Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization

Kaufmann S, Fuchs C, Gonik M, Khrameeva EE, Mironov AA, Frishman D (2015)
PLOS ONE 10(5): e0126125.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Kaufmann, Stefanie; Fuchs, ChristianeUniBi; Gonik, Mariya; Khrameeva, Ekaterina E.; Mironov, Andrey A.; Frishman, Dmitrij
Abstract / Bemerkung
The recent advent of conformation capture techniques has provided unprecedented insights into the spatial organization of chromatin. We present a large-scale investigation of the inter-chromosomal segment and gene contact networks in embryonic stem cells of two mammalian organisms: humans and mice. Both interaction networks are characterized by a high degree of clustering of genome regions and the existence of hubs. Both genomes exhibit similar structural characteristics such as increased flexibility of certain Y chromosome regions and co-localization of centromere-proximal regions. Spatial proximity is correlated with the functional similarity of genes in both species. We also found a significant association between spatial proximity and the co-expression of genes in the human genome. The structural properties of chromatin are also species specific, including the presence of two highly interactive regions in mouse chromatin and an increased contact density on short, gene-rich human chromosomes, thereby indicating their central nuclear position. Trans-interacting segments are enriched in active marks in human and had no distinct feature profile in mouse. Thus, in contrast to interactions within individual chromosomes, the inter-chromosomal interactions in human and mouse embryonic stem cells do not appear to be conserved.
Erscheinungsjahr
2015
Zeitschriftentitel
PLOS ONE
Band
10
Ausgabe
5
Art.-Nr.
e0126125
ISSN
1932-6203
eISSN
1932-6203
Page URI
https://pub.uni-bielefeld.de/record/2934021

Zitieren

Kaufmann S, Fuchs C, Gonik M, Khrameeva EE, Mironov AA, Frishman D. Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization. PLOS ONE. 2015;10(5): e0126125.
Kaufmann, S., Fuchs, C., Gonik, M., Khrameeva, E. E., Mironov, A. A., & Frishman, D. (2015). Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization. PLOS ONE, 10(5), e0126125. doi:10.1371/journal.pone.0126125
Kaufmann, S., Fuchs, C., Gonik, M., Khrameeva, E. E., Mironov, A. A., and Frishman, D. (2015). Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization. PLOS ONE 10:e0126125.
Kaufmann, S., et al., 2015. Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization. PLOS ONE, 10(5): e0126125.
S. Kaufmann, et al., “Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization”, PLOS ONE, vol. 10, 2015, : e0126125.
Kaufmann, S., Fuchs, C., Gonik, M., Khrameeva, E.E., Mironov, A.A., Frishman, D.: Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization. PLOS ONE. 10, : e0126125 (2015).
Kaufmann, Stefanie, Fuchs, Christiane, Gonik, Mariya, Khrameeva, Ekaterina E., Mironov, Andrey A., and Frishman, Dmitrij. “Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization”. PLOS ONE 10.5 (2015): e0126125.

7 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Nuclear organization mediates cancer-compromised genetic and epigenetic control.
Zaidi SK, Fritz AJ, Tracy KM, Gordon JA, Tye CE, Boyd J, Van Wijnen AJ, Nickerson JA, Imbalzano AN, Lian JB, Stein JL, Stein GS., Adv Biol Regul 69(), 2018
PMID: 29759441
Superresolution imaging of nanoscale chromosome contacts.
Wang Y, Ratna P, Shivashankar GV., Sci Rep 7(), 2017
PMID: 28186153
Gene Team in Blood Pressure Genetics.
Morris BJ., Circ Cardiovasc Genet 10(3), 2017
PMID: 28506961
FOXO3 longevity interactome on chromosome 6.
Donlon TA, Morris BJ, Chen R, Masaki KH, Allsopp RC, Willcox DC, Elliott A, Willcox BJ., Aging Cell 16(5), 2017
PMID: 28722347
Structure of the human chromosome interaction network.
Sarnataro S, Chiariello AM, Esposito A, Prisco A, Nicodemi M., PLoS One 12(11), 2017
PMID: 29141034
Exploring the mechanisms of genome-wide long-range interactions: interpreting chromosome organization.
Wang J, Meng X, Chen H, Yuan C, Li X, Zhou Y, Chen M., Brief Funct Genomics 15(5), 2016
PMID: 26769147
Long noncoding RNA TUG1 is downregulated in non-small cell lung cancer and can regulate CELF1 on binding to PRC2.
Lin PC, Huang HD, Chang CC, Chang YS, Yen JC, Lee CC, Chang WH, Liu TC, Chang JG., BMC Cancer 16(), 2016
PMID: 27485439

