Journal ArticleDOI
A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms
Nazar Mashtalir,Nazar Mashtalir,Hiroshi Suzuki,Daniel P. Farrell,Akshay Sankar,Akshay Sankar,Jie Luo,Martin Filipovski,Martin Filipovski,Andrew R. D’Avino,Andrew R. D’Avino,Roodolph St. Pierre,Roodolph St. Pierre,Alfredo M. Valencia,Alfredo M. Valencia,Takashi Onikubo,Robert G. Roeder,Yan Han,Yuan He,Jeffrey A. Ranish,Frank DiMaio,Thomas Walz,Cigall Kadoch,Cigall Kadoch +23 more
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TLDR
A structural model of the endogenously purified human canonical BAF complex bound to the nucleosome, generated using cryoelectron microscopy, cross-linking mass spectrometry, and homology modeling provides important biophysical foundations for understanding the mechanisms of BAFcomplex function in normal and disease states.About:
This article is published in Cell.The article was published on 2020-10-29. It has received 79 citations till now. The article focuses on the topics: Chromatin remodeling & ATP-dependent chromatin remodeling.read more
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The trRosetta server for fast and accurate protein structure prediction
Zongyang Du,Hong Su,Wenkai Wang,Lisha Ye,Hong Wei,Zhenling Peng,Ivan Anishchenko,David Baker,Jianyi Yang +8 more
TL;DR: The trRosetta (transform-restrained Rosetta) server as discussed by the authors is a web-based platform for fast and accurate protein structure prediction, powered by deep learning and Rosetta.
Journal ArticleDOI
Acute BAF perturbation causes immediate changes in chromatin accessibility
Sandra Schick,Sarah Grosche,Katharina Eva Kohl,Danica Drpic,Martin G. Jaeger,Nara C. Marella,Hana Imrichova,Jung-Ming G. Lin,Gerald Hofstätter,Michael Schuster,André F. Rendeiro,Anna Koren,Mark Petronczki,Christoph Bock,Christoph Bock,André C. Müller,Georg E. Winter,Stefan Kubicek +17 more
TL;DR: In this article, the authors used the dTAG system to induce acute degradation of BAF subunits and showed that chromatin alterations are established faster than the duration of one cell cycle using a pharmacological inhibitor and a chemical degrader of the BAF complex ATPase subunits.
Journal ArticleDOI
Cross-Linking Mass Spectrometry for Investigating Protein Conformations and Protein-Protein Interactions─A Method for All Seasons.
TL;DR: In this paper, the contributions of chemical cross-linking combined with mass spectrometry (XL-MS) for studying three-dimensional structures of proteins and for investigating protein-protein interactions are outlined.
Journal ArticleDOI
Chromatin landscape signals differentially dictate the activities of mSWI/SNF family complexes.
Nazar Mashtalir,Nazar Mashtalir,Hai T. Dao,Akshay Sankar,Akshay Sankar,Hengyuan Liu,Aaron J. Corin,Aaron J. Corin,John D. Bagert,Eva J. Ge,Andrew R. D’Avino,Andrew R. D’Avino,Martin Filipovski,Martin Filipovski,Brittany C. Michel,Brittany C. Michel,Geoffrey P. Dann,Tom W. Muir,Cigall Kadoch,Cigall Kadoch +19 more
TL;DR: In this paper, the histone modification-, variant-, and mutation-specific effects, alone and in combination, on mSWI/SNF activities and chromatin interactions are defined.
Journal ArticleDOI
Exploiting vulnerabilities of SWI/SNF chromatin remodelling complexes for cancer therapy.
Marek Wanior,Andreas Krämer,Andreas Krämer,Stefan Knapp,Andreas C. Joerger,Andreas C. Joerger +5 more
TL;DR: In this article, the authors reviewed the importance of SWI/SNF chromatin remodellers in gene regulation as well as mechanisms leading to assembly defects and their role in cancer development.
References
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MotionCor2: Anisotropic Correction of Beam-Induced Motion for Improved Cryo-Electron Microscopy
Shawn Q. Zheng,Eugene Palovcak,Jean Paul Armache,Kliment A. Verba,Yifan Cheng,David A. Agard +5 more
TL;DR: MotionCor2 software corrects for beam-induced sample motion, improving the resolution of cryo-EM reconstructions.
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cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
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New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov,Takanori Nakane,Björn O. Forsberg,Dari Kimanius,Wim J. H. Hagen,Erik Lindahl,Erik Lindahl,Sjors H.W. Scheres +7 more
TL;DR: CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations in the third major release of RELION.
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CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou,Nikolaus Grigorieff +1 more
TL;DR: Modifications to the CTFFIND algorithm are described which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates.
Related Papers (5)
Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes
Nazar Mashtalir,Nazar Mashtalir,Andrew R. D’Avino,Andrew R. D’Avino,Brittany C. Michel,Brittany C. Michel,Jie Luo,Joshua Pan,Joshua Pan,Jordan E. Otto,Jordan E. Otto,Hayley J. Zullow,Hayley J. Zullow,Zachary M. McKenzie,Rachel L. Kubiak,Roodolph St. Pierre,Roodolph St. Pierre,Alfredo M. Valencia,Alfredo M. Valencia,Steven J. Poynter,Steven J. Poynter,Seth H. Cassel,Seth H. Cassel,Jeffrey A. Ranish,Cigall Kadoch,Cigall Kadoch +25 more