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The condensed chromatin fiber: an allosteric chemo-mechanical machine for signal transduction and genome processing

Annick Lesne, Christophe Bécavin, Jean–Marc Victor
2012 Physical Biology  
The structural, mechanical and topological features of the chromatin fiber endow chromosomes with a tunable signal transduction from specific (or non specific) effectors to specific (or non specific) active  ...  We revisit here allostery in the context of chromatin and argue that allosteric principles underlie and explain the functional architecture required for space-time coordination of gene expression at all  ...  Acknowledgments Christophe Bécavin ackowledges the Institut des HautesÉtudes Scientifiques (IHÉS), Génopole, the Centre National de la Recherche Scientifique (CNRS) and the Agence Nationale pour la Recherche  ... 
doi:10.1088/1478-3975/9/1/013001 pmid:22314931 fatcat:h4jf6qobezb2jmjpcyysozlpae

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

Boryana Doyle, Geoffrey Fudenberg, Maxim Imakaev, Leonid A. Mirny, Marc A. Marti-Renom
2014 PLoS Computational Biology  
Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator.  ...  Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact  ...  Author Contributions Conceived and designed the experiments: BD MI GF LAM. Performed the experiments: BD. Analyzed the data: BD. Contributed reagents/materials/ analysis tools: BD MI GF LAM.  ... 
doi:10.1371/journal.pcbi.1003867 pmid:25340767 pmcid:PMC4207457 fatcat:lguii6kdwvd25pkuhlpsnkt464

How Xenopus Embryos Complete DNA Replication Reliably: Solution to the Random-completion Problem

Scott Cheng-Hsin Yang, John Bechhoefer
2009 Biophysical Journal  
demonstrates that a wide range of biological phenomena can be explained by interactions between TFs and chromatin, and provides a quantitative description of the following processes: cooperative binding  ...  These loop elongation mutants fold properly as determined by far-UV circular dichroism spectroscopy, suggesting that loop 2 is well tolerant of loop insertions without affecting GB1's native structure.  ... 
doi:10.1016/j.bpj.2008.12.3719 fatcat:rkgtt3fufrhtxn6m23l3qgasru

Chromatin fiber functional organization: Some plausible models

A. Lesne, J. -M. Victor
2006 The European Physical Journal E : Soft matter  
We conclude that a major role of the chromatin fiber structure might be to endow DNA with allosteric potentialities and to control DNA transactions by an epigenetic tuning of its mechanical and topological  ...  We here present a modeling study of the chromatin fiber functional organization. Multi-scale modeling is required to unravel the complex interplay between the fiber and the DNA levels.  ...  We warmly acknowledge Arndt Benecke for sharing with us his views and results before publication.  ... 
doi:10.1140/epje/i2005-10050-6 pmid:16501875 fatcat:f52hraenvnayrb6mvsudtdcwfi

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions [article]

Boryana Doyle, Geoffrey Fudenberg, Maxim Imakaev, Leonid Mirny
2014 bioRxiv   pre-print
Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator.  ...  Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact  ...  Thus, for generality, we model chromatin as a long homogeneous flexible fiber with only a few additional looping interactions between specific elements, as described below.  ... 
doi:10.1101/003087 fatcat:h53slp2mgrf4xgsebiuf7wurre

PARP Goes Transcription

W.Lee Kraus, John T Lis
2003 Cell  
In the absence of Cornell University Ithaca, New York 14853 DNA damage, the length of the polymer is considerably shorter, ranging from single residues to oligo(ADP-) units.  ...  The structural motifs and functional domains that are critical for PARP-1's role in chromatin ranging from archaebacteria to mammals, although it is apparently absent in yeast (Hassa and Hottiger, 2002  ...  mode of allosteric regulation of Regulation of Chromatin Structure and Transcription by PARP-1 PARP-1 enzymatic activity.  ... 
doi:10.1016/s0092-8674(03)00433-1 pmid:12809599 fatcat:hizvx3kupfadjenwtogav57jk4

Regulation of Poly(ADP-ribose) Polymerase-1 by DNA Structure-specific Binding

Irina Lonskaya, Vladimir N. Potaman, Luda S. Shlyakhtenko, Elena A. Oussatcheva, Yuri L. Lyubchenko, Viatcheslav A. Soldatenkov
2005 Journal of Biological Chemistry  
DNA hairpins, cruciforms, and stably unpaired regions are all effective co-activators of PARP-1 auto-modification and poly(ADP-ribosyl)ation of histone H1 in the absence of free DNA ends.  ...  PARP-1 interactions with non-B DNA structures are functional and lead to its catalytic activation.  ...  Sinden, and S. Fuchs for valuable discussions and critical suggestions and V. Forrester for manuscript proofreading.  ... 
doi:10.1074/jbc.m413483200 pmid:15737996 fatcat:xb2rnc5vcfhnnebalkuwe7b5iu

Radioisotope [chapter]

