Manipulating nuclear architecture

Current Opinion in Genetics and Development

Volumn 25, Issue 1, 2014, Pages 1-7

  Deng, Wulan ^a   Blobel, Gerd A ^b  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEMOGLOBIN BETA CHAIN; HISTONE H3; LAMIN A; MESSENGER RNA; TRANSCRIPTION FACTOR GATA 1; CHROMATIN;

BINDING SITE; CAENORHABDITIS ELEGANS; CELL NUCLEUS; CHROMOSOME STRUCTURE; DOWN REGULATION; ERYTHROID CELL; EUKARYOTE; GENE EXPRESSION; GENE INTERACTION; GENE LOCATION; GENE LOCUS; HETEROCHROMATIN; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; NUCLEOLUS; PRIORITY JOURNAL; PROTEIN CROSS LINKING; PROTEIN DOMAIN; PROTEIN MOTIF; REGULATOR GENE; REVIEW; RNA PROCESSING; ANIMAL; CHEMISTRY; CHROMATIN; GENETICS; GENOME; HUMAN;

ANIMALS; CELL NUCLEUS; CHROMATIN; GENE EXPRESSION; GENOME; HUMANS;

EID: 84890206727     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2013.10.014     Document Type: Review

References (60)

1. Cremer T., Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol 2010, 2:a003889.
2. 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.
3. Zhao R., Bodnar M.S., Spector D.L. Nuclear neighborhoods and gene expression. Curr Opin Genet Dev 2009, 19:172-179.
4. Pickersgill H., Kalverda B., de Wit E., Talhout W., Fornerod M., van Steensel B. Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 2006, 38:1005-1014.
5. Nemeth A., Langst G. Genome organization in and around the nucleolus. Trends Genet 2011, 27:149-156.
6. Ragoczy T., Bender M.A., Telling A., Byron R., Groudine M. The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev 2006, 20:1447-1457.
7. Hubner M.R., Eckersley-Maslin M.A., Spector D.L. Chromatin organization and transcriptional regulation. Curr Opin Genet Dev 2013, 23:89-95.
8. 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.
9. 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.
10. Sexton T., Yaffe E., Kenigsberg E., Bantignies F., Leblanc B., Hoichman M., Parrinello H., Tanay A., Cavalli G. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell 2012, 148:458-472.
11. 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.
12. Sanyal A., Lajoie B.R., Jain G., Dekker J. The long-range interaction landscape of gene promoters. Nature 2012, 489:109-113.
13. Kadauke S., Blobel G.A. Chromatin loops in gene regulation. Biochim Biophys Acta 2009, 1789:17-25.
14. Krivega I., Dean A. Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev 2012, 22:79-85.
15. O'Sullivan J.M., Tan-Wong S.M., Morillon A., Lee B., Coles J., Mellor J., Proudfoot N.J. Gene loops juxtapose promoters and terminators in yeast. Nat Genet 2004, 36:1014-1018.
16. O'Reilly D., Greaves D.R. Cell-type-specific expression of the human CD68 gene is associated with changes in Pol II phosphorylation and short-range intrachromosomal gene looping. Genomics 2007, 90:407-415.
17. Tan-Wong S.M., Wijayatilake H.D., Proudfoot N.J. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev 2009, 23:2610-2624.
18. Andrulis E.D., Neiman A.M., Zappulla D.C., Sternglanz R. Perinuclear localization of chromatin facilitates transcriptional silencing. Nature 1998, 394:592-595.
19. Finlan L.E., Sproul D., Thomson I., Boyle S., Kerr E., Perry P., Ylstra B., Chubb J.R., Bickmore W.A. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 2008, 4:e1000039.
20. Kumaran R.I., Spector D.L. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J Cell Biol 2008, 180:51-65.
21. Reddy K.L., Zullo J.M., Bertolino E., Singh H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 2008, 452:243-247.
