Role of Histone Deacetylases in Gene Regulation at Nuclear Lamina

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Milon, Beatrice C ^a   Cheng, Haibo ^a   Tselebrovsky, Mikhail V ^b   Lavrov, Sergei A ^b   Nenasheva, Valentina V ^b   Mikhaleva, Elena A ^b   Shevelyov, Yuri Y ^b   Nurminsky, Dmitry I ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^b INSTITUTE OF MOLECULAR GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED RNA; HISTONE DEACETYLASE; LAMIN;

ANIMAL CELL; ARTICLE; CELL INTERACTION; CHROMATIN CONDENSATION; CONTROLLED STUDY; DEACYLATION; DOWN REGULATION; DROSOPHILA; ENZYME ACTIVITY; ENZYME MECHANISM; GENE CONTROL; GENE EXPRESSION REGULATION; GENE REPRESSION; GENE SILENCING; GENETIC VARIABILITY; HISTONE ACETYLATION; NONHUMAN; NUCLEAR LAMINA; PREDICTION; PROTEIN DEPLETION; PROTEIN DOMAIN;

ACETYLATION; ANIMALS; BLOTTING, WESTERN; CELL LINE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GENE EXPRESSION REGULATION; GENE SILENCING; HISTONE DEACETYLASE 1; HISTONE DEACETYLASES; HISTONES; LAMIN TYPE B; MULTIGENE FAMILY; NUCLEAR LAMINA; RNA, DOUBLE-STRANDED; TRANSCRIPTION, GENETIC;

EID: 84870689701     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049692     Document Type: Article

References (48)

1. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI, (2002) Large clusters of co-expressed genes in the Drosophila genome. Nature 420: 666-669.
2. Hurst LD, Pal C, Lercher MJ, (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5: 299-310.
3. Peric-Hupkes D, van Steensel B, (2010) Role of the nuclear lamina in genome organization and gene expression. Cold Spring Harb Symp Quant Biol 75: 517-524.
4. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, et al. (2008) Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453: 948-951.
5. Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, et al. (2010) Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 38: 603-613.
6. Pickersgill H, Kalverda B, de Wit E, Talhout W, Fornerod M, et al. (2006) Characterization of the Drosophila melanogaster genome at the nuclear lamina. Nat Genet 38: 1005-1014.
7. Shevelyov YY, Lavrov SA, Mikhaylova LM, Nurminsky ID, Kulathinal RJ, et al. (2009) The B-type lamin is required for somatic repression of testis-specific gene clusters. Proc Natl Acad Sci U S A 106: 3282-3287.
8. van Bemmel JG, Pagie L, Braunschweig U, Brugman W, Meuleman W, et al. (2010) The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome. PLoS One 5: e15013.
9. Lee HY, Johnson KD, Boyer ME, Bresnick EH, (2011) Relocalizing genetic loci into specific subnuclear neighborhoods. J Biol Chem 286: 18834-18844.
10. Elcock LS, Bridger JM, (2010) Exploring the relationship between interphase gene positioning, transcriptional regulation and the nuclear matrix. Biochem Soc Trans 38: 263-267.
11. Dialynas G, Speese S, Budnik V, Geyer PK, Wallrath LL, (2010) The role of Drosophila Lamin C in muscle function and gene expression. Development 137: 3067-3077.
12. Reddy KL, Singh H, (2008) Using molecular tethering to analyze the role of nuclear compartmentalization in the regulation of mammalian gene activity. Methods 45: 242-251.
13. Finlan LE, Sproul D, Thomson I, Boyle S, Kerr E, et al. (2008) Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 4: e1000039.
14. Wagner N, Krohne G, (2007) LEM-Domain proteins: new insights into lamin-interacting proteins. Int Rev Cytol 261: 1-46.
15. Montes de OR, Shoemaker CJ, Gucek M, Cole RN, Wilson KL, (2009) Barrier-to-autointegration factor proteome reveals chromatin-regulatory partners. PLoS One 4: e7050.
16. Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, et al. (2010) Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 143: 212-224.
17. Ikegami K, Egelhofer TA, Strome S, Lieb JD, (2010) Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. Genome Biol 11: R120.
18. Schwartz YB, Kahn TG, Nix DA, Li XY, Bourgon R, et al. (2006) Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 38: 700-705.
19. Ye Q, Worman HJ, (1996) Interaction between an integral protein of the nuclear envelope inner membrane and human chromodomain proteins homologous to Drosophila HP1. J Biol Chem 271: 14653-14656.
20. Towbin BD, Meister P, Pike BL, Gasser SM, (2010) Repetitive transgenes in C. elegans accumulate heterochromatic marks and are sequestered at the nuclear envelope in a copy-number- and lamin-dependent manner. Cold Spring Harb Symp Quant Biol 75: 555-565.
21. Pindyurin AV, Moorman C, de Wit E, Belyakin SN, Belyaeva ES, et al. (2007) SUUR joins separate subsets of PcG, HP1 and B-type lamin targets in Drosophila. J Cell Sci 120: 2344-2351.
22. Sadoni N, Langer S, Fauth C, Bernardi G, Cremer T, et al. (1999) Nuclear organization of mammalian genomes. Polar chromosome territories build up functionally distinct higher order compartments. J Cell Biol 146: 1211-1226.
23. Gilchrist S, Gilbert N, Perry P, Bickmore WA, (2004) Nuclear organization of centromeric domains is not perturbed by inhibition of histone deacetylases. Chromosome Res 12: 505-516.
24. Holaska JM, Wilson KL, (2007) 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: 8897-8908.
25. Somech R, Shaklai S, Geller O, Amariglio N, Simon AJ, et al. (2005) The nuclear-envelope protein and transcriptional repressor LAP2beta interacts with HDAC3 at the nuclear periphery, and induces histone H4 deacetylation. J Cell Sci 118: 4017-4025.
26. Eskeland R, Freyer E, Leeb M, Wutz A, Bickmore WA, (2010) Histone acetylation and the maintenance of chromatin compaction by Polycomb repressive complexes. Cold Spring Harb Symp Quant Biol 75: 71-78.
27. Gregory PD, Wagner K, Horz W, (2001) Histone acetylation and chromatin remodeling. Exp Cell Res 265: 195-202.
28. Ridsdale JA, Hendzel MJ, Delcuve GP, Davie JR, (1990) Histone acetylation alters the capacity of the H1 histones to condense transcriptionally active/competent chromatin. J Biol Chem 265: 5150-5156.
29. Hansen JC, Wolffe AP, (1992) Influence of chromatin folding on transcription initiation and elongation by RNA polymerase III. Biochemistry 31: 7977-7988.
30. Lande-Diner L, Cedar H, (2005) Silence of the genes-mechanisms of long-term repression. Nat Rev Genet 6: 648-654.
31. Lucio-Eterovic AK, Cortez MA, Valera ET, Motta FJ, Queiroz RG, et al. (2008) Differential expression of 12 histone deacetylase (HDAC) genes in astrocytomas and normal brain tissue: class II and IV are hypoexpressed in glioblastomas. BMC Cancer 19: 243.
32. Foglietti C, Filocamo G, Cundari E, De Rinaldis E, Lahm A, et al. (2006) Dissecting the biological functions of Drosophila histone deacetylases by RNA interference and transcriptional profiling. J Biol Chem 281: 17968-17976.
33. Cho Y, Griswold A, Campbell C, Min KT, (2005) Individual histone deacetylases in Drosophila modulate transcription of distinct genes. Genomics 86: 606-617.
34. Kalmykova AI, Nurminsky DI, Ryzhov DV, Shevelyov YY, (2005) Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster. Nucleic Acids Res 33: 1435-1444.
35. Gemkow MJ, Verveer PJ, Arndt-Jovin DJ, (1998) Homologous association of the Bithorax-Complex during embryogenesis: consequences for transvection in Drosophila melanogaster. Development 125: 4541-4552.
36. Wagner N, Schmitt J, Krohne G, (2004) Two novel LEM-domain proteins are splice products of the annotated Drosophila melanogaster gene CG9424 (Bocksbeutel). Eur J Cell Biol 82: 605-616.
37. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, et al. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471: 480-485.
38. Davie JR, Candido EP, (1980) DNase I sensitive chromatin is enriched in the acetylated species of histone H4. FEBS Lett 110: 164-168.
39. Sperling K, Kerem BS, Goitein R, Kottusch V, Cedar H, et al. (1985) DNase I sensitivity in facultative and constitutive heterochromatin. Chromosoma 93: 38-42.
40. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
41. Chintapalli VR, Wang J, Dow JA, (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39: 715-720.
42. Wilmington S, Hornick E, Pinto B, Wallrath L, Geyer P (2008) Genetic analyses of bocksbeutel and otefin: genes encoding nuclear lamina LEM domain proteins. Program and Abstracts. 49th Annual Drosophila Research Conference, San Diego, CA. Abstract 540C.
43. Zink D, Amaral MD, Englmann A, Lang S, Clarke LA, et al. (2004) Transcription-dependent spatial arrangements of CFTR and adjacent genes in human cell nuclei. J Cell Biol 166: 815-825.
44. Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, et al. (2012) DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell 149: 1474-1487.
45. Cohen BA, Mitra RD, Hughes JD, Church GM, (2000) A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 26: 183-186.
46. Lee JM, Sonnhammer EL, (2003) Genomic gene clustering analysis of pathways in eukaryotes. Genome Res 13: 875-882.
47. Pennings JL, van Dartel DA, Robinson JF, Pronk TE, Piersma AH, (2011) Gene set assembly for quantitative prediction of developmental toxicity in the embryonic stem cell test. Toxicology 284: 63-71.
48. Maraldi NM, Capanni C, Cenni V, Fini M, Lattanzi G, (2011) Laminopathies and lamin-associated signaling pathways. J Cell Biochem 112: 979-992.