Transcription and the nuclear periphery: edge of darkness?

Current Opinion in Genetics and Development

Volumn 19, Issue 2, 2009, Pages 187-191

  Deniaud, Emmanuelle ^a   Bickmore, Wendy A ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS MEMBRANE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE REPLICATION; GENETIC TRANSCRIPTION; HUMAN; NONHUMAN; PRIORITY JOURNAL; REVIEW;

ANIMALS; CHROMATIN; DNA REPLICATION; GENE EXPRESSION REGULATION; HUMANS; MODELS, BIOLOGICAL; NUCLEAR ENVELOPE; NUCLEAR PROTEINS; TRANSCRIPTION, GENETIC;

MAMMALIA;

EID: 65349142073     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2009.01.005     Document Type: Review

References (39)

1. Ahmed S., and Brickner J.H. Regulation and epigenetic control of transcription at the nuclear periphery. Trends Genet 23 (2007) 396-402
2. Akhtar A., and Gasser S.M. The nuclear envelope and transcriptional control. Nat Rev Genet 8 (2007) 507-517
3. Gilchrist S., Gilbert N., Perry P., and Bickmore W.A. Nuclear organization of centromeric domains is not perturbed by inhibition of histone deacetylases. Chromosome Res 12 (2004) 505-516
4. Weierich C., Brero A., Stein S., von H.J., Cremer C., Cremer T., and Solovei I. Three-dimensional arrangements of centromeres and telomeres in nuclei of human and murine lymphocytes. Chromosome Res 11 (2003) 485-502
5. Boyle S., Gilchrist S., Bridger J.M., Mahy N.L., Ellis J.A., and Bickmore W.A. The spatial organization of human chromosomes within the nuclei of normal and emerin-mutant cells. Hum Mol Genet 10 (2001) 211-219
6. Croft J.A., Bridger J.M., Boyle S., Perry P., Teague P., and Bickmore W.A. Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol 145 (1999) 1119-1131
7. Mayer R., Brero A., von H.J., Schroeder T., Cremer T., and Dietzel S. Common themes and cell type specific variations of higher order chromatin arrangements in the mouse. BMC Cell Biol 6 (2005) 44
8. Bolzer A., Kreth G., Solovei I., Koehler D., Saracoglu K., Fauth C., Muller S., Eils R., Cremer C., Speicher M.R., and Cremer T. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol 3 (2005) e157
9. Ferreira J., Paolella G., Ramos C., and Lamond A.I. Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories. J Cell Biol 139 (1997) 1597-1610
10. Shopland L.S., Lynch C.R., Peterson K.A., Thornton K., Kepper N., Hase J., Stein S., Vincent S., Molloy K.R., Kreth G., et al. Folding and organization of a contiguous chromosome region according to the gene distribution pattern in primary genomic sequence. J Cell Biol 174 (2006) 27-38
11. Kupper K., Kolbl A., Biener D., Dittrich S., von H.J., Thormeyer T., Fiegler H., Carter N.P., Speicher M.R., Cremer T., and Cremer M. Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 116 (2007) 285-306
12. Guelen L., Pagie L., Brasset E., Meuleman W., Faza M.B., Talhout W., Eussen B.H., de K.A., Wessels L., de Laat W., and van Steensel B. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453 (2008) 948-951. The authors provide a genome-wide mapping of the sites interacting with the nuclear lamina in mammalian cells. These sites have the characteristics of inactive chromatin and have well-defined boundaries.
13. Pickersgill H., Kalverda B., de W.E., Talhout W., Fornerod M., and van Steensel B. Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 38 (2006) 1005-1014
14. Levsky J.M., Shenoy S.M., Chubb J.R., Hall C.B., Capodieci P., and Singer R.H. The spatial order of transcription in mammalian cells. J Cell Biochem 102 (2007) 609-617
15. Kosak S.T., Scalzo D., Alworth S.V., Li F., Palmer S., Enver T., Lee J.S., and Groudine M. Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol 5 (2007) e309
16. Kosak S.T., Skok J.A., Medina K.L., Riblet R., Le Beau M.M., Fisher A.G., and Singh H. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296 (2002) 158-162
17. Ballester M., Kress C., Hue-Beauvais C., Kieu K., Lehmann G., Adenot P., and Devinoy E. The nuclear localization of WAP and CSN genes is modified by lactogenic hormones in HC11 cells. J Cell Biochem 105 (2008) 262-270
18. Hewitt S.L., High F.A., Reiner S.L., Fisher A.G., and Merkenschlager M. Nuclear repositioning marks the selective exclusion of lineage-inappropriate transcription factor loci during T helper cell differentiation. Eur J Immunol 34 (2004) 3604-3613
19. Williams R.R., Azuara V., Perry P., Sauer S., Dvorkina M., Jorgensen H., Roix J., McQueen P., Misteli T., Merkenschlager M., and Fisher A.G. Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J Cell Sci 119 (2006) 132-140. This study reports a spatial reorganisation of chromatin away from the nuclear periphery during the differentiation of ES cells towards a neural state. Accompanying long-range effects on replication time, but gene-specific effects on transcription, reorganisation are reported.
