Unraveling architecture of the pluripotent genome

Current Opinion in Cell Biology

Volumn 28, Issue 1, 2014, Pages 96-104

  Phillips Cremins, Jennifer E ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ANIMAL; CELL LINEAGE; CHROMOSOME; CYTOLOGY; GENE EXPRESSION REGULATION; GENETICS; GENOME; HUMAN; METABOLISM; PLURIPOTENT STEM CELL;

ANIMALS; CELL LINEAGE; CHROMOSOMES; GENE EXPRESSION REGULATION; GENOME; HUMANS; PLURIPOTENT STEM CELLS; TRANSCRIPTION FACTORS;

EID: 84900028471     PISSN: 09550674     EISSN: 18790410     Source Type: Journal    
DOI: 10.1016/j.ceb.2014.04.006     Document Type: Review

References (47)

1. Misteli T. Beyond the sequence: cellular organization of genome function. Cell 2007, 128:787-800.
2. Schardin M., Cremer T., Hager H.D., Lang M. Specific staining of human chromosomes in Chinese hamster×man hybrid cell lines demonstrates interphase chromosome territories. Hum Genet 1985, 71:281-287.
3. Lanctot C., Cheutin T., Cremer M., Cavalli G., Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 2007, 8:104-115.
4. de Wit E., de Laat W. A decade of 3C technologies: insights into nuclear organization. Genes Dev 2012, 26:11-24.
5. Dekker J., Marti-Renom M.A., Mirny L.A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 2013, 14:390-403.
6. Li G., Fullwood M.J., Xu H., Mulawadi F.H., Velkov S., Vega V., Ariyaratne P.N., Mohamed Y.B., Ooi H.S., Tennakoon C., et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 2010, 11:R22.
7. van Steensel B., Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol 2010, 28:1089-1095.
8. Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
9. Zhang Y., McCord R.P., Ho Y.J., Lajoie B.R., Hildebrand D.G., Simon A.C., Becker M.S., Alt F.W., Dekker J. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell 2012, 148:908-921.
10. Dixon J.R., Selvaraj S., Yue F., Kim A., Li Y., Shen Y., Hu M., Liu J.S., Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012, 485:376-380.
11. Nora E.P., Lajoie B.R., Schulz E.G., Giorgetti L., Okamoto I., Servant N., Piolot T., van Berkum N.L., Meisig J., Sedat J., et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012, 485:381-385.
12. Sanyal A., Lajoie B.R., Jain G., Dekker J. The long-range interaction landscape of gene promoters. Nature 2012, 489:109-113.
13. Phillips-Cremins J.E., Sauria M.E., Sanyal A., Gerasimova T.I., Lajoie B.R., Bell J.S., Ong C.T., Hookway T.A., Guo C., Sun Y., et al. Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 2013, 153:1281-1295.
14. Jin F., Li Y., Dixon J.R., Selvaraj S., Ye Z., Lee A.Y., Yen C.A., Schmitt A.D., Espinoza C.A., Ren B. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 2013, 503:290-294.
15. Zhang Y., Wong C.H., Birnbaum R.Y., Li G., Favaro R., Ngan C.Y., Lim J., Tai E., Poh H.M., Wong E., et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 2013, 504:306-310.
16. Dostie J., Richmond T.A., Arnaout R.A., Selzer R.R., Lee W.L., Honan T.A., Rubio E.D., Krumm A., Lamb J., Nusbaum C., et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res 2006, 16:1299-1309.
17. de Wit E., Bouwman B.A., Zhu Y., Klous P., Splinter E., Verstegen M.J., Krijger P.H., Festuccia N., Nora E.P., Welling M., et al. The pluripotent genome in three dimensions is shaped around pluripotency factors. Nature 2013, 501:227-231.
18. Schoenfelder S., Sexton T., Chakalova L., Cope N.F., Horton A., Andrews S., Kurukuti S., Mitchell J.A., Umlauf D., Dimitrova D.S., et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 2010, 42:53-61.
19. Gibcus J.H., Dekker J. The hierarchy of the 3D genome. Mol Cell 2013, 49:773-782.
20. Lin Y.C., Benner C., Mansson R., Heinz S., Miyazaki K., Miyazaki M., Chandra V., Bossen C., Glass C.K., Murre C. Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate. Nat Immunol 2012, 13:1196-1204.
21. Andrey G., Montavon T., Mascrez B., Gonzalez F., Noordermeer D., Leleu M., Trono D., Spitz F., Duboule D. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science 2013, 340:1234167.
22. Apostolou E., Ferrari F., Walsh R.M., Bar-Nur O., Stadtfeld M., Cheloufi S., Stuart H.T., Polo J.M., Ohsumi T.K., Borowsky M.L., et al. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell 2013, 12:699-712.
