Nucleoporins and chromatin metabolism

Current Opinion in Cell Biology

Volumn 40, Issue , 2016, Pages 153-160

  Ptak, Christopher ^a   Wozniak, Richard W ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOPORIN; CHROMATIN;

CELL INTERACTION; CELL METABOLISM; CHROMATIN; CHROMATIN STRUCTURE; DNA REPAIR; DOUBLE STRANDED DNA BREAK; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE SILENCING; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; HUMAN; MOLECULAR BIOLOGY; NONHUMAN; NUCLEAR PORE COMPLEX; PRIORITY JOURNAL; REVIEW; TRINUCLEOTIDE REPEAT; VIRUS INFECTION; ANIMAL; CELL NUCLEUS; CELL NUCLEUS MEMBRANE; CHEMISTRY; CYTOPLASM; EUKARYOTIC CELL; METABOLISM; NUCLEAR PORE;

ANIMALS; CELL NUCLEUS; CHROMATIN; CYTOPLASM; DNA REPAIR; EUKARYOTIC CELLS; GENE EXPRESSION REGULATION; HUMANS; NUCLEAR ENVELOPE; NUCLEAR PORE; NUCLEAR PORE COMPLEX PROTEINS;

EID: 84962786478     PISSN: 09550674     EISSN: 18790410     Source Type: Journal    
DOI: 10.1016/j.ceb.2016.03.024     Document Type: Review

References (55)

