1,549
Views
25
CrossRef citations to date
0
Altmetric
Review

Mapping of protein- and chromatin-interactions at the nuclear lamina

, &
Pages 460-471 | Received 30 Jul 2010, Accepted 03 Sep 2010, Published online: 31 Dec 2010

References

  • Foisner R. Collas P. Dynamic connections of nuclear envelope proteins to chromatin and the nuclear matrix. Nuclear Envelope Dynamics in Embryos and Somatic Cells 2003; 4:43 - 59
  • Mattout-Drubezki A, Gruenbaum Y. Dynamic interactions of nuclear lamina proteins with chromatin and transcriptional machinery. Cell Mol Life Sci 2003; 60:2053 - 2063
  • Broers JL, Hutchison CJ, Ramaekers FC. Laminopathies. J Pathol 2004; 204:478 - 488
  • Broers JL, Ramaekers FC, Bonne G, Yaou RB, Hutchison CJ. Nuclear lamins: laminopathies and their role in premature ageing. Physiol Rev 2006; 86:967 - 1008
  • Lloyd DJ, Trembath RC, Shackleton S. A novel interaction between lamin A and SREBP1: implications for parial lipodystrophy and other laminopathies. Human Molecular Genetics 2002; 11:769 - 777
  • Pegoraro G, Kubben N, Wickert U, Gohler H, Hoffmann K, Misteli T. Ageing-related chromatin defects through loss of the NURD complex. Nat Cell Biol 2009; 11:1261 - 1267
  • Taimen P, Pfleghaar K, Shimi T, Moller D, Ben-Harush K, Erdos MR, et al. A progeria mutation reveals functions for lamin A in nuclear assembly, architecture and chromosome organization. Proc Natl Acad Sci USA 2009; 106:20788 - 20793
  • Wu CC, Yates JR 3rd. The application of mass spectrometry to membrane proteomics. Nat Biotechnol 2003; 21:262 - 267
  • Yates JR, Ruse CI, Nakorchevsky A. Proteomics by mass spectrometry: approaches, advances and applications. Annu Rev Biomed Eng 2009; 11:49 - 79
  • Werner T. Next generation sequencing in functional genomics. Brief Bioinform 2010; 11:499 - 511
  • Sutherland HG, Mumford GK, Newton K, Ford LV, Farrall R, Dellaire G, et al. Large-scale identification of mammalian proteins localized to nuclear sub-compartments. Hum Mol Genet 2001; 10:1995 - 2011
  • Van Berlo JH, Voncken JW, Kubben N, Broers JL, Duisters R, van Leeuwen RE, et al. A-type lamins are essential for TGFbeta1 induced PP2A to dephosphorylate transcription factors. Hum Mol Genet 2005; 14:2839 - 2849
  • Ivorra C, Kubicek M, Gonzalez JM, Sanz-Gonzalez SM, Alvarez-Barrientos A, O'Connor JE, et al. A mechanism of AP-1 suppression through interaction of c-Fos with lamin A/C. Genes Dev 2006; 20:307 - 320
  • Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A, Jansen R, et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 1999; 402:413 - 418
  • Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, et al. Subcellular localization of the yeast proteome. Genes Dev 2002; 16:707 - 719
  • Simpson JC, Wellenreuther R, Poustka A, Pepperkok R, Wiemann S. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. EMBO Rep 2000; 1:287 - 292
  • Simpson JC, Pepperkok R. Localizing the proteome. Genome Biol 2003; 4:240
  • Kahsay RY, Gao G, Liao L. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics 2005; 21:1853 - 1858
  • Shen HB, Chou KC. Nuc-PLoc: a new web-server for predicting protein subnuclear localization by fusing PseAA composition and PsePSSM. Protein Eng Des Sel 2007; 20:561 - 567
  • Rolls MM, Stein PA, Taylor SS, Ha E, McKeon F, Rapoport TA. A visual screen of a GFP-fusion library identifies a new type of nuclear envelope membrane protein. J Cell Biol 1999; 146:29 - 44
