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Models of Polymer Physics for the 3D Structure of Chromosomes Nicodemi, Mario
Description
<p class=MsoNormal><span style='font-size:9.0pt;font-family:Helvetica;
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
color:black;mso-ansi-language:EN-CA'>Principled approaches from polymer physics are important to make sense of
the complexity of experimental data on chromosome 3D architecture and to
explain their underlying molecular mechanisms. I discuss first the current
picture of the spatial organisation of our DNA across genomic scales at
the single cell level, as emerging from technologies such as microscopy,
Hi-C, SPRITE or GAM [1]. Next, I discuss how different models of polymer
physics can help understanding the origin of the patterns in the data and
the underlying folding mechanisms [2,3,4]. Finally, I show that polymer
physics can be used to predict the impact of large mutations (Structural
Variants) on chromosome structure, in particular on how the network of
contacts between genes and regulators is rewired, hence enabling the
identification of their pathogenic potential [5,6].
[1] R.A. Beagrie, A. Scialdone, M. Schueler, D.C.A. Kraemer, M. Chotalia,
S.Q. Xie, M. Barbieri, I. de Santiago, L.-M. Lavitas, M.R. Branco, J.
Fraser, J. Dostie, L. Game, N. Dillon, P.A.W. Edwards, M. Nicodemi*, A.
Pombo*, Complex multi-enhancer contacts captured by Genome Architecture
Mapping (GAM), a novel ligation-free approach. Nature 543, 519 (2017).
[2] A.M. Chiariello, S. Bianco, C. Annunziatella, A. Esposito, M.
Nicodemi, Polymer physics of chromosome large-scale 3D organisation,
Scientific Reports 6, 29775 (2016).
[3] M. Barbieri, S.Q. Xie, E. Torlai Triglia, A.M. Chiariello, S. Bianco,
I. de Santiago, M.R. Branco, D. Rueda, M. Nicodemi*, A. Pombo*, Active and
poised promoter states drive folding of the extended HoxB locus in mouse
embryonic stem cells. Nature Struct. Mol. Bio, 24, 515 (2017).
[4] C.A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M.
Nicodemi*, P. R. Cook*, and D. Marenduzzo*, Nonequilibrium Chromosome
Looping via Molecular Slip Links, Phys. Rev. Lett. 108, 158103 (2017)
[5] S. Bianco, D.G. Lupiáñez, A.M. Chiariello, C. Annunziatella, K. Kraft,
R. Schöpflin, L. Wittler, G. Andrey, M. Vingron, A. Pombo, S. Mundlos*, M.
Nicodemi*, Polymer physics predicts the effects of structural variants on
chromatin architecture, Nature Genetics 50, 662 (2018).
[6] B.K. Kragesteen, M. Spielmann, C. Paliou, V. Heinrich, R. Schoepflin,
A. Esposito, C. Annunziatella, S. Bianco, A.M. Chiariello, I.
Jerkovi&#263;, I. Harabula, P. Guckelberger, M. Pechstein, L. Wittler,
W.-L. Chan, M. Franke, D.G. Lupiáñez, K. Kraft, B. Timmermann, M. Vingron,
A. Visel, M. Nicodemi*, S. Mundlos* and G. Andrey*, Dynamic 3D Chromatin
Architecture Determines Enhancer Specificity and Morphogenetic Identity in
Limb Development, Nature Genetics 50, 1463 (2018).</span><span
style='font-size:10.0pt;font-family:"Times New Roman";mso-fareast-font-family:
"Times New Roman";mso-ansi-language:EN-CA'><o:p></o:p></span></p>
Item Metadata
Title |
Models of Polymer Physics for the 3D Structure of Chromosomes
|
Creator | |
Publisher |
Banff International Research Station for Mathematical Innovation and Discovery
|
Date Issued |
2019-03-26T10:33
|
Description |
<p class=MsoNormal><span style='font-size:9.0pt;font-family:Helvetica;
mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:"Times New Roman";
color:black;mso-ansi-language:EN-CA'>Principled approaches from polymer physics are important to make sense of
the complexity of experimental data on chromosome 3D architecture and to
explain their underlying molecular mechanisms. I discuss first the current
picture of the spatial organisation of our DNA across genomic scales at
the single cell level, as emerging from technologies such as microscopy,
Hi-C, SPRITE or GAM [1]. Next, I discuss how different models of polymer
physics can help understanding the origin of the patterns in the data and
the underlying folding mechanisms [2,3,4]. Finally, I show that polymer
physics can be used to predict the impact of large mutations (Structural
Variants) on chromosome structure, in particular on how the network of
contacts between genes and regulators is rewired, hence enabling the
identification of their pathogenic potential [5,6].