47 References

Daten bereitgestellt von Europe PubMed Central.

Capturing chromosome conformation.
Dekker J, Rippe K, Dekker M, Kleckner N., Science 295(5558), 2002
PMID: 11847345
Meet the neighbours: tools to dissect nuclear structure and function.
Osborne CS, Ewels PA, Young AN., Brief Funct Genomics 10(1), 2011
PMID: 21258046
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J., Science 326(5950), 2009
PMID: 19815776
Chromosome territories--a functional nuclear landscape.
Cremer T, Cremer M, Dietzel S, Muller S, Solovei I, Fakan S., Curr. Opin. Cell Biol. 18(3), 2006
PMID: 16687245
A fractal model for nuclear organization: current evidence and biological implications.
Bancaud A, Lavelle C, Huet S, Ellenberg J., Nucleic Acids Res. 40(18), 2012
PMID: 22790985
Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B., Nature 485(7398), 2012
PMID: 22495300
A high-resolution map of the three-dimensional chromatin interactome in human cells.
Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B., Nature 503(7475), 2013
PMID: 24141950
Spatial proximity and similarity of the epigenetic state of genome domains.
Khrameeva EE, Mironov AA, Fedonin GG, Khaitovich P, Gelfand MS., PLoS ONE 7(4), 2012
PMID: 22496774
A complex network framework for unbiased statistical analyses of DNA-DNA contact maps.
Kruse K, Sewitz S, Babu MM., Nucleic Acids Res. 41(2), 2012
PMID: 23175602
A three-dimensional model of the yeast genome.
Duan Z, Andronescu M, Schutz K, McIlwain S, Kim YJ, Lee C, Shendure J, Fields S, Blau CA, Noble WS., Nature 465(7296), 2010
PMID: 20436457
BootES: an R package for bootstrap confidence intervals on effect sizes.
Kirby KN, Gerlanc D., Behav Res Methods 45(4), 2013
PMID: 23519455
Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing
AUTHOR UNKNOWN, 1995
Ensembl 2012
AUTHOR UNKNOWN, 2012
The UCSC Genome Browser Database: update 2006
AUTHOR UNKNOWN, 2006
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T., Genome Res. 13(11), 2003
PMID: 14597658
Understanding network concepts in modules.
Dong J, Horvath S., BMC Syst Biol 1(), 2007
PMID: 17547772
The ENCODE (ENCyclopedia Of DNA Elements) Project.
ENCODE Project Consortium., Science 306(5696), 2004
PMID: 15499007
HOX genes: seductive science, mysterious mechanisms.
Lappin TR, Grier DG, Thompson A, Halliday HL., Ulster Med J 75(1), 2006
PMID: 16457401
Inflation of correlation in the pursuit of drug-likeness.
Kenny PW, Montanari CA., J. Comput. Aided Mol. Des. 27(1), 2013
PMID: 23306465
Finding What Is Not There through the Unfortunate Binning of Results: The Mendel Effect
AUTHOR UNKNOWN, 2006
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products.
Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S., Bioinformatics 26(7), 2010
PMID: 20179076
Genome wide profiling of human embryonic stem cells (hESCs), their derivatives and embryonal carcinoma cells to develop base profiles of U.S. Federal government approved hESC lines.
Liu Y, Shin S, Zeng X, Zhan M, Gonzalez R, Mueller FJ, Schwartz CM, Xue H, Li H, Baker SC, Chudin E, Barker DL, McDaniel TK, Oeser S, Loring JF, Mattson MP, Rao MS., BMC Dev. Biol. 6(), 2006
PMID: 16672070
Distinctive nuclear organisation of centromeres and regions involved in pluripotency in human embryonic stem cells.
Wiblin AE, Cui W, Clark AJ, Bickmore WA., J. Cell. Sci. 118(Pt 17), 2005
PMID: 16105879
Arrangement of centromeres in mouse cells.
Hsu TC, Cooper JE, Mace ML Jr, Brinkley BR., Chromosoma 34(1), 1971
PMID: 4105528
Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.
Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L., Nat. Biotechnol. 30(1), 2011
PMID: 22198700
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.
Nagano T, Lubling Y, Stevens TJ, Schoenfelder S, Yaffe E, Dean W, Laue ED, Tanay A, Fraser P., Nature 502(7469), 2013
PMID: 24067610
Chromatin and epigenetic features of long-range gene regulation.
Harmston N, Lenhard B., Nucleic Acids Res. 41(15), 2013
PMID: 23766291

