Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM).
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
16 07 2022
16 07 2022
Historique:
received:
10
01
2022
accepted:
04
07
2022
entrez:
16
7
2022
pubmed:
17
7
2022
medline:
20
7
2022
Statut:
epublish
Résumé
Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei.
Identifiants
pubmed: 35842472
doi: 10.1038/s41598-022-16028-2
pii: 10.1038/s41598-022-16028-2
pmc: PMC9288481
doi:
Substances chimiques
Chromatin
0
DNA
9007-49-2
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
12198Subventions
Organisme : NCI NIH HHS
ID : U54 CA261694
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA225002
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA268084
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008152
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA228272
Pays : United States
Commentaires et corrections
Type : ErratumIn
Informations de copyright
© 2022. The Author(s).
Références
EMBO Rep. 2012 Nov 6;13(11):992-6
pubmed: 22986547
Genome Res. 2016 Jan;26(1):70-84
pubmed: 26518482
Nucleus. 2017 Nov 2;8(6):625-640
pubmed: 28960120
Science. 2018 Aug 31;361(6405):924-928
pubmed: 30166492
J Cell Biol. 1994 Oct;127(2):287-302
pubmed: 7929576
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
J Mol Biol. 2002 Jun 21;319(5):1097-113
pubmed: 12079350
J Cell Biol. 2018 Jun 4;217(6):1973-1984
pubmed: 29572382
Cell. 1999 Aug 6;98(3):285-94
pubmed: 10458604
J Struct Biol. 1996 Jan-Feb;116(1):71-6
pubmed: 8742726
Sci Adv. 2020 Jan 08;6(2):eaax6232
pubmed: 31934628
Chromosome Res. 2011 Jan;19(1):37-51
pubmed: 21274616
Curr Opin Cell Biol. 1999 Jun;11(3):307-11
pubmed: 10395564
Mol Cell. 2017 Jul 20;67(2):282-293.e7
pubmed: 28712725
J Struct Biol. 2015 Feb;189(2):135-46
pubmed: 25433274
J Colloid Interface Sci. 1998 Aug 15;204(2):357-62
pubmed: 9698415
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Science. 2017 Jul 28;357(6349):
pubmed: 28751582
Bioessays. 2020 Feb;42(2):e1900132
pubmed: 31994771
Biochem Soc Trans. 2018 Feb 19;46(1):67-76
pubmed: 29263138
Proc Natl Acad Sci U S A. 1976 Jun;73(6):1897-901
pubmed: 1064861
J Synchrotron Radiat. 2014 Sep;21(Pt 5):1188-93
pubmed: 25178011
Nat Rev Mol Cell Biol. 2003 Oct;4(10):809-14
pubmed: 14570061
Sci Adv. 2020 Sep 23;6(39):
pubmed: 32967822
Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65
pubmed: 26499245
Science. 2016 Aug 5;353(6299):598-602
pubmed: 27445307
Biophys J. 2014 Apr 15;106(8):1801-10
pubmed: 24739179
Curr Opin Genet Dev. 2011 Apr;21(2):175-86
pubmed: 21342762
Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12168-12173
pubmed: 27688758
Cell. 2013 Jun 6;153(6):1281-95
pubmed: 23706625
J Cell Biol. 1987 Jul;105(1):77-92
pubmed: 3112167
Trends Genet. 2016 Apr;32(4):225-237
pubmed: 26862051
Cold Spring Harb Perspect Biol. 2010 Aug;2(8):a000794
pubmed: 20591991
Nucleic Acids Res. 2013 Jan 7;41(1):63-75
pubmed: 23143266
Mol Biol Cell. 2021 Mar 15;32(6):470-474
pubmed: 33476183
Sci Adv. 2018 Feb 28;4(2):eaar8082
pubmed: 29503869
Sci Adv. 2020 Jan 10;6(2):eaay4055
pubmed: 31950084
Curr Opin Genet Dev. 2016 Apr;37:36-45
pubmed: 26826680
Annu Rev Genomics Hum Genet. 2013;14:67-84
pubmed: 23875797
Curr Opin Cell Biol. 2019 Jun;58:95-104
pubmed: 30908980
Curr Opin Cell Biol. 2010 Jun;22(3):291-7
pubmed: 20346642
Nucleus. 2012 Sep-Oct;3(5):404-10
pubmed: 22825571
Epigenetics. 2014 May;9(5):653-7
pubmed: 24561903
Science. 2018 Oct 26;362(6413):
pubmed: 30361340
Annu Rev Biophys Biomol Struct. 1993;22:27-65
pubmed: 7688609
Proc Natl Acad Sci U S A. 2018 Jul 17;115(29):E6697-E6706
pubmed: 29967174
Sci Rep. 2017 Jan 24;7:41061
pubmed: 28117353
Biophys J. 2020 Mar 24;118(6):1479-1488
pubmed: 32097622
Proc Natl Acad Sci U S A. 2008 Dec 16;105(50):19732-7
pubmed: 19064912
Cell. 2012 Nov 9;151(4):724-737
pubmed: 23141535
Nature. 2012 Apr 11;485(7398):376-80
pubmed: 22495300
PLoS Genet. 2018 Dec 26;14(12):e1007872
pubmed: 30586358
Front Genet. 2013 Dec 04;4:274
pubmed: 24363663
Sci Adv. 2021 Jan 1;7(1):
pubmed: 33523864
Nat Biomed Eng. 2017 Nov;1(11):902-913
pubmed: 29450107
Annu Rev Biophys. 2019 May 6;48:231-253
pubmed: 30835504
J Cell Biochem. 2005 Jan 1;94(1):126-38
pubmed: 15523671
Cell. 2015 Mar 12;160(6):1145-58
pubmed: 25768910
Cell. 2015 Jul 2;162(1):108-19
pubmed: 26119342
BMC Cell Biol. 2009 Dec 16;10:88
pubmed: 20015367
Curr Opin Cell Biol. 2020 Jun;64:77-89
pubmed: 32283330
Cell. 2012 Feb 3;148(3):458-72
pubmed: 22265598
J Struct Biol. 1997 Dec;120(3):343-52
pubmed: 9441937
Epigenetics Chromatin. 2017 Aug 7;10(1):39
pubmed: 28784182