Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Wu, Feinan ^a   Yao, Jie ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

DamID; High throughput sequencing; Histone modification; Nuclear lamina; Nuclear periphery; Transcription

Indexed keywords

DNA ADENINE METHYLTRANSFERASE; HISTONE H3;

ANIMAL CELL; ARTICLE; CELL COMPARTMENTALIZATION; CELL NUCLEUS; CELLULAR DISTRIBUTION; DNA SEQUENCE; FIBROBLAST; GENOMICS; HIGH THROUGHPUT SEQUENCING; HISTONE MODIFICATION; MOUSE; MYOBLAST; NONHUMAN; NUCLEAR LAMINA; TRANSCRIPTION INITIATION SITE;

MAMMALIA;

ANIMALS; CELL NUCLEUS; CHROMOSOME MAPPING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONES; MICE; MYOBLASTS; NIH 3T3 CELLS; NUCLEAR LAMINA; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION INITIATION SITE;

EID: 84883199983     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-591     Document Type: Article

References (41)

1. Akhtar A, Gasser SM. The nuclear envelope and transcriptional control. Nat Rev Genet 2007, 8(7):507-517. 10.1038/nrg2122, 17549064.
2. Dechat T, Pfleghaar K, Sengupta K, Shimi T, Shumaker DK, Solimando L, Goldman RD. Nuclear lamins: major factors in the structural organization and function of the nucleus and chromatin. Genes Dev 2008, 22(7):832-853. 10.1101/gad.1652708, 2732390, 18381888.
3. Kosak ST, Skok JA, Medina KL, Riblet R, Le Beau MM, Fisher AG, Singh H. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 2002, 296(5565):158-162. 10.1126/science.1068768, 11935030.
4. Takizawa T, Meaburn KJ, Misteli T. The meaning of gene positioning. Cell 2008, 135(1):9-13. 10.1016/j.cell.2008.09.026, 3478881, 18854147.
5. Meister P, Mango SE, Gasser SM. Locking the genome: nuclear organization and cell fate. Curr Opin Genet Dev 2011, 21(2):167-174. 10.1016/j.gde.2011.01.023, 21345665.
6. Finlan LE, Sproul D, Thomson I, Boyle S, Kerr E, Perry P, Ylstra B, Chubb JR, Bickmore WA. Recruitment to the nuclear periphery can alter expression of genes in human cells. PLoS Genet 2008, 4(3):e1000039. 10.1371/journal.pgen.1000039, 2265557, 18369458.
7. Kumaran RI, Spector DL. A genetic locus targeted to the nuclear periphery in living cells maintains its transcriptional competence. J Cell Biol 2008, 180(1):51-65. 10.1083/jcb.200706060, 2213611, 18195101.
8. Reddy KL, Zullo JM, Bertolino E, Singh H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature 2008, 452(7184):243-247. 10.1038/nature06727, 18272965.
9. Dialynas G, Speese S, Budnik V, Geyer PK, Wallrath LL. The role of Drosophila Lamin C in muscle function and gene expression. Development 2010, 137(18):3067-3077. 10.1242/dev.048231, 2926956, 20702563.
10. Geyer PK, Vitalini MW, Wallrath LL. Nuclear organization: taking a position on gene expression. Curr Opin Cell Biol 2011, 23(3):354-359. 10.1016/j.ceb.2011.03.002, 21450447.
11. Belmont AS, Zhai Y, Thilenius A. Lamin B distribution and association with peripheral chromatin revealed by optical sectioning and electron microscopy tomography. J Cell Biol 1993, 123(6 Pt 2):1671-1685. 2290888, 8276889.
12. Haithcock E, Dayani Y, Neufeld E, Zahand AJ, Feinstein N, Mattout A, Gruenbaum Y, Liu J. Age-related changes of nuclear architecture in Caenorhabditis elegans. Proc Natl Acad Sci USA 2005, 102(46):16690-16695. 10.1073/pnas.0506955102, 1283819, 16269543.
13. Taimen P, Pfleghaar K, Shimi T, Moller D, Ben-Harush K, Erdos MR, Adam SA, Herrmann H, Medalia O, Collins FS, et al. A progeria mutation reveals functions for lamin A in nuclear assembly, architecture, and chromosome organization. Proc Natl Acad Sci USA 2009, 106(49):20788-20793. 10.1073/pnas.0911895106, 2779830, 19926845.
14. Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008, 453(7197):948-951. 10.1038/nature06947, 18463634.
15. Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Graf S, Flicek P, Kerkhoven RM, van Lohuizen M, et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell 2010, 38(4):603-613. 10.1016/j.molcel.2010.03.016, 20513434.
16. Zullo JM, Demarco IA, Pique-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, et al. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell 2012, 149(7):1474-1487. 10.1016/j.cell.2012.04.035, 22726435.