1. Stancheva I., Schirmer E.C. Nuclear envelope: connecting structural genome organization to regulation of gene expression. Adv Exp Med Biol 2014, 773:209-244.
2. Krull S., Dorries J., Boysen B., Reidenbach S., Maginus L., Norder H., Thyberg J., Cordes V.C. Protein Tpr is required for establishing nuclear pore-associated zones of heterochromatin exclusion. EMBO J 2010, 29:1659-1673.
3. Pascual-Garcia P., Capelson M. Nuclear pores as versatile platforms for gene regulation. Curr Opin Genet Dev 2014, 25:110-117.
4. Ptak C., Aitchison J.D., Wozniak W. The multifunctional nuclear pore complex: a platform for controlling gene expression. Curr Opin Cell Biol 2014, 28:46-53.
5. Field M.C., Koreny L., Rout M.P. Enriching the pore: splendid complexity from humble origins. Traffic 2014, 2:141-156.
6. Shi Y., Fernandez-Martinez J., Tjioe E., Pellarin R., Kim S.J., Williams R., Schneidman-Duhovny D., Sali A., Rout M.P., Chait B.T. Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex. Mol Cell Proteomics 2014, 11:2927-2943.
7. Hoelz A., Debler E.W., Blobel G. The structure of the nuclear pore complex. Annu Rev Biochem 2011, 80:613-643.
8. Aitchison J.D., Rout M.J. The yeast nuclear pore complex and transport through it. Genetics 2012, 190:855-883.
9. Ibarra A., Hetzer M.W. Nuclear pore proteins and the control of genome functions. Genes Dev 2015, 4:337-349.
10. Taddei A., Gasser S.M. Structure and function in the budding yeast nucleus. Genetics 2012, 192:107-129.
11. Kehat I., Accornero F., Aronow B.J., Molkentin J.D. Modulation of chromatin position and gene expression by HDAC4 interaction with nucleoporins. J Cell Biol 2011, 193:21-29.
12. Gilchrist D.A., Fargo D.C., Adelman K. Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation. Methods 2009, 48:398-408.
13. Orian A., Abed M., Kenyagin-Karsenti D., Boico O. DamID: a methylation based chromatin profiling approach. Methods Mol Biol 2009, 567:155-169.
14. Egecioglu D.E., D'Urso A., Brickner D.G., Light W.H., Brickner J.H. Approaches to studying subnuclear organization and gene-nuclear pore interactions. Methods Cell Biol 2014, 122:463-485.
15. Talamas J.A., Capelson M. Nuclear envelope and genome interactions in cell fate. Front Genet 2015, 6:95.
16. Vaquerizas J.M., Suyama R., Kind J., Miura K., Luscombe N.M., Akhtar A. Nuclear pore proteins Nup153 and megator define transcriptionally active regions in the Drosophila genome. PLoS Genet 2010, 2:e1000846.
17. Sharma R., Jost D., Kind J., Gomez-Saldivar G., van Steensel B., Askjaer P., Vaillant C., Meister P. Differential spatial and structural organization of the X chromosome underlies dosage compensation in C. elegans. Genes Dev 2014, 28:2591-2596.
18. Chen M., Gartenberg M.R. Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast. Genes Dev 2014, 28:959-970.
19. Fischer T., Strässer K., Rácz A., Rodriguez-Navarro S., Oppizzi M., Ihrig P., Lechner J., Hurt E. The mRNA export machinery requires the novel Sac3p-Thp1p complex to dock at the nucleoplasmic entrance of the nuclear pores. EMBO J 2002, 21:5843-5852.
20. Jani D., Valkov E., Stewart M. Structural basis for binding the TREX2 complex to nuclear pores, GAL1 localisation and mRNA export. Nucleic Acid Res 2014, 42:6686-6697.
21. Schneider M., Hellerschmied D., Schubert T., Amlacher S., Vinayachandran V., Reja R., Pugh B.F., Clausen T., Köhler A. The nuclear pore-associated TREX-2 complex employs mediator to regulate gene expression. Cell 2015, 162:1016-1028.
22. Breuer M., Ohkura H. A negative loop within the nuclear pore complex controls global chromatin organization. Genes Dev 2015, 29:1789-1794.
23. Van de Vosse D.W., Wan Y., Lapetina D.L., Chen W.-M., Chiang J.-H., Aitchison J.D., Wozniak R.W. A role for the nucleoporin Nup170p in chromatin structure and gene silencing. Cell 2013, 152:969-983.
24. Makhnevych T., Lusk C.P., Anderson A.M., Aitchison J.D., Wozniak R.W. Cell cycle regulated transport controlled by alterations in the nuclear pore complex. Cell 2003, 115:813-823.
25. Kalverda B., Pickergill H., Shloma V.V., Fornerod M. Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 2010, 140:360-371.
26. Capelson M., Liang Y., Schulte R., Mair W., Wagner U., Hetzer M.W. Chromatin-bound nuclear pore components regulate gene expression in higher eukaryotes. Cell 2010, 140:372-383.
27. Buchwalter A.L., Liang Y., Hetzer M.W. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Mol Biol Cell 2014, 25:2472-2482.
28. Griffis E.R., Altan N., Lippincott-Schwartz J., Powers M.A. Nup98 is a mobile nucleoporin with transcription-dependent dynamics. Mol Biol Cell 2002, 13:1282-1297.
29. Griffis E.R., Craige B., Dimaano C., Ullman K.S., Powers M.A. Distinct functional domains within nucleoporins Nup153 and Nup98 mediate transcription-dependent mobility. Mol Biol Cell 2004, 15:1991-2002.