22. Zullo J.M., Demarco I.A., Pique-Regi R., Gaffney D.J., Epstein C.B., Spooner C.J., Luperchio T.R., Bernstein B.E., Pritchard J.K., Reddy K.L., et al. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell 2012, 149:1474-1487.
23. Mattout A., Pike B.L., Towbin B.D., Bank E.M., Gonzalez-Sandoval A., Stadler M.B., Meister P., Gruenbaum Y., Gasser S.M. An EDMD mutation in C. elegans lamin blocks muscle-specific gene relocation and compromises muscle integrity. Curr Biol 2011, 21:1603-1614.
24. Towbin B.D., Gonzalez-Aguilera C., Sack R., Gaidatzis D., Kalck V., Meister P., Askjaer P., Gasser S.M. Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery. Cell 2012, 150:934-947.
25. Kubben N., Adriaens M., Meuleman W., Voncken J.W., van Steensel B., Misteli T. Mapping of lamin A- and progerin-interacting genome regions. Chromosoma 2012, 121:447-464.
26. Akhtar W., de Jong J., Pindyurin A.V., Pagie L., Meuleman W., de Ridder J., Berns A., Wessels L.F., van Lohuizen M., van Steensel B. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 2013, 154:914-927.
27. Casolari J.M., Brown C.R., Komili S., West J., Hieronymus H., Silver P.A. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 2004, 117:427-439.
28. Brickner J.H., Walter P. Gene recruitment of the activated INO1 locus to the nuclear membrane. PLoS Biol 2004, 2:e342.
29. Brown C.R., Kennedy C.J., Delmar V.A., Forbes D.J., Silver P.A. Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. Genes Dev 2008, 22:627-639.
30. Taddei A., Van Houwe G., Hediger F., Kalck V., Cubizolles F., Schober H., Gasser S.M. Nuclear pore association confers optimal expression levels for an inducible yeast gene. Nature 2006, 441:774-778.
31. Brickner D.G., Cajigas I., Fondufe-Mittendorf Y., Ahmed S., Lee P.C., Widom J., Brickner J.H. H2A.Z-mediated localization of genes at the nuclear periphery confers epigenetic memory of previous transcriptional state. PLoS Biol 2007, 5:e81.
32. Casolari J.M., Brown C.R., Drubin D.A., Rando O.J., Silver P.A. Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev 2005, 19:1188-1198.
33. Dieppois G., Iglesias N., Stutz F. Cotranscriptional recruitment to the mRNA export receptor Mex67p contributes to nuclear pore anchoring of activated genes. Mol Cell Biol 2006, 26:7858-7870.
34. Abruzzi K.C., Belostotsky D.A., Chekanova J.A., Dower K., Rosbash M. 3'-End formation signals modulate the association of genes with the nuclear periphery as well as mRNP dot formation. EMBO J 2006, 25:4253-4262.
35. Ahmed S., Brickner D.G., Light W.H., Cajigas I., McDonough M., Froyshteter A.B., Volpe T., Brickner J.H. DNA zip codes control an ancient mechanism for gene targeting to the nuclear periphery. Nat Cell Biol 2010, 12:111-118.
36. Brickner D.G., Ahmed S., Meldi L., Thompson A., Light W., Young M., Hickman T.L., Chu F., Fabre E., Brickner J.H. Transcription factor binding to a DNA zip code controls interchromosomal clustering at the nuclear periphery. Dev Cell 2012, 22:1234-1246.
37. Brown J.M., Green J., das Neves R.P., Wallace H.A., Smith A.J., Hughes J., Gray N., Taylor S., Wood W.G., Higgs D.R., et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol 2008, 182:1083-1097.
38. Ishii K., Arib G., Lin C., Van Houwe G., Laemmli U.K. Chromatin boundaries in budding yeast: the nuclear pore connection. Cell 2002, 109:551-562.
39. Wallace J.A., Felsenfeld G. We gather together: insulators and genome organization. Curr Opin Genet Dev 2007, 17:400-407.
