Temporally correlated active forces drive chromosome structure and dynamics

Autor: Sumitabha Brahmachari, Tomer Markovich, Fred C. MacKintosh, José N. Onuchic

Understanding the mechanisms governing the structure and dynamics of flexible polymers like chromosomes, especially, the signatures of motor-driven active processes is of great interest in genome biology. We study chromosomes as a coarse-grained poly

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1d44a36d92eb67487a0f4e3c6dc913fa
https://doi.org/10.1101/2023.04.23.528410

DNA supercoiling-mediated collective behavior of co-transcribing RNA polymerases

Autor: Shubham Tripathi, Sumitabha Brahmachari, José N Onuchic, Herbert Levine

Publikováno v: Nucleic Acids Research. 50:1269-1279

Multiple RNA polymerases (RNAPs) transcribing a gene have been known to exhibit collective group behavior, causing the transcription elongation rate to increase with the rate of transcription initiation. Such behavior has long been believed to be dri

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::da15760cd8d9a220216eb86717a0e849
https://doi.org/10.1093/nar/gkab1252

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Autor: Judy St. Leger, Bram van den Broek, Ahmed M.O. Elbatsh, Leonid L. Moroz, Evin Hildebrandt, Namita Mitra, Parwinder Kaur, Roger D. Kornberg, Federica Di Palma, Nils Stein, Weijie Yao, Theresa L.U. Burnham, Christopher J. Knight, Suhas S.P. Rao, Kazuhiro Maeshima, Asha S. Multani, Veronica F. Hinman, Aditya N. Mhaskar, José N. Onuchic, David Weisz, Sen Pathak, René H. Medema, Kevin A. Hovel, Arina D. Omer, Alexandria Mena, Andrea B. Kohn, Andrew J. Beel, Liesl Nel-Themaat, Benjamin D. Rowland, José Luis Gómez-Skarmeta, Bas van Steensel, Maria Cristina Gambetta, Claire Hoencamp, Christopher Lui, Roy G.H.P. van Heesbeen, Emma K. Farley, Olga Dudchenko, Michele Di Pierro, Neil D. Young, Meng C. Wang, Kerstin Lindblad-Toh, Pierre Jean Mattei, Tom van Schaik, Melanie Pham, Ruqayya Khan, Fabian Lim, Wesley C. Warren, Vinícius G. Contessoto, Richard R. Behringer, Hans H. Cheng, Alexander Haddad, Gregory A. Cary, Daniel Chauss, Zane Colaric, Hans Teunissen, Ayse Sena Mutlu, Zhenzhen Yang, Ángela Sedeño Cacciatore, Elzo de Wit, Sumitabha Brahmachari, Erez Lieberman Aiden, Karen Holcroft, Jonne A. Raaijmakers, Brian Glenn St Hilaire

Publikováno v: Science
Science (New York, N.Y.), vol 372, iss 6545
Digital.CSIC. Repositorio Institucional del CSIC
instname
Scopus
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP

We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional(3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedlyduring eukaryotic evolution. The type of genome arc

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7def7f95c1bea4f8af665cc0bb48a7cb

Measurement of the torque in braided DNAs using a thermodynamic Maxwell relation

Autor: John F. Marko, Yang Liu, Sumitabha Brahmachari, Ke Ding, Botao Xiao

Braided DNAs are significant structural intermediates in cellular processes, yet little has been experimentally demonstrated about their higher-order structure and twisting torques. We use magnetic tweezers to measure braid extensions at forces rangi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6312acbec8b89c215d7a709adb3c41c7
https://doi.org/10.1101/2020.02.07.938209

Chromosome disentanglement driven via optimal compaction of loop-extruded brush structures

Autor: John F. Marko, Sumitabha Brahmachari

Publikováno v: Proc Natl Acad Sci U S A

Eukaryote cell division features cyclical manipulation of the compaction state of chromosomes that is synchronized with their physical and topological segregation. It has been proposed that lengthwise compaction of chromatin into mitotic chromosomes

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fdafd8ce479e784eeeabd216f50e7cbb