30. Pascual-Garcia P., Jeong J., Capelson M. Nucleoporin Nup98 associates with Trx/MLL and NSL histone-modifying complexes and regulates HOX gene expression. Cell Rep 2014, 9:433-442.
31. Prestel M., Feller C., Straub T., Mitlöhner H., Becker P.B. The activation potential of MOF is constrained for dosage compensation. Mol Cell 2010, 38:815-826.
32. Raja S.J., Charapitsa I., Conrad T., Vaquerizas J.M., Gebhardt P., Holz H., Kadlec J., Fraterman S., Luscombe N.M., Akhtar A. The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell 2010, 38:827-841.
33. Jacinto F.V., Benner C., Hetzer M.W. The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing. Genes Dev 2015, 29:1224-1238.
34. Simon D.N., Rout M.P. Cancer and the nuclear pore complex. Adv Exp Med Biol 2014, 773:285-307.
35. Panda D., Pascual-Garciab P., Dunaginc M., Tudorb M., Hopkinsa K.C., Xua J., Golda B., Raj A., Capelson M., Cherry S. Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila. Proc Natl Acad Sci U S A 2014, 111:3890-3899.
36. Liang Y., Franks T.M., Marchetto M.C., Gage F.H., Hetzer M.W. Dynamic association of Nup98 with the human genome. PLOS Genet 2013, 9:e1003308.
37. Light W.H., Freany J., Sood V., Thompson A., D'Urso A., Horvath C.M., Brickenr J.H. A conserved role for human Nup98 in altering chromatin structure and promoting epigenetic transcriptional memory. PLOS Biol 2013, 11:e1001524.
38. Panda D., Gold B., Tartell M.A., Rausch K., Casas-Tinto S., Cherry S. The transcription factor FoxK participates with Nup98 to regulate antiviral gene expression. mBio 2015, 6:e02509.
39. Benayoun B.A., Caburet S., Veitia R.A. Forkhead transcription factors: key players in health and disease. Trends Genet 2011, 27:224-232.
40. Le Sage V., Mouland A.J. Viral subversion of the nuclear pore complex. Viruses 2013, 5:2019-2042.
41. Yarbrough M.L., Mata M.A., Sakthivel R., Fontoura B.M.A. Viral subversion of nucleocytoplasmic trafficking. Traffic 2014, 15:127-140.
42. Mettenleiter T.C. Breaching the barrier - the nuclear envelope in virus infection. J Mol Biol 2015, 10.1016/j.jmb.2015.10.001.
43. Koh Y., Wu X., Ferris A.L., Matreyek K.A., Smith S.J., Lee K., KewalRamani V.N., Hughes S.H., Engelman A. Differential effects of human immunodeficiency virus type 1 capsid and cellular factors nucleoporin 153 and LEDGF/p75 on the efficiency and specificity of viral DNA integration. J Virol 2013, 87:648-658.
44. Marini B., Kertesz-Farkas A., Ali H., Lucic B., Lisek K., Manganaro L., Pongor S., Luzzati R., Recchia A., Mavilio F., et al. Nuclear architecture dictates HIV-1 integration site selection. Nature 2015, 521:227-231.
45. Lelek M., Casartelli M., Pellin D., Rizzi E., Souque P., Severgnini M., Di Serio C., Fricke T., Diaz-Griffero F., Zimmer C., et al. Chromatin organization at the nuclear pore favours HIV replication. Nat Commun 2015, 6:6483.
46. Hase M.E., Cordes V.C. Direct interaction with Nup153 mediates binding of Tpr to the periphery of the nuclear pore complex. Mol Biol Cell 2003, 14:1923-1940.
47. Therizols P., Fairhead C., Cabal G.G., Genovesio A., Olivo-Marin J.C., Dujon B., Fabre E. Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region. J Cell Biol 2006, 172:189-199.
48. Nagai S., Dubrana K., Tsai-Pflugfelder M., Davidson M.B., Roberts T.M., Brown G.W., Varela E., Hediger F., Gasser S.M., Krogan N.J. Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase. Science 2008, 322:597-602.
49. Horigome C., Oma Y., Konishi T., Schmid R., Marcomini I., Hauer M.H., Dion V., Harata M., Gasser S.M. SWR1 and INO80 chromatin remodelers contribute to DNA double-strand break perinuclear anchorage site choice. Mol Cell 2014, 55:626-639.
50. Chung D.K., Chan J.N., Strecker J., Zhang W., Ebrahimi-Ardebili S., Lu T., Abraham K.J., Durocher D., Mekhail K. Perinuclear tethers license telomeric DSBs for a broad kinesin- and NPC-dependent DNA repair process. Nat Commun 2015, 6:7742.
51. Khadaroo B., Teixeira M.T., Luciano P., Eckert-Boulet N., Germann S.M., Simon M.N., Gallina I., Abdallah P., Gilson E., Géli V., Lisby M. The DNA damage response at eroded telomeres and tethering to the nuclear pore complex. Nat Cell Biol 2009, 11:980-987.
52. Su X.A., Dion V., Gasser S.M., Freudenreich C.H. Regulation of recombination at yeast nuclear pores controls repair and triplet repeat stability. Genes Dev 2015, 29:1006-1017.
53. Kalocsay M., Hiller N.J., Jentsch S. Chromosome-wide Rad51 spreading and SUMO-H2A.Z-dependent chromosome fixation in response to a persistent DNA double-strand break. Mol Cell 2009, 33:335-343.
54. Oza P., Jaspersen S.L., Miele A., Dekker J., Peterson C.L. Mechanisms that regulate localization of a DNA double-strand break to the nuclear periphery. Genes Dev 2009, 23:912-927.
55. Pearson C.E., Nichol Edamura K., Cleary J.D. Repeat instability: mechanisms of dynamic mutations. Nat Rev Genet 2005, 6:729-742.