Results 51 to 60 of about 2,219,993 (156)

Prediction of CTCF loop anchor based on machine learning

Frontiers in Genetics, 2023
Introduction: Various activities in biological cells are affected by three-dimensional genome structure. The insulators play an important role in the organization of higher-order structure.
Xiao Zhang, Xiao Zhang, Xiao Zhang, Wen Zhu, Wen Zhu, Huimin Sun, Yijie Ding, Li Liu   +7 more
doaj   +1 more source

Chromatin jets define the properties of cohesin-driven in vivo loop extrusion [PDF]

, 2022
Complex genomes show intricate organization in three-dimensional (3D) nuclear space. Current models posit that cohesin extrudes loops to form self-interacting domains delimited by the DNA binding protein CTCF.
King, James WD, Al-Jibury, Ediem, Fisher, Amanda G., Merkenschlager, Matthias, Pruessner, Gunnar, Garcia-Millan, Rosalba, King, James W.D., Guo, Ya, Ntagiantas, Konstantinos, Lenhard, Boris, Nash, Alex J., Galjart, Niels; id_orcid, Galjart, Niels, Fisher, Amanda G, Rueckert, Daniel, Nash, Alex J, Guo, Ya;Al-Jibury, Ediem;Garcia-Millan, Rosalba;Ntagiantas, Konstantinos;King, James W.D.;Nash, Alex J.;Galjart, Niels;Lenhard, Boris;Rueckert, Daniel;Fisher, Amanda G.;Pruessner, Gunnar;Merkenschlager, Matthias, Garcia-Millan, Rosalba; id_orcid   +17 more
core   +1 more source

Limits of Chromosome Compaction by Loop-Extruding Motors

Physical Review X, 2019
During mitosis, human chromosomes are linearly compacted about 1000-fold by loop-extruding motors. Recent experiments have shown that condensins extrude DNA loops but in a “one-sided” manner.
Edward J. Banigan, Leonid A. Mirny
doaj   +1 more source

DNA hypermethylation/boundary control loss identified in retinoblastomas associated with genetic and epigenetic inactivation of the RB1 gene promoter

Epigenetics, 2021
DNA hypermethylation events occur frequently in human cancers, but less is known of the mechanisms leading to their initiation. Retinoblastoma, an intraocular cancer affecting young children, involves bi-allelic inactivation of the RB1 gene (RB−/-).
AM Raizis, HM Racher, A Foucal, H Dimaras, BL Gallie, PM George   +5 more
doaj   +1 more source

CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism

Nucleus, 2020
Mammalian genome structure is closely linked to function. At the scale of kilobases to megabases, CTCF and cohesin organize the genome into chromatin loops.
Anders S. Hansen
doaj   +1 more source

High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL

, 2023
3D chromatin organization plays a critical role in regulating gene expression, DNA replication, recombination, and repair. While initially discovered for its role in sister chromatid cohesion, emerging evidence suggests that the cohesin complex (SMC1 ...
Qi Xu, Parminder Kaur, Tao, Yizhi Jane, Zhang, Hongshan, Xu, Qi, Pappas, Colette, Ilya J. Finkelstein, Hongtao Yu, Zhubing Shi, Lu, Xiaotong, Shi, Zhubing, Xiaotong Lu, Finkelstein, Ilya J., Elizabeth Marie Irvin, Yu, Hongtao, Wang, Hong, Irvin, Elizabeth Marie, Yizhi Jane Tao, Kaur, Parminder, Colette Pappas, Hongshan Zhang, Hong Wang   +21 more
core   +1 more source

Scc2/Nipbl hops between chromosomal cohesin rings after loading

eLife, 2017
The cohesin complex mediates DNA-DNA interactions both between (sister chromatid cohesion) and within chromosomes (DNA looping). It has been suggested that intra-chromosome loops are generated by extrusion of DNAs through the lumen of cohesin’s ring ...
James Rhodes, Davide Mazza, Kim Nasmyth, Stephan Uphoff   +3 more
doaj   +1 more source

The accessory subunit of mitochondrial DNA polymerase {gamma} determines the DNA content of mitochondrial nucleoids in human cultured cells [PDF]

, 2009
The accessory subunit of mitochondrial DNA polymerase γ, POLGβ, functions as a processivity factor in vitro. Here we show POLGβ has additional roles in mitochondrial DNA metabolism.
H. Sembongi, T. Yasukawa, Yasukawa, T, Di Re, M., I. J. Holt, L. J. Bailey, Fersht, A.R., Boyd-Kirkup, JD, Martinsson, P., Holt, I.J., J. N. Spelbrink, Sembongi, H, Spelbrink, JN, Bailey, LJ, Sembongi, H., Goffart, S, P. Martinsson, A. R. Fersht, Di Re, M, Martinsson, P, Reyes, A., J. D. Boyd-kirkup, S. Goffart, Bailey, L.J., Fersht, AR, Wong, TS, T. S. Wong, Reyes, A, M. Di Re, Holt, IJ, J. He, He, J., Goffart, S., A. Reyes, Boyd-Kirkup, J.D., Wong, T.S., He, J, Yasukawa, T., Spelbrink, J.N.   +38 more
core   +2 more sources

USP7 promotes IgA class switching through stabilizing RUNX3 for germline transcription activation

Cell Reports
Summary: Class switch recombination (CSR) diversifies the effector functions of antibodies and involves complex regulation of transcription and DNA damage repair.
Bo Zhao, Zhigang Xia, Beibei Yang, Yao Guo, Ruizhi Zhou, Mingyu Gu, Meiling Liu, Qingcheng Li, Wanyu Bai, Junbin Huang, Xuefei Zhang, Chengming Zhu, Kam Tong Leung, Chun Chen, Junchao Dong   +14 more
doaj   +1 more source

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

, 2018
Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs
Stephan Gruber, Paolo De Los Rios, Alessandro Barducci, John F. Marko   +3 more
core   +1 more source