  • Hofemeister H, O'Hare P. Analysis of the localization and topology of nurim, a polytopic protein tightly associated with the inner nuclear membrane. J Biol Chem 2005; 280:2512 - 2521
  • Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, et al. Global analysis of protein localization in budding yeast. Nature 2003; 425:686 - 691
  • Thirkettle HJ, Mills IG, Whitaker HC, Neal DE. Nuclear LYRIC/AEG-1 interacts with PLZF and relieves PLZF-mediated repression. Oncogene 2009; 28:3663 - 3670
  • Wu CC, MacCoss MJ, Howell KE, Yates JR 3rd. A method for the comprehensive proteomic analysis of membrane proteins. Nat Biotechnol 2003; 21:532 - 538
  • Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, et al. A mammalian organelle map by protein correlation profiling. Cell 2006; 125:187 - 199
  • Clawson GA, Moody DE, James J, Smuckler EA. Nuclear envelope alterations accompanying thioacetamide-related enlargement of the nucleus. Cancer Res 1981; 41:519 - 526
  • Cronshaw JM, Krutchinsky AN, Zhang W, Chait BT, Matunis MJ. Proteomic analysis of the mammalian nuclear pore complex. J Cell Biol 2002; 158:915 - 927
  • Dreger M, Bengtsson L, Schoneberg T, Otto H, Hucho F. Nuclear envelope proteomics: novel integral membrane proteins of the inner nuclear membrane. Proc Natl Acad Sci USA 2001; 98:11943 - 11948
  • Korfali N, Fairley EA, Swanson SK, Florens L, Schirmer EC. Use of sequential chemical extractions to purify nuclear membrane proteins for proteomics identification. Methods Mol Biol 2009; 528:201 - 225
  • Sutherland HG, Lam YW, Briers S, Lamond AI, Bickmore WA. 3D3/lyric: a novel transmembrane protein of the endoplasmic reticulum and nuclear envelope, which is also present in the nucleolus. Exp Cell Res 2004; 294:94 - 105
  • Siniossoglou S, Wimmer C, Rieger M, Doye V, Tekotte H, Weise C, et al. A novel complex of nucleoporins, which includes Sec13p and a Sec13p homolog, is essential for normal nuclear pores. Cell 1996; 84:265 - 275
  • Goodchild RE, Dauer WT. Mislocalization to the nuclear envelope: an effect of the dystonia-causing torsinA mutation. Proc Natl Acad Sci USA 2004; 101:847 - 852
  • Holaska JM, Wilson KL. 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 2007; 46:8897 - 8908
  • Nikolakaki E, Simos G, Georgatos SD, Giannakouros T. A nuclear envelope-associated kinase phosphorylates arginine-serine motifs and modulates interactions between the lamin B receptor and other nuclear proteins. J Biol Chem 1996; 271:8365 - 8372
  • Muralikrishna B, Thanumalayan S, Jagatheesan G, Rangaraj N, Karande AA, Parnaik VK. Immunolocalization of detergent-susceptible nucleoplasmic lamin A/C foci by a novel monoclonal antibody. J Cell Biochem 2004; 91:730 - 739
  • Lin F, Morrison JM, Wu W, Worman HJ. MAN1, an integral protein of the inner nuclear membrane, binds Smad2 and Smad3 and antagonizes transforming growth factor-beta signaling. Hum Mol Genet 2005; 14:437 - 445
  • Zhong N, Radu G, Ju W, Brown WT. Novel progerininteractive partner proteins hnRNP E1, EGF, Mel 18 and UBC9 interact with lamin A/C. Biochem Biophys Res Commun 2005; 338:855 - 861
  • Capanni C, Mattioli E, Columbaro M, Lucarelli E, Parnaik VK, Novelli G, et al. Altered pre-lamin A processing is a common mechanism leading to lipodystrophy. Hum Mol Genet 2005; 14:1489 - 1502