Jan W. Gooch
2011 Encyclopedic Dictionary of Polymers  
The number of monomers in a polymer may range up to millions. (2) A long chain of repeating subunits.  ...  Allosteric With respect to enzymes, an effect that is produced on the activity of one part of an enzyme (such as an active site) by the binding of an effector to a different part of the enzyme.  ...  Noncompetitive Inhibitor A molecule that attaches to an enzyme at an allosteric site (a site other than the active site), distorting the shape of the active site so that the enzyme can no longer function  ... 
doi:10.1007/978-1-4419-6247-8_14640 fatcat:kebxan2fczapph46wnsudadjc4

Coronavirus [chapter]

Jan W. Gooch
2011 Encyclopedic Dictionary of Polymers  
The number of monomers in a polymer may range up to millions. (2) A long chain of repeating subunits.  ...  Allosteric With respect to enzymes, an effect that is produced on the activity of one part of an enzyme (such as an active site) by the binding of an effector to a different part of the enzyme.  ...  Noncompetitive Inhibitor A molecule that attaches to an enzyme at an allosteric site (a site other than the active site), distorting the shape of the active site so that the enzyme can no longer function  ... 
doi:10.1007/978-1-4419-6247-8_13476 fatcat:btluws7qzvahvjm4g3abak2zh4

Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications

Pavel Semenyuk, Vladimir Muronetz
2019 International Journal of Molecular Sciences  
Firstly, there are many naturally occurred charged polymers such as DNA and RNA, polyphosphates, sulfated glycosaminoglycans, etc., as well as pronouncedly charged proteins such as histones or actin.  ...  Finally, protein behavior can be altered due to post-translational modifications such as phosphorylation, sulfation, and glycation, which change a local charge of the protein region.  ...  Electrostatic interactions are important for the interaction of DNA with histones and chromatin condensation [10] , interactions of ribosomal proteins with ribosomal RNA [11] , as well as for the formation  ... 
doi:10.3390/ijms20051252 fatcat:umxqy27wyrfnrouhcfxayx6huq

Chromatin dynamics controls epigenetic domain formation [article]

Marina Katava, Guang Shi, Dave Thirumalai
2021 bioRxiv   pre-print
Surprisingly, we predict that the bounded domains arise without the need for any boundary elements as long as the spreading is slow.  ...  In the opposite limit, finite-sized modified domains emerge, with the chromatin remaining in an expanded state, by a positive feedback mechanism involving contacts between nucleosomes through a looping  ...  Acknowledgements: We are thankful to Bassem Al-Sady and Ilya Finkelstein for advice and useful discussions.  ... 
doi:10.1101/2021.01.18.427115 fatcat:4kn2klrngfepvmnmuc5zqkljvu

Theory and Simulations of condensin mediated loop extrusion in DNA [article]

Ryota Takaki, Atreya Dey, Guang Shi, Dave Thirumalai
2021 arXiv   pre-print
ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops.  ...  as a function of external load.  ...  Author contributions statement R.T and D.T. conceived the theory, R.T., A.D., G.S., and D.T performed the calculations and simulations, the experiment(s), R.T., A.D., FG. S., and D.  ... 
arXiv:2006.00129v4 fatcat:3rypkihgcvbyhfldy63rdc4qmy

Capturing the essence of folding and functions of biomolecules using coarse-grained models

Changbong Hyeon, D. Thirumalai
2011 Nature Communications  
Theoretical ideas, in particular, concepts from polymer physics, have guided the development of coarse-grained models to study folding of DNA, RNA, and proteins.  ...  The distances over which biological molecules and their complexes can function range from a few nanometres, in the case of folded structures, to millimetres, for example during chromosome organization.  ...  A number of models, such as the random walk model, and models that connect mega-based size domains by chromatin loops have been used to describe higher structures of chromatin.  ... 
doi:10.1038/ncomms1481 pmid:21952221 fatcat:tqrb4bwtm5ac7h7r4kwpxjuebq

Biology and physics of heterochromatin-like domains/complexes [article]

Prim B. Singh, Stepan N. Belyakin, Petr P. Laktionov
2020 bioRxiv   pre-print
Instead, a more dynamic structure, the oligo-nucleosomal 'clutch', consisting of between 2 to 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility  ...  They are present in the genomes of organisms ranging from fission yeast to man, with an expansion in size and number in mammals.  ...  Polymers are very long molecules formed from small repeating units called monomers.  ... 
doi:10.1101/2020.07.19.210518 fatcat:z2it6mibbfc57m7jnn6qixykbe

Core protein: A pleiotropic keystone in the HBV lifecycle

Adam Zlotnick, Balasubramanian Venkatakrishnan, Zhenning Tan, Eric Lewellyn, William Turner, Samson Francis
2015 Antiviral Research  
Cp is bound to nuclear viral DNA and affects its epigenetics. Cp correlates with RNA specificity.  ...  Cp can be targeted by antivirals -while self-assembly is the most accessible of Cp activities, we argue that it makes sense to engage the broader spectrum of Cp function.  ...  Uri Lopatin and Dr. Lisa Selzer for their helpful comments. AZ and BV were supported by NIH grants R56-AI077688 and R01-AI067417. The Zlotnick lab has also received support from Assembly Biosciences.  ... 
doi:10.1016/j.antiviral.2015.06.020 pmid:26129969 pmcid:PMC4537649 fatcat:hcn3u5fikvalxbhchsm5o3agnu
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