20. Finlan L.E., Sproul D., Thomson I., Boyle S., Kerr E., Perry P., Ylstra B., Chubb J.R., and Bickmore W.A. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 4 (2008) e1000039. Artificial tethering of two distinct regions of the human genome to the nuclear periphery results in the suppression of expression from some genes but not from others. Histone deacetylation is implicated in transcriptional suppression.
21. Reddy K.L., Zullo J.M., Bertolino E., and Singh H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 452 (2008) 243-247. Artificial tethering to the nuclear periphery in mouse cells can repress transcription and this is associated with recruitment of lamins and proteins of inner nuclear membrane.
22. Kumaran R.I., and Spector D.L. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J Cell Biol 180 (2008) 51-65. This study provides evidence of transcriptional activity at the nuclear periphery by showing that lamin B-targeted reporter gene can still be transcribed.
23. Dimitrova D.S., and Berezney R. The spatio-temporal organization of DNA replication sites is identical in primary, immortalized and transformed mammalian cells. J Cell Sci 115 (2002) 4037-4051
24. Hiratani I., Ryba T., Itoh M., Yokochi T., Schwaiger M., Chang C.W., Lyou Y., Townes T.M., Schubeler D., and Gilbert D.M. Global reorganization of replication domains during embryonic stem cell differentiation. PLoS Biol 6 (2008) e245. This study establishes the replication timing profile of the entire genome of murine ES cells before and after differentiation and reveals a correlation between the change in replication timing and a spatial reorganisation.
25. Sadoni N., Langer S., Fauth C., Bernardi G., Cremer T., Turner B.M., and Zink D. Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments. J Cell Biol 146 (1999) 1211-1226
26. Holaska J.M., and Wilson K.L. An emerin "proteome": purification of distinct emerin-containing complexes from HeLa cells suggests molecular basis for diverse roles including gene regulation, mRNA splicing, signaling, mechanosensing, and nuclear architecture. Biochemistry 46 (2007) 8897-8908
27. Somech R., Shaklai S., Geller O., Amariglio N., Simon A.J., Rechavi G., and Gal-Yam E.N. The nuclear-envelope protein and transcriptional repressor LAP2beta interacts with HDAC3 at the nuclear periphery, and induces histone H4 deacetylation. J Cell Sci 118 (2005) 4017-4025
28. Nili E., Cojocaru G.S., Kalma Y., Ginsberg D., Copeland N.G., Gilbert D.J., Jenkins N.A., Berger R., Shaklai S., Amariglio N., et al. Nuclear membrane protein LAP2beta mediates transcriptional repression alone and together with its binding partner GCL (germ-cell-less). J Cell Sci 114 (2001) 3297-3307
29. Chubb J.R., Boyle S., Perry P., and Bickmore W.A. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr Biol 12 (2002) 439-445
30. Zink D., Amaral M.D., Englmann A., Lang S., Clarke L.A., Rudolph C., Alt F., Luther K., Braz C., Sadoni N., et al. Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166 (2004) 815-825
31. Brown C.R., Kennedy C.J., Delmar V.A., Forbes D.J., and Silver P.A. Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. Genes Dev 22 (2008) 627-639
32. Malhas A., Lee C.F., Sanders R., Saunders N.J., and Vaux D.J. Defects in lamin B1 expression or processing affect interphase chromosome position and gene expression. J Cell Biol 176 (2007) 593-603
33. Shumaker D.K., Dechat T., Kohlmaier A., Adam S.A., Bozovsky M.R., Erdos M.R., Eriksson M., Goldman A.E., Khuon S., Collins F.S., et al. Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. Proc Natl Acad Sci U S A 103 (2006) 8703-8708
34. Meaburn K.J., Cabuy E., Bonne G., Levy N., Morris G.E., Novelli G., Kill I.R., and Bridger J.M. Primary laminopathy fibroblasts display altered genome organization and apoptosis. Aging Cell 6 (2007) 139-153
35. Chuang C.H., Carpenter A.E., Fuchsova B., Johnson T., de L.P., and Belmont A.S. Long-range directional movement of an interphase chromosome site. Curr Biol 16 (2006) 825-831
36. Shimi T., Pfleghaar K., Kojima S., Pack C.-G., Solovei I., Goldman A.E., Adam S.A., Shumaker D.K., Kinjo M., Cremer T., and Goldman R.D. The A- and B-type nuclear lamin networks: microdomains involved in chromatin organization and transcription. Genes Dev 22 (2008) 3409-3421. The authors identify distinct microdomains of the nuclear lamina, composed of either A-type or B-type lamins. Lamin A blebs induced by lamin B1 depletion associate preferentially with active regions of the genome.
37. Schermelleh L., Carlton P.M., Haase S., Shao L., Winoto L., Kner P., Burke B., Cardoso M.C., Agard D.A., Gustafsson M.G., et al. Subdiffraction multicolor imaging of the nuclear periphery with 3D structured illumination microscopy. Science 320 (2008) 1332-1336. A technical breakthrough in light microscopy, allowing the high-resolution imaging of subnuclear structures, reveals that the nuclear periphery below NPCs is depleted of chromatin.
38. Taddei A. Active genes at the nuclear pore complex. Curr Opin Cell Biol 19 (2007) 305-310
39. Brown C.R., and Silver P.A. Transcriptional regulation at the nuclear pore complex. Curr Opin Genet Dev 17 (2007) 100-106