  • Farnum M, Zukoski C. Effect of glycerol on the interactions and solubility of bovine pancreatic trypsin inhibitor. Biophys J 1999; 76:2716 - 2726
  • Lang C, Krohne G. Lamina-associated polypeptide 2beta (LAP2beta) is contained in a protein complex together with A- and B-type lamins. Eur J Cell Biol 2003; 82:143 - 153
  • Grandi P, Dang T, Pane N, Shevchenko A, Mann M, Forbes D, et al. Nup93, a vertebrate homologue of yeast Nic96p, forms a complex with a novel 205-kDa protein and is required for correct nuclear pore assembly. Mol Biol Cell 1997; 8:2017 - 2038
  • Zhang SX, Garcia-Gras E, Wycuff DR, Marriot SJ, Kadeer N, Yu W, et al. Identification of direct serum-response factor gene targets during Me2SO-induced P19 cardiac cell differentiation. J Biol Chem 2005; 280:19115 - 1926
  • Doufexis M, Storr HL, King PJ, Clark AJ. Interaction of the melanocortin 2 receptor with nucleoporin 50: evidence for a novel pathway between a G-protein-coupled receptor and the nucleus. FASEB J 2007; 21:4095 - 4100
  • Montes de Oca R, Shoemaker CJ, Gucek M, Cole RNW. Barrier-to-Autointegration Factor Proteome Reveals Chromatin-Regulatory Partners. PLoS One 2009; 4:7050
  • Libotte T, Zaim H, Abraham S, Padmakumar VC, Schneider M, Lu W, et al. Lamin A/C-dependent localization of Nesprin-2, a giant scaffolder at the nuclear envelope. Mol Biol Cell 2005; 16:3411 - 3424
  • Kubben N, Voncken J, Demmers JA, Calis C, van Almen G, Misteli T, et al. Identification of differential protein interactiors of lamin A and progerin. Nucleus 2010; 1:460 - 471
  • Junttila MR, Saarinen S, Schmidt T, Kast J, Westermarck J. Single-step Strep-tag purification for the isolation and identification of protein complexes from mammalian cells. Proteomics 2005; 5:1199 - 1203
  • Witte CP, Noel LD, Gielbert J, Parker JE, Romeis T. Rapid one-step protein purification from plant material using the eight-amino acid StrepII epitope. Plant Mol Biol 2004; 55:135 - 147
  • Sakaki M, Koike H, Takahashi N, Sasagawa N, Tomioka S, Arahata K, et al. Interaction between emerin and nuclear lamins. J Biochem 2001; 129:321 - 327
  • Goldberg M, Lu H, Stuurman N, Ashery-Padan R, Weiss AM, Yu J, et al. Interactions among Drosophila nuclear envelope proteins lamin, otefin and YA. Mol Cell Biol 1998; 18:4315 - 4323
  • Maraldi NM, Lattanzi G, Capanni C, Columbaro M, Mattioli E, Sabatelli P, et al. Laminopathies: a chromatin affair. Adv Enzyme Regul 2006; 46:33 - 49
  • Ruault M, Dubarry M, Taddei A. Re-positioning genes to the nuclear envelope in mammalian cells: impact on transcription. Trends Genet 2008; 24:574 - 581
  • Schneider R, Grosschedl R. Dynamics and interplay of nuclear architecture, genome organization and gene expression. Genes Dev 2007; 21:3027 - 3043
  • Casolari JM, Brown CR, Komili S, West J, Hieronymus H, Silver PA. Genome-wide localization of the nuclear transport machinery couples transcriptional status and nuclear organization. Cell 2004; 117:427 - 439
  • Partridge JF, Borgstrom B, Allshire RC. Distinct protein interaction domains and protein spreading in a complex centromere. Genes Dev 2000; 14:783 - 791
  • Grund SE, Fischer T, Cabal GG, Antunez O, Perez-Ortin JE, Hurt E. The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression. J Cell Biol 2008; 182:897 - 910
  • Brown CR, Kennedy CJ, Delmar VA, Forbes DJ, Silver PA. Global histone acetylation induces functional genomic reorganization at mammalian nuclear pore complexes. Genes Dev 2008; 22:627 - 639
