Abstract
About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming nucleosomes. Even though the histone proteins that make up the core of nucleosomes are highly conserved in evolution, nucleosomes can be very different from each other due to posttranslational modifications of the histones. Another crucial factor in making nucleosomes unique has so far been underappreciated: the sequence of their DNA. This review provides an overview of the experimental and theoretical progress that increasingly points to the importance of the nucleosomal base pair sequence. Specifically, we discuss the role of the underlying base pair sequence in nucleosome positioning, sliding, breathing, force-induced unwrapping, dissociation and partial assembly and also how the sequence can influence higher-order structures. A new view emerges: the physical properties of nucleosomes, especially their dynamical properties, are determined to a large extent by the mechanical properties of their DNA, which in turn depends on DNA sequence.
Citations
Mar 19, 2019·Annual Review of Biophysics·Beat Fierz, Michael G Poirier
Jan 9, 2020·Nature Communications·Artur KaczmarczykNynke H Dekker
Jul 10, 2019·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Tommy StormbergYuri L Lyubchenko
Jun 25, 2016·FEBS Letters·Andrew LeungChristopher J Nelson
Dec 1, 2017·The European Physical Journal. E, Soft Matter·Jamie CulkinHelmut Schiessel
Nov 10, 2017·The Journal of Chemical Physics·J A J WondergemM Tompitak
Oct 29, 2017·Proceedings of the National Academy of Sciences of the United States of America·Joshua LequieuJuan J de Pablo
Aug 31, 2018·Nucleic Acids Research·Rajbir SinghMark R Parthun
Oct 21, 2018·Nature Protocols·Alexey K ShaytanAnna R Panchenko
Apr 8, 2019·The Journal of Chemical Physics·Michele CaraglioEnrico Carlon
Mar 28, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Slawomir KubikDavid Shore
Mar 23, 2017·Protein Science : a Publication of the Protein Society·Sergei RudnizkyAriel Kaplan
Jun 28, 2018·Nanoscale·Luciano D'Agostino
Sep 8, 2018·Physical Review Letters·Enrico SkoruppaEnrico Carlon
Jun 18, 2017·Physical Review. E·M TompitakH Schiessel
Mar 9, 2017·BMC Bioinformatics·Marco TompitakHelmut Schiessel
Nov 1, 2020·Communications Biology·Xiangyan ShiLars Nordenskiöld
Dec 18, 2020·Soft Matter·Yair Augusto Gutiérrez FosadoTakahiro Sakaue
Sep 16, 2019·Biophysical Journal·Orkide OrduNynke H Dekker
Jan 3, 2021·Journal of Molecular Biology·Deniz DoğanSeyit Kale
Feb 17, 2021·Nucleic Acids Research·Thomas BrouwerJohn van Noort
Apr 23, 2020·Biophysical Journal·Joshua Moller, Juan J de Pablo
Apr 4, 2017·Acta Biomaterialia·Jaspreet Singh, Prashant K Purohit
Jan 27, 2020·IScience·Max SchnepfUlrike Gaul
Dec 29, 2019·Biophysical Journal·Koen van DeelenLennart de Bruin
Apr 21, 2021·Nucleic Acids Research·Govardhan Reddy, D Thirumalai
May 19, 2021·Nature Communications·Stephen E FarrRosana Collepardo-Guevara
Dec 22, 2017·Journal of Chemical Theory and Computation·Ahmad ElbahnsiChristophe Oguey