Genomic Energy Landscapes.
Energy landscape theory, developed in the context of protein folding, provides, to our knowledge, a new perspective on chromosome architecture. We review what has been learned concerning the topology and structure of both the interphase and mitotic chromosomes from effective energy landscapes constructed using Hi-C data. Energy landscape thinking raises new questions about the nonequilibrium dynamics of the chromosome and gene regulation.
Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas.
Bin
B
Zhang
Department of Chemistry and Center for Theoretical Biological Physics, Rice University, Houston, Texas; Department of Physics and Astronomy, Rice University, Houston, Texas. Electronic address: pwolynes@rice.edu.
Peter G
PG
Wolynes
D020090:Chromosome Segregation; D002875:Chromosomes / Q000235:genetics* / Q000378:metabolism; D023281:Genomics; D006801:Humans; D050866:Liquid Crystals; D013816:Thermodynamics
PLoS Comput Biol. 2015 Aug 11;11(8):e1004443
26262925
Nat Rev Genet. 2005 Jun;6(6):451-64
15883588
Curr Opin Cell Biol. 2014 Feb;26:69-78
24529248
Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16173-8
22988072
Proc Natl Acad Sci U S A. 1992 Jun 1;89(11):4918-22
1594594
Biochimie. 2015 Dec;119:218-30
25530262
Nat Methods. 2008 Jul;5(7):621-8
18516045
Science. 2013 Nov 22;342(6161):948-53
24200812
PLoS Comput Biol. 2008 Aug 22;4(8):e1000153
18725929
HFSP J. 2008 Dec;2(6):307-13
19436496
Chromosome Res. 2011 Jan;19(1):37-51
21274616
Nucleic Acids Res. 2016 Jul 8;44(12):5540-9
27257057
Isr J Chem. 2014 Aug;54(8-9):1311-1337
25308991
Science. 2009 Oct 9;326(5950):289-93
19815776
Cell. 2014 Dec 18;159(7):1665-80
25497547
Chromosome Res. 2008;16(3):469-97
18461485
Sci Rep. 2015 Nov 19;5:16746
26581803
Nat Rev Genet. 2014 Apr;15(4):234-46
24614316
Nucleic Acids Res. 2014 Sep;42(15):9553-61
25092923
Phys Rev Lett. 1985 Nov 25;55(22):2425-2428
10032141
Proc Natl Acad Sci U S A. 1997 Jun 10;94(12):6170-5
9177189
Biophys J. 2016 Mar 29;110(6):1234-45
27028634
Cell Rep. 2016 May 31;15(9):2038-49
27210764
Cell. 1993 Apr 9;73(1):97-108
8384932
Nucleic Acids Res. 2014 Jul;42(13):8223-30
24990374
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65
26499245
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1996 Dec;54(6):6618-6622
9965887
FEBS Lett. 2015 Oct 7;589(20 Pt A):2931-43
26028501
Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10185-90
24946805
J Chem Phys. 2012 Apr 14;136(14):145102
22502548
Proteins. 1995 Mar;21(3):167-95
7784423
Sci Rep. 2015 Nov 25;5:17038
26602160
J Biol Chem. 2012 Feb 17;287(8):5183-91
22157002
Nat Genet. 2006 Sep;38(9):1005-14
16878134
Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):14930-5
23980160
J Am Chem Soc. 2016 Jul 6;138(26):8126-33
27300314
Q Rev Biophys. 2005 Aug;38(3):245-88
16780604
Cold Spring Harb Perspect Biol. 2010 Mar;2(3):a003889
20300217
Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12168-12173
27688758
Cell. 2013 Jun 6;153(6):1281-95
23706625
Genes Dev. 2014 Oct 1;28(19):2151-62
25274727
Phys Rev Lett. 2014 Oct 17;113(16):168101
25361282
Nature. 2012 Apr 11;485(7398):381-5
22495304
J Chem Phys. 2011 Aug 7;135(5):051101
21823683
Proc Natl Acad Sci U S A. 2009 Feb 10;106(6):1796-801
19181849
Phys Rev Lett. 2016 Jun 17;116(24):248101
27367409
J Cell Biol. 2004 Sep 13;166(6):775-85
15353545
Cell. 2014 May 8;157(4):950-63
24813616
Nature. 1953 May 30;171(4361):964-7
13063483
J Phys Chem B. 2016 Aug 25;120(33):8642-53
27218881
Proc Natl Acad Sci U S A. 2011 Sep 13;108(37):15184-9
21876141
J Phys Condens Matter. 2015 Feb 18;27(6):064112
25564155
Proc Natl Acad Sci U S A. 2015 May 12;112(19):6062-7
25918364
Nat Struct Mol Biol. 2013 Mar;20(3):387-95
23416946
Biophys J. 2016 May 24;110(10):2162-8
27224481
Science. 2008 Oct 17;322(5900):442-6
18927393
Proc Natl Acad Sci U S A. 2003 Mar 4;100(5):2374-9
12606710
Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8061-6
24847063
Nature. 2013 Oct 3;502(7469):59-64
24067610
Nature. 2012 Apr 11;485(7398):376-80
22495300
Science. 2016 Feb 12;351(6274):720-4
26912859
Cell. 1988 Dec 23;55(6):937-44
2849511
J Am Chem Soc. 2009 Oct 21;131(41):15005-13
19778017
Biophys J. 2002 Jun;82(6):2847-59
12023209
Science. 2002 Feb 15;295(5558):1306-11
11847345
Cell. 2015 Dec 17;163(7):1611-27
26686651
Cell. 2010 Oct 15;143(2):212-24
20888037
Nucleic Acids Res. 2014 Mar;42(5):2848-55
24366878
Philos Trans A Math Phys Eng Sci. 2005 Feb 15;363(1827):453-64; discussion 464-7
15664893