Quantifying Chromosome Structural Reorganizations During Differentiation, Reprogramming, and Transdifferentiation

被引：9
作者：
Chu, Xiakun [1 ,3 ]
Wang, Jin [2 ,3 ]
机构：
[1] Hong Kong Univ Sci & Technol Guangzhou, Adv Mat Thrust, Guangzhou 511400, Guangdong, Peoples R China
[2] Univ Chinese Acad Sci, Ctr Theoret Interdisciplinary Sci, Wenzhou Inst, Wenzhou 325001, Zhejiang, Peoples R China
[3] SUNY Stony Brook, Dept Chem & Phys, Stony Brook, NY 11794 USA
来源：
PHYSICAL REVIEW LETTERS | 2022年 / 129卷 / 06期
关键词：
PLURIPOTENT STEM-CELLS; CHROMATIN-STRUCTURE; PHASE-SEPARATION; TOPOISOMERASE-II; REVEALS; GENOME; ORGANIZATION; LANDSCAPE; PRINCIPLES; TOPOLOGY;
D O I：
10.1103/PhysRevLett.129.068102
中图分类号：
O4 [物理学];
学科分类号：
0702 ;
摘要：
We developed a nonequilibrium model to study chromosome structural reorganizations within a simplified cell developmental system. From the chromosome structural perspective, we predicted that the neural progenitor cell is on the neural developmental path and very close to the transdifferentiation path from the fibroblast to the neuron cell. We identified an early bifurcation of stem cell differentiation processes and the cell-of-origin-specific reprogramming pathways. Our theoretical results are in good agreement with available experimental evidence, promoting future applications of our approach.
引用
收藏
页数：7
相关论文
共 93 条
[1]   A chromosome folding intermediate at the condensin-to-cohesin transition during telophase [J].
Abramo, Kristin ;
Valton, Anne-Laure ;
Venev, Sergey V. ;
Ozadam, Hakan ;
Fox, A. Nicole ;
Dekker, Job .
NATURE CELL BIOLOGY, 2019, 21 (11) :1393-+
[2]   Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming [J].
Ashwin, S. S. ;
Sasai, Masaki .
SCIENTIFIC REPORTS, 2015, 5
[3]   Cell Reprogramming: The Many Roads to Success [J].
Aydin, Begum ;
Mazzoni, Esteban O. .
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 35, 2019, 35 :433-452
[4]   Polymer physics predicts the effects of structural variants on chromatin architecture [J].
Bianco, Simona ;
Lupianez, Dario G. ;
Chiariello, Andrea M. ;
Annunziatella, Carlo ;
Kraft, Katerina ;
Schoepflin, Robert ;
Wittler, Lars ;
Andrey, Guillaume ;
Vingron, Martin ;
Pombo, Ana ;
Mundlos, Stefan ;
Nicodemi, Mario .
NATURE GENETICS, 2018, 50 (05) :662-+
[5]   Concise Review: Induced Pluripotent Stem Cells Versus Embryonic Stem Cells: Close Enough or Yet Too Far Apart? [J].
Bilic, Josipa ;
Izpisua Belmonte, Juan Carlos .
STEM CELLS, 2012, 30 (01) :33-41
[6]   Mechanistic modeling of chromatin folding to understand function [J].
Brackey, Chris A. ;
Marenduzzo, Davide ;
Gilbert, Nick .
NATURE METHODS, 2020, 17 (08) :767-775
[7]   Mouse embryonic stem cells can differentiate via multiple paths to the same state [J].
Briggs, James Alexander ;
Li, Victor C. ;
Lee, Seungkyu ;
Woolf, Clifford J. ;
Klein, Allon ;
Krischner, Marc W. .
ELIFE, 2017, 6
[8]   Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency [J].
Cacchiarelli, Davide ;
Trapnell, Cole ;
Ziller, Michael J. ;
Soumillon, Magali ;
Cesana, Marcella ;
Karnik, Rahul ;
Donaghey, Julie ;
Smith, Zachary D. ;
Ratanasirintrawoot, Sutheera ;
Zhang, Xiaolan ;
Sui, Shannan J. Ho ;
Wu, Zhaoting ;
Akopian, Veronika ;
Gifford, Casey A. ;
Doench, John ;
Rinn, John L. ;
Daley, George Q. ;
Meissner, Alexander ;
Lander, Eric S. ;
Mikkelsen, Tarjei S. .
CELL, 2015, 162 (02) :412-424
[9]   Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments [J].
Cesari, Andrea ;
Reisser, Sabine ;
Bussi, Giovanni .
COMPUTATION, 2018, 6 (01)
[10]   Pre-mitotic genome re-organisation bookends the B cell differentiation process [J].
Chan, Wing Fuk ;
Coughlan, Hannah D. ;
Zhou, Jie H. S. ;
Keenan, Christine R. ;
Bediaga, Naiara G. ;
Hodgkin, Philip D. ;
Smyth, Gordon K. ;
Johanson, Timothy M. ;
Allan, Rhys S. .
NATURE COMMUNICATIONS, 2021, 12 (01)
12345678910