17. Carmo-Fonseca M. The contribution of nuclear compartmentalization to gene regulation. Cell 2002, 108(4):513-521. 10.1016/S0092-8674(02)00650-5, 11909522.
18. Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326(5950):289-293. 10.1126/science.1181369, 2858594, 19815776.
19. Singer RH, Green MR. Compartmentalization of eukaryotic gene expression: causes and effects. Cell 1997, 91(3):291-294. 10.1016/S0092-8674(00)80411-0, 9363936.
20. Meldi L, Brickner JH. Compartmentalization of the nucleus. Trends Cell Biol 2011, 21(12):701-708. 10.1016/j.tcb.2011.08.001, 21900010.
21. Yao J, Tjian R. Sub-nuclear compartmentalization of core promoter factors and target genes. Cell Cycle 2011, 10(15):2405-2406. 10.4161/cc.10.15.16199, 21670597.
22. Singh K, Dilworth FJ. Redirecting traffic in the nucleus. Dev Cell 2011, 21(3):390-392. 10.1016/j.devcel.2011.08.025, 21920308.
23. Yao J, Fetter RD, Hu P, Betzig E, Tjian R. Subnuclear segregation of genes and core promoter factors in myogenesis. Genes Dev 2011, 25(6):569-580. 10.1101/gad.2021411, 3059831, 21357673.
24. Wang J, Kumar RM, Biggs VJ, Lee H, Chen Y, Kagey MH, Young RA, Abate-Shen C. The msx1 homeoprotein recruits polycomb to the nuclear periphery during development. Dev Cell 2011, 21(3):575-588. 10.1016/j.devcel.2011.07.003, 3673563, 21852201.
25. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010, 11(1):31-46. 10.1038/nrg2626, 19997069.
26. van Steensel B, Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 2000, 18(4):424-428. 10.1038/74487, 10748524.
27. Vogel MJ, Peric-Hupkes D, van Steensel B. Detection of in vivo protein-DNA interactions using DamID in mammalian cells. Nat Protoc 2007, 2(6):1467-1478. 10.1038/nprot.2007.148, 17545983.
28. Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 2009, 25(15):1952-1958. 10.1093/bioinformatics/btp340, 2732366, 19505939.
29. Qi HH, Sarkissian M, Hu GQ, Wang Z, Bhattacharjee A, Gordon DB, Gonzales M, Lan F, Ongusaha PP, Huarte M, et al. Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development. Nature 2010, 466(7305):503-507. 10.1038/nature09261, 3072215, 20622853.
30. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006. 186604, 12045153.
31. Chuang CH, Belmont AS. Moving chromatin within the interphase nucleus-controlled transitions?. Semin Cell Dev Biol 2007, 18(5):698-706. 10.1016/j.semcdb.2007.08.012, 2117624, 17905613.
32. Liu Y, Chu A, Chakroun I, Islam U, Blais A. Cooperation between myogenic regulatory factors and SIX family transcription factors is important for myoblast differentiation. Nucleic Acids Res 2010, 38(20):6857-6871. 10.1093/nar/gkq585, 2978361, 20601407.
33. Wu R, Terry AV, Singh PB, Gilbert DM. Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states. Mol Biol Cell 2005, 16(6):2872-2881. 10.1091/mbc.E04-11-0997, 1142431, 15788566.
34. Delest A, Sexton T, Cavalli G. Polycomb: a paradigm for genome organization from one to three dimensions. Curr Opin Cell Biol 2012, 24(3):405-414. 10.1016/j.ceb.2012.01.008, 22336329.
35. Asp P, Blum R, Vethantham V, Parisi F, Micsinai M, Cheng J, Bowman C, Kluger Y, Dynlacht BD. Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci USA 2011, 108(22):E149-E158. 10.1073/pnas.1102223108, 3107312, 21551099.
36. The ENCODE, Consortium P. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS biology 2011, 9(4):e1001046. 10.1371/journal.pbio.1001046, 3079585, 21526222.
37. ENCODE Caltech Histone Modification ChIP-seq. http://genome.ucsc.edu/cgi-bin/hgFileUi?db=mm9&g=wgEncodeCaltechHist.
38. Luo L, Gassman KL, Petell LM, Wilson CL, Bewersdorf J, Shopland LS. The nuclear periphery of embryonic stem cells is a transcriptionally permissive and repressive compartment. J Cell Sci 2009, 122(Pt 20):3729-3737. 2758804, 19773359.
39. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359. 10.1038/nmeth.1923, 3322381, 22388286.
40. Koehler R, Issac H, Cloonan N, Grimmond SM. The uniqueome: a mappability resource for short-tag sequencing. Bioinformatics 2011, 27(2):272-274. 10.1093/bioinformatics/btq640, 3018812, 21075741.
41. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC table browser data retrieval tool. Nucleic Acids Res 2004, 32(Database issue):D493-D496. 308837, 14681465.