AUTHOR UNKNOWN, 2008
The nuclear envelope--a scaffold for silencing?
Towbin BD, Meister P, Gasser SM., Curr. Opin. Genet. Dev. 19(2), 2009
PMID: 19303765
Characterization of the Drosophila melanogaster genome at the nuclear lamina.
Pickersgill H, Kalverda B, de Wit E, Talhout W, Fornerod M, van Steensel B., Nat. Genet. 38(9), 2006
PMID: 16878134
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions.
Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B., Nature 453(7197), 2008
PMID: 18463634
Interphase chromosomes undergo constrained diffusional motion in living cells.
Marshall WF, Straight A, Marko JF, Swedlow J, Dernburg A, Belmont A, Murray AW, Agard DA, Sedat JW., Curr. Biol. 7(12), 1997
PMID: 9382846
A chromatin remodelling complex that loads cohesin onto human chromosomes.
Hakimi MA, Bochar DA, Schmiesing JA, Dong Y, Barak OG, Speicher DW, Yokomori K, Shiekhattar R., Nature 418(6901), 2002
PMID: 12198550
Cohesin and chromatin organisation
AUTHOR UNKNOWN, 2011
Cohesin-mediated chromatin interactions--into the third dimension of gene regulation.
Sofueva S, Hadjur S., Brief Funct Genomics 11(3), 2012
PMID: 22278832
Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus.
Hadjur S, Williams LM, Ryan NK, Cobb BS, Sexton T, Fraser P, Fisher AG, Merkenschlager M., Nature 460(7253), 2009
PMID: 19458616
Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus.
Nativio R, Wendt KS, Ito Y, Huddleston JE, Uribe-Lewis S, Woodfine K, Krueger C, Reik W, Peters JM, Murrell A., PLoS Genet. 5(11), 2009
PMID: 19956766
Cohesin mediates chromatin interactions that regulate mammalian β-globin expression.
Chien R, Zeng W, Kawauchi S, Bender MA, Santos R, Gregson HC, Schmiesing JA, Newkirk DA, Kong X, Ball AR Jr, Calof AL, Lander AD, Groudine MT, Yokomori K., J. Biol. Chem. 286(20), 2011
PMID: 21454523
Cell type specificity of chromatin organization mediated by CTCF and cohesin.
Hou C, Dale R, Dean A., Proc. Natl. Acad. Sci. U.S.A. 107(8), 2010
PMID: 20133600
CTCF physically links cohesin to chromatin.
Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A., Proc. Natl. Acad. Sci. U.S.A. 105(24), 2008
PMID: 18550811
CTCF: master weaver of the genome.
Phillips JE, Corces VG., Cell 137(7), 2009
PMID: 19563753
Cohesin mediates transcriptional insulation by CCCTC-binding factor.
Wendt KS, Yoshida K, Itoh T, Bando M, Koch B, Schirghuber E, Tsutsumi S, Nagae G, Ishihara K, Mishiro T, Yahata K, Imamoto F, Aburatani H, Nakao M, Imamoto N, Maeshima K, Shirahige K, Peters JM., Nature 451(7180), 2008
PMID: 18235444

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