Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers

Nucleic Acids Research
He MengJohn van Noort

Abstract

Single-molecule techniques allow for picoNewton manipulation and nanometer accuracy measurements of single chromatin fibers. However, the complexity of the data, the heterogeneity of the composition of individual fibers and the relatively large fluctuations in extension of the fibers complicate a structural interpretation of such force-extension curves. Here we introduce a statistical mechanics model that quantitatively describes the extension of individual fibers in response to force on a per nucleosome basis. Four nucleosome conformations can be distinguished when pulling a chromatin fiber apart. A novel, transient conformation is introduced that coexists with single wrapped nucleosomes between 3 and 7 pN. Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT. Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway. These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays.

References

Jan 5, 2000·Proceedings of the National Academy of Sciences of the United States of America·Y Cui, C Bustamante
Jun 14, 2000·Current Opinion in Structural Biology·C BustamanteD Smith
Dec 12, 2001·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·E Ben-HaïmJ M Victor
Feb 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Brent D Brower-TolandMichelle D Wang
May 4, 2002·Annual Review of Biophysics and Biomolecular Structure·Jeffrey C Hansen
Mar 12, 2004·The European Physical Journal. E, Soft Matter·S CoccoJ Yan
Jul 13, 2004·Physical Review Letters·I M Kulić, H Schiessel
Nov 30, 2004·Science·Benedetta DorigoTimothy J Richmond
Mar 18, 2005·The Journal of Biological Chemistry·Cyril ClaudetJan Bednar
Dec 31, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Igor M KulićHelmut Schiessel
Feb 3, 2006·The European Physical Journal. E, Soft Matter·H Schiessel
Apr 18, 2006·Proceedings of the National Academy of Sciences of the United States of America·Philip J J RobinsonDaniela Rhodes
Apr 20, 2006·Nature Structural & Molecular Biology·Aurélien BancaudJean-Louis Viovy
Oct 18, 2006·Proceedings of the National Academy of Sciences of the United States of America·Shirley MihardjaCarlos Bustamante
Feb 27, 2007·Cell·Bing LiJerry L Workman
Sep 11, 2007·Biophysical Journal·Brian C CarterSteven P Gross
Sep 26, 2007·Proceedings of the National Academy of Sciences of the United States of America·Karsten RippeGernot Längst
Dec 11, 2007·Biophysical Journal·M KruithofJ van Noort
Jun 28, 2008·Proceedings of the National Academy of Sciences of the United States of America·Andrew RouthDaniela Rhodes
Mar 5, 2009·Physical Review Letters·Daniel Klaue, Ralf Seidel
Apr 7, 2009·Current Opinion in Genetics & Development·Andrew BassettAndrew Travers
Apr 21, 2009·Nature Structural & Molecular Biology·Maarten KruithofJohn van Noort
May 6, 2009·Biophysical Journal·M Kruithof, J van Noort
Aug 5, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sergei A GrigoryevTamar Schlick
Aug 25, 2009·Nature Structural & Molecular Biology·Michael G PoirierJonathan Widom
Sep 23, 2010·Biophysical Journal·Nikolay KorolevLars Nordenskiöld
Nov 5, 2010·Nucleic Acids Research·Abdollah AllahverdiLars Nordenskiöld
Dec 16, 2010·Biophysical Journal·Elena F KosloverAndrew J Spakowitz
Dec 24, 2010·Nucleic Acids Research·Vera BöhmJörg Langowski
Jan 20, 2011·Proceedings of the National Academy of Sciences of the United States of America·B SudhanshuA J Spakowitz
Feb 24, 2011·Current Opinion in Genetics & Development·Guohong Li, Danny Reinberg
Jul 20, 2011·Proceedings of the National Academy of Sciences of the United States of America·Marek SimonMichael G Poirier
Aug 4, 2011·The FEBS Journal·Andrew Flaus, Tom Owen-Hughes
Oct 4, 2011·Biophysical Journal·Rosana Collepardo-Guevara, Tamar Schlick
Apr 5, 2012·The EMBO Journal·Sarah J CorrellSergei A Grigoryev
Jun 23, 2012·Nature Reviews. Molecular Cell Biology·Karolin LugerDavid J Tremethick

❮ Previous
Next ❯

Citations

Dec 27, 2015·Analytical Biochemistry·Chenyi WuColyn Crane-Robinson
Mar 19, 2016·The Journal of Physical Chemistry. B·Lennart de BruinHelmut Schiessel
Jul 1, 2016·ACS Nano·Jenny V LeCarlos E Castro
Feb 6, 2017·Biophysical Journal·Gavin Bascom, Tamar Schlick
Mar 6, 2018·PLoS Computational Biology·Hidetoshi KonoHisashi Ishida
Nov 18, 2017·Nucleic Acids Research·Anatoly ZinchenkoLars Nordenskiöld
Sep 1, 2017·The Journal of Biological Chemistry·Artur KaczmarczykJohn van Noort
Nov 24, 2017·Cold Spring Harbor Symposia on Quantitative Biology·Ping Chen, Guohong Li
Aug 7, 2018·ELife·Ramasubramanian SundaramoorthyTom Owen-Hughes
Feb 1, 2017·Science Advances·Jonas J FunkeHendrik Dietz
Oct 31, 2018·Scientific Reports·Eugen OstrofetDavid Dulin
Jan 26, 2018·Scientific Reports·Nikolay KorolevLars Nordenskiöld
Jan 9, 2020·Nature Communications·Artur KaczmarczykNynke H Dekker
May 15, 2020·Soft Matter·Fatemeh KhodabandehFarshid Mohammad-Rafiee
Aug 12, 2020·Scientific Reports·Christian AermesClaudia Tanja Mierke
Jul 10, 2019·Physical Review Letters·Daniel A VegaMariano Febbo
Apr 25, 2019·Essays in Biochemistry·Thomas O Tolsma, Jeffrey C Hansen
Feb 20, 2019·Physical Review. E·Martijn Zuiddam, Helmut Schiessel
Apr 11, 2019·Essays in Biochemistry·Manuela Moraru, Thomas Schalch
Nov 9, 2017·Scientific Reports·D MichielettoD Marenduzzo
May 10, 2017·The Journal of Chemical Physics·Shuangshuang ZhangDadong Yan
Dec 21, 2020·Nucleic Acids Research·Bram HennemanRemus T Dame
Sep 16, 2019·Biophysical Journal·Orkide OrduNynke H Dekker
Nov 5, 2019·Current Opinion in Chemical Biology·Xiaodan ZhaoJie Yan
Feb 10, 2021·Proceedings of the National Academy of Sciences of the United States of America·Hisashi Ishida, Hidetoshi Kono
Feb 17, 2021·Nucleic Acids Research·Thomas BrouwerJohn van Noort
Apr 23, 2020·Biophysical Journal·Joshua Moller, Juan J de Pablo

❮ Previous
Next ❯

Methods Mentioned

BETA
electron microscopy
force measurements
salt dialysis
electrophoresis
optical tweezers
FRET

Software Mentioned

LabVIEW

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.