A Polymer Physics Model to Dissect Genome Organization in Healthy and Pathological Phenotypes

2021 ◽  
pp. 307-316
Author(s):  
Mattia Conte ◽  
Luca Fiorillo ◽  
Simona Bianco ◽  
Andrea M. Chiariello ◽  
Andrea Esposito ◽  
...  
2018 ◽  
Vol 114 (3) ◽  
pp. 563a ◽  
Author(s):  
Quinn MacPherson ◽  
Sarah Sandholtz ◽  
Andrew Spakowitz

2019 ◽  
Vol 19 (2) ◽  
pp. 119-127 ◽  
Author(s):  
Surya K Ghosh ◽  
Daniel Jost

Abstract Understanding how genomes fold and organize is one of the main challenges in modern biology. Recent high-throughput techniques like Hi-C, in combination with cutting-edge polymer physics models, have provided access to precise information on 3D chromosome folding to decipher the mechanisms driving such multi-scale organization. In particular, structural maintenance of chromosome (SMC) proteins play an important role in the local structuration of chromatin, putatively via a loop extrusion process. Here, we review the different polymer physics models that investigate the role of SMCs in the formation of topologically associated domains (TADs) during interphase via the formation of dynamic loops. We describe the main physical ingredients, compare them and discuss their relevance against experimental observations.


2018 ◽  
Author(s):  
Ofer Kimchi ◽  
Tristan Cragnolini ◽  
Michael P. Brenner ◽  
Lucy J. Colwell

The accurate prediction of RNA secondary structure from primary sequence has had enormous impact on research from the past forty years. While many algorithms are available to make these predictions, the inclusion of non-nested loops, termed pseudoknots, still poses challenges. Here, we describe a new method to compute the entire free energy landscape of secondary structures of RNA resulting from a primary RNA sequence, by combining a polymer physics model for the entropy of pseudoknots with exhaustive enumeration of the set of possible structures. Our polymer physics model can address arbitrarily complex pseudoknots and has only two free loop entropy parameters that correspond to concrete physical quantities, over an order of magnitude fewer than even the sparsest state-of-the-art algorithms. Our model outperforms previously published methods in predicting pseudoknots, while performing on par with current methods in the prediction of non-pseudoknotted structures. For RNA sequences of ~ 45 nucleotides, or ~ 90 with minimal heuristics, the complet–e enumeration of possible secondary structures can be accomplished quickly despite the NP-complete nature of the problem.


2021 ◽  
Vol 120 (3) ◽  
pp. 223a
Author(s):  
Biao Wan ◽  
Xinliang Xu ◽  
Jin Yu

Author(s):  
Andrea Esposito ◽  
Simona Bianco ◽  
Luca Fiorillo ◽  
Mattia Conte ◽  
Alex Abraham ◽  
...  

The development of new experimental technologies is opening the way to a deeper investigation of the three-dimensional organization of chromosomes inside the cell nucleus. Genome architecture is linked to vital functional purposes, yet a full comprehension of the mechanisms behind DNA folding is still far from being accomplished. Theoretical approaches based on polymer physics have been employed to understand the complexity of chromatin architecture data and to unveil the basic mechanisms shaping its structure. Here, we review some recent advances in the field to discuss how Polymer Physics, combined with numerical Molecular Dynamics simulation and Machine Learning based inference, can capture important aspects of genome organization, including the description of tissue-specific structural rearrangements, the detection of novel, regulatory-linked architectural elements and the structural variability of chromatin at the single-cell level.


Author(s):  
Fumihiko Tanaka
Keyword(s):  

2014 ◽  
Vol 134 (5) ◽  
pp. 486-495 ◽  
Author(s):  
Takeshi Horiguchi ◽  
Kohei Tsukamoto ◽  
Shinji Tominaga ◽  
Tadashi Nishimura ◽  
Hideaki Fujita ◽  
...  

PIERS Online ◽  
2008 ◽  
Vol 4 (4) ◽  
pp. 425-428
Author(s):  
Pavel Fiala ◽  
Karel Bartusek ◽  
Miloslav Steinbauer

Author(s):  
A.N. Volobuev ◽  
◽  
E.S. Petrov ◽  
N.P. Romanchuk ◽  
V.F. Pyatin ◽  
...  
Keyword(s):  

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