) structure shaped by folding and interactions, with chromatin loops serving as fundamental organizational units.
Junfeng Wang, Bingzi Zheng, Lili Wu, Xiaoyan Liu, Haixia Zhai, Junwei Luo   +5 more
doaj   +1 more source

Characterizing meiotic chromosomes' structure and pairing using a designer sequence optimized for Hi‐C

Molecular Systems Biology, 2018
In chromosome conformation capture experiments (Hi‐C), the accuracy with which contacts are detected varies due to the uneven distribution of restriction sites along genomes.
Héloïse Muller, Vittore F Scolari, Nicolas Agier, Aurèle Piazza, Agnès Thierry, Guillaume Mercy, Stéphane Descorps‐Declere, Luciana Lazar‐Stefanita, Olivier Espeli, Bertrand Llorente, Gilles Fischer, Julien Mozziconacci, Romain Koszul   +12 more
doaj   +1 more source

Loops determine the mechanical properties of mitotic chromosomes. [PDF]

PLoS ONE, 2011
We introduce a new polymer model for mitotic chromosomes. The key assumption of the model is the ability of the chromatin fibre to cross-link to itself due to binding proteins.
Yang Zhang, Dieter W Heermann
doaj   +1 more source

Chronobiology of Cancer: How Aging Fuels Oncogenesis at the Molecular Level

Aging and Cancer, EarlyView.
This graphical abstract illustrates the key biological pathways linking aging with cancer development and progression. In the upper left, cumulative exposure to ultraviolet radiation, toxins, and reactive oxygen species (ROS) causes DNA damage and genomic instability, whereas age‐related decline in repair mechanisms, such as ATM/ATR, BER, and NER ...
Anu Singh, Aroonima Misra, Sufian Zaheer
wiley   +1 more source

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL

eLife, 2020
Eukaryotic genomes are folded into loops. It is thought that these are formed by cohesin complexes via extrusion, either until loop expansion is arrested by CTCF or until cohesin is removed from DNA by WAPL.
Gordana Wutz, Rene Ladurner, Brian Glenn St Hilaire, Roman R Stocsits, Kota Nagasaka, Benoit Pignard, Adrian Sanborn, Wen Tang, Csilla Várnai, Miroslav P Ivanov, Stefan Schoenfelder, Petra van der Lelij, Xingfan Huang, Gerhard Dürnberger, Elisabeth Roitinger, Karl Mechtler, Iain Finley Davidson, Peter Fraser, Erez Lieberman-Aiden, Jan-Michael Peters   +19 more
doaj   +1 more source

Clinical, Histologic, and Serological Predictors of Renal Function Loss in Lupus Nephritis

Arthritis Care &Research, EarlyView.
Objective Kidney survival is the ultimate goal in lupus nephritis (LN) management, but long‐term predictors remain inadequately studied, requiring long‐term follow‐up. This study aimed to identify baseline and early longitudinal predictors of kidney survival in the Accelerating Medicines Partnership LN longitudinal cohort.
Shangzhu Zhang, Laurence Magder, Daniel Goldman, Judith A. James, Joel M. Guthridge, Carla Guthridge, Peter Izmirly, Jill P. Buyon, H. Michael Belmont, Richard A. Furie, Noa Schwartz, Chaim Putterman, Jennifer L. Barnas, Jennifer H. Anolik, Sarah French, Maria Dall'Era, Avi Z. Rosenberg, Jeffrey Hodgin, Dawit S. Demeke, the Accelerating Medicines Partnership Rheumatoid Arthritis and Systemic Lupus Erythematosus (RA/SLE) Network, Michelle Petri, Andrea Fava   +21 more
wiley   +1 more source

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   +3 more sources

RNAP II antagonizes mitotic chromatin folding and chromosome segregation by condensin

Cell Reports
Summary: Condensin shapes mitotic chromosomes by folding chromatin into loops, but whether it does so by DNA-loop extrusion remains speculative. Although loop-extruding cohesin is stalled by transcription, the impact of transcription on condensin, which ...
Jérémy Lebreton, Léonard Colin, Elodie Chatre, Pascal Bernard   +3 more
doaj   +1 more source

The chromatin assembly factor 1 promotes Rad51-dependent template switches at replication forks by counteracting D-loop disassembly by the RecQ-type helicase Rqh1.

PLoS Biology, 2014
At blocked replication forks, homologous recombination mediates the nascent strands to switch template in order to ensure replication restart, but faulty template switches underlie genome rearrangements in cancer cells and genomic disorders ...
Violena Pietrobon, Karine Fréon, Julien Hardy, Audrey Costes, Ismail Iraqui, Françoise Ochsenbein, Sarah A E Lambert   +6 more
doaj   +1 more source

Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data

BMC Genomics, 2019
Background Chromosomal architecture, which is constituted by chromatin loops, plays an important role in cellular functions. Gene expression and cell identity can be regulated by the chromatin loop, which is formed by proximal or distal enhancers and ...
Ruimin Wang, Yunlong Wang, Xueying Zhang, Yaliang Zhang, Xiaoyong Du, Yaping Fang, Guoliang Li   +6 more
doaj   +1 more source