40. Gerasimova T.I., Byrd K., Corces V.G. A chromatin insulator determines the nuclear localization of DNA. Mol Cell 2000, 6:1025-1035.
41. Yusufzai T.M., Tagami H., Nakatani Y., Felsenfeld G. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol Cell 2004, 13:291-298.
42. Tolhuis B., Palstra R.J., Splinter E., Grosveld F., de Laat W. Looping and interaction between hypersensitive sites in the active beta-globin locus. Mol Cell 2002, 10:1453-1465.
43. Mueller-Storm H.P., Sogo J.M., Schaffner W. An enhancer stimulates transcription in trans when attached to the promoter via a protein bridge. Cell 1989, 58:767-777.
44. Mahmoudi T., Katsani K.R., Verrijzer C.P. GAGA can mediate enhancer function in trans by linking two separate DNA molecules. EMBO J 2002, 21:1775-1781.
45. Petrascheck M., Escher D., Mahmoudi T., Verrijzer C.P., Schaffner W., Barberis A. DNA looping induced by a transcriptional enhancer in vivo. Nucleic Acids Res 2005, 33:3743-3750.
46. Nolis I.K., McKay D.J., Mantouvalou E., Lomvardas S., Merika M., Thanos D. Transcription factors mediate long-range enhancer-promoter interactions. Proc Natl Acad Sci U S A 2009, 106:20222-20227.
47. De Gobbi M., Viprakasit V., Hughes J.R., Fisher C., Buckle V.J., Ayyub H., Gibbons R.J., Vernimmen D., Yoshinaga Y., de Jong P., et al. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science 2006, 312:1215-1217.
48. Ameres S.L., Drueppel L., Pfleiderer K., Schmidt A., Hillen W., Berens C. Inducible DNA-loop formation blocks transcriptional activation by an SV40 enhancer. EMBO J 2005, 24:358-367.
49. Hou C., Zhao H., Tanimoto K., Dean A. CTCF-dependent enhancer-blocking by alternative chromatin loop formation. Proc Natl Acad Sci U S A 2008, 105:20398-20403.
50. Jing H., Vakoc C.R., Ying L., Mandat S., Wang H., Zheng X., Blobel G.A. Exchange of GATA factors mediates transitions in looped chromatin organization at a developmentally regulated gene locus. Mol Cell 2008, 29:232-242.
51. 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.
52. Engreitz J.M., Pandya-Jones A., McDonel P., Shishkin A., Sirokman K., Surka C., Kadri S., Xing J., Goren A., Lander E.S., et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 2013, 341:1237973-1-1237973-8.
53. Yadon A.N., Singh B.N., Hampsey M., Tsukiyama T. DNA looping facilitates targeting of a chromatin remodeling enzyme. Mol Cell 2013, 50:93-103.
54. Deng W., Blobel G.A. Do chromatin loops provide epigenetic gene expression states?. Curr Opin Genet Dev 2010, 20:548-554.
55. Brickner J.H. Transcriptional memory at the nuclear periphery. Curr Opin Cell Biol 2009, 21:127-133.
56. Thomson I., Gilchrist S., Bickmore W.A., Chubb J.R. The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1. Curr Biol 2004, 14:166-172.
57. Kind J., Pagie L., Ortabozkoyun H., Boyle S., de Vries S.S., Janssen H., Amendola M., Nolen L.D., Bickmore W.A., van Steensel B. Single-cell dynamics of genome-nuclear lamina interactions. Cell 2013, 153:178-192.
58. Wang F., Higgins J.M. Histone modifications and mitosis: countermarks, landmarks, and bookmarks. Trends Cell Biol 2013, 23:175-184.
59. Kadauke S., Blobel G.A. Mitotic bookmarking by transcription factors. Epigenetics Chromatin 2013, 6:6.
60. Burke L.J., Zhang R., Bartkuhn M., Tiwari V.K., Tavoosidana G., Kurukuti S., Weth C., Leers J., Galjart N., Ohlsson R., et al. CTCF binding and higher order chromatin structure of the H19 locus are maintained in mitotic chromatin. EMBO J 2005, 24:3291-3300.