  • 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
  • Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008; 453:948 - 951
  • Vogel MJ, Peric-Hupkes D, van Steensel B. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2007; 2:1467 - 1478
  • Kurshakova MM, Krasnov AN, Kopytova DV, Shidlovskii YV, Nikolenko JV, Nabirochkina EN, et al. SAGA and a novel Drosophila export complex anchor efficient transcription and mRNA export to NPC. EMBO J 2007; 26:4956 - 4965
  • Scaffidi P, Misteli T. Reversal of the cellular phenotype in the premature aging disease Hutchinson-Gilford progeria syndrome. Nat Med 2005; 11:440 - 445
  • Schmid M, Arib G, Laemmli C, Nishikawa J, Durussel T, Laemmli UK. Nup-PI: the nucleopore-promoter interaction of genes in yeast. Mol Cell 2006; 21:379 - 391
  • Schmid M, Durussel T, Laemmli UK. ChIC and ChEC; genomic mapping of chromatin proteins. Mol Cell 2004; 16:147 - 157
  • Schirmer EC, Gerace L. The nuclear membrane proteome: extending the envelope. Trends Biochem Sci 2005; 30:551 - 558
  • Fink JL, Karunaratne S, Mittal A, Gardiner DM, Hamilton N, Mahony D, et al. Towards defining the nuclear proteome. Genome Biol 2008; 9:R15
  • Miller BR, Forbes DJ. Purification of the vertebrate nuclear pore complex by biochemical criteria. Traffic 2000; 1:941 - 951
  • Schirmer EC, Florens L, Guan T, Yates JR 3rd, Gerace L. Nuclear membrane proteins with potential disease links found by subtractive proteomics. Science 2003; 301:1380 - 1382
  • Batrakou DG, Kerr AR, Schirmer EC. Comparative proteomic analyses of the nuclear envelope and pore complex suggests a wide range of heretofore unexpected functions. J Proteomics 2009; 72:56 - 70
  • Maison C, Pyrpasopoulou A, Theodoropoulos PA, Georgatos SD. The inner nuclear membrane protein LAP1 forms a native complex with B-type lamins and partitions with spindle-associated mitotic vesicles. EMBO J 1997; 16:4839 - 4850
  • Dreuillet C, Tillit J, Kress M, Ernoult-Lange M. In vivo and in vitro interaction between human transcription factor MOK2 and nuclear lamin A/C. Nucleic Acids Res 2002; 30:4634 - 4642
  • Wagner N, Weber D, Seitz S, Krohne G. The lamin B receptor of Drosophila melanogaster. J Cell Sci 2004; 117:2015 - 2028
  • Rasala BA, Orjalo AV, Shen Z, Briggs S, Forbes DJ. ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division. Proc Natl Acad Sci USA 2006; 103:17801 - 17806
  • Apel ED, Lewis RM, Grady RM, Sanes JR. Syne-1, a dystrophin- and Klarsicht-related protein associated with synaptic nuclei at the neuromuscular junction. J Biol Chem 2000; 275:31986 - 31995
  • Menon BB, Sarma NJ, Pasula S, Deminoff SJ, Willis KA, Barbara KE, et al. Reverse recruitment: the Nup84 nuclear pore subcomplex mediates Rap1/Gcr1/Gcr2 transcriptional activation. Proc Natl Acad Sci USA 2005; 102:5749 - 5754
  • Casolari JM, Brown CR, Drubin DA, Rando OJ, Silver PA, et al. Developmentally induced changes in transcriptional program alter spatial organization across chromosomes. Genes Dev 2005; 19:1188 - 1198
  • Cabal GG, Genovesio A, Rodriguez-Navarro S, Zimmer C, Gadal O, Lesne A, et al. SAGA interacting factors confine sub-diffusion of transcribed genes to the nuclear envelope. Nature 2006; 441:770 - 773
  • Schirmer EC. The epigenetics of nuclear envelope organization and disease. Mutat Res 2008; 647:112 - 121