[1] R.A. Beagrie, A. Scialdone, M. Schueler, D.C.A. Kraemer, M. Chotalia, S.Q. Xie, M. Barbieri, I. de Santiago, L.-M. Lavitas, M.R. Branco, J. Fraser, J. Dostie, L. Game, N. Dillon, P.A.W. Edwards, M. Nicodemi*, A. Pombo*, Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM), a novel ligation-free approach. Nature 543, 519 (2017). [2] A.M. Chiariello, S. Bianco, C. Annunziatella, A. Esposito, M. Nicodemi, Polymer physics of chromosome large-scale 3D organisation, Scientific Reports 6, 29775 (2016). [3] M. Barbieri, S.Q. Xie, E. Torlai Triglia, A.M. Chiariello, S. Bianco, I. de Santiago, M.R. Branco, D. Rueda, M. Nicodemi*, A. Pombo*, Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells. Nature Struct. Mol. Bio, 24, 515 (2017). [4] C.A. Brackley, J. Johnson, D. Michieletto, A. N. Morozov, M. Nicodemi*, P. R. Cook*, and D. Marenduzzo*, Nonequilibrium Chromosome Looping via Molecular Slip Links, Phys. Rev. Lett. 108, 158103 (2017) [5] S. Bianco, D.G. Lupiáñez, A.M. Chiariello, C. Annunziatella, K. Kraft, R. Schöpflin, L. Wittler, G. Andrey, M. Vingron, A. Pombo, S. Mundlos*, M. Nicodemi*, Polymer physics predicts the effects of structural variants on chromatin architecture, Nature Genetics 50, 662 (2018). [6] B.K. Kragesteen, M. Spielmann, C. Paliou, V. Heinrich, R. Schoepflin, A. Esposito, C. Annunziatella, S. Bianco, A.M. Chiariello, I. Jerkovi&#263;, I. Harabula, P. Guckelberger, M. Pechstein, L. Wittler, W.-L. Chan, M. Franke, D.G. Lupiáñez, K. Kraft, B. Timmermann, M. Vingron, A. Visel, M. Nicodemi*, S. Mundlos* and G. Andrey*, Dynamic 3D Chromatin Architecture Determines Enhancer Specificity and Morphogenetic Identity in Limb Development, Nature Genetics 50, 1463 (2018).</span><span style='font-size:10.0pt;font-family:"Times New Roman";mso-fareast-font-family: "Times New Roman";mso-ansi-language:EN-CA'><o:p></o:p></span></p> |
Extent |
31.0 minutes
|
Subject | |
Type | |
File Format |
video/mp4
|
Language |
eng
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Notes |
Author affiliation: Universita' di Napoli
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Series | |
Date Available |
2019-09-23
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Provider |
Vancouver : University of British Columbia Library
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Rights |
Attribution-NonCommercial-NoDerivatives 4.0 International
|
DOI |
10.14288/1.0380938
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URI | |
Affiliation | |
Peer Review Status |
Unreviewed
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Scholarly Level |
Faculty
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Rights URI | |
Aggregated Source Repository |
DSpace
|
Item Media
Item Citations and Data
Rights
Attribution-NonCommercial-NoDerivatives 4.0 International