23. Denholtz M., Bonora G., Chronis C., Splinter E., de Laat W., Ernst J., Pellegrini M., Plath K. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell 2013, 13:602-616.
24. Wei Z., Gao F., Kim S., Yang H., Lyu J., An W., Wang K., Lu W. Klf4 organizes long-range chromosomal interactions with the oct4 locus in reprogramming and pluripotency. Cell Stem Cell 2013, 13:36-47.
25. Zhang H., Jiao W., Sun L., Fan J., Chen M., Wang H., Xu X., Shen A., Li T., Niu B., et al. Intrachromosomal looping is required for activation of endogenous pluripotency genes during reprogramming. Cell Stem Cell 2013, 13:30-35.
26. Adelman K., Lis J.T. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet 2012, 13:720-731.
27. Kagey M.H., Newman J.J., Bilodeau S., Zhan Y., Orlando D.A., van Berkum N.L., Ebmeier C.C., Goossens J., Rahl P.B., Levine S.S., et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature 2010, 467:430-435.
28. Levasseur D.N., Wang J., Dorschner M.O., Stamatoyannopoulos J.A., Orkin S.H. Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. Genes Dev 2008, 22:575-580.
29. Rada-Iglesias A., Bajpai R., Swigut T., Brugmann S.A., Flynn R.A., Wysocka J. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2011, 470:279-283.
30. Creyghton M.P., Cheng A.W., Welstead G.G., Kooistra T., Carey B.W., Steine E.J., Hanna J., Lodato M.A., Frampton G.M., Sharp P.A., et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A 2010, 107:21931-21936.
31. DeMare L.E., Leng J., Cotney J., Reilly S.K., Yin J., Sarro R., Noonan J.P. The genomic landscape of cohesin-associated chromatin interactions. Genome Res 2013, 23:1224-1234.
32. Deng W., Lee J., Wang H., Miller J., Reik A., Gregory P.D., Dean A., Blobel G.A. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 2012, 149:1233-1244.
33. Soufi A., Donahue G., Zaret K.S. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 2012, 151:994-1004.
34. Taberlay P.C., Kelly T.K., Liu C.C., You J.S., De Carvalho D.D., Miranda T.B., Zhou X.J., Liang G., Jones P.A. Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell 2011, 147:1283-1294.
35. Fudenberg G., Mirny L.A. Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev 2012, 22:115-124.
36. Peric-Hupkes D., Meuleman W., Pagie L., Bruggeman S.W., Solovei I., Brugman W., Graf S., Flicek P., Kerkhoven R.M., van Lohuizen M., et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 2010, 38:603-613.
37. Splinter E., Heath H., Kooren J., Palstra R.J., Klous P., Grosveld F., Galjart N., de Laat W. CTCF mediates long-range chromatin looping and local histone modification in the beta-globin locus. Genes Dev 2006, 20:2349-2354.
38. Hadjur S., Williams L.M., Ryan N.K., Cobb B.S., Sexton T., Fraser P., Fisher A.G., Merkenschlager M. Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 2009, 460:410-413.
39. Phillips J.E., Corces V.G. CTCF: master weaver of the genome. Cell 2009, 137:1194-1211.
40. Handoko L., Xu H., Li G., Ngan C.Y., Chew E., Schnapp M., Lee C.W., Ye C., Ping J.L., Mulawadi F., et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011, 43:630-638.
41. Seitan V.C., Faure A.J., Zhan Y., McCord R.P., Lajoie B.R., Ing-Simmons E., Lenhard B., Giorgetti L., Heard E., Fisher A.G., et al. Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res 2013, 23:2066-2077.
42. Sofueva S., Yaffe E., Chan W.C., Georgopoulou D., Vietri Rudan M., Mira-Bontenbal H., Pollard S.M., Schroth G.P., Tanay A., Hadjur S. Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J 2013, 32:3119-3129.
43. Yan J., Enge M., Whitington T., Dave K., Liu J., Sur I., Schmierer B., Jolma A., Kivioja T., Taipale M., et al. Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 2013, 154:801-813.
44. Merkenschlager M., Odom D.T. CTCF and cohesin: linking gene regulatory elements with their targets. Cell 2013, 152:1285-1297.
45. Nagano T., Lubling Y., Stevens T.J., Schoenfelder S., Yaffe E., Dean W., Laue E.D., Tanay A., Fraser P. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 2013, 502:59-64.
46. Ran F.A., Hsu P.D., Wright J., Agarwala V., Scott D.A., Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc 2013, 8:2281-2308.
47. Naumova N., Imakaev M., Fudenberg G., Zhan Y., Lajoie B.R., Mirny L.A., Dekker J. Organization of the mitotic chromosome. Science 2013, 342:948-953.