Human transcriptional interactome of chromatin contribute to gene co-expression

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Dong, Xiao ^a,b   Li, Chao ^a,b,c   Chen, Yunqin ^d   Ding, Guohui ^a,e   Li, Yixue ^a,e  

^a Chinese Academy of Sciences   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^d TONGJI UNIVERSITY   (China)

^e SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; GENE; GENE EXPRESSION; GENE FUNCTION; GENOMICS; HUMAN GENOME; TRANSCRIPTION REGULATION; TRANSCRIPTIONAL INTERACTOME; CONFORMATION; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; HUMAN; HUMAN CHROMOSOME; METABOLISM; PROTEIN BINDING;

CHROMATIN; CHROMOSOMES, HUMAN; GENE EXPRESSION REGULATION; HUMANS; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 78649983246     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-704     Document Type: Article

References (19)

1. Dekker J, Rippe K, Dekker M, Kleckner N. Capturing chromosome conformation. Science 2002, 295(5558):1306-1311. 10.1126/science.1067799, 11847345.
2. Fraser P, Bickmore W. Nuclear organization of the genome and the potential for gene regulation. Nature 2007, 447(7143):413-417. 10.1038/nature05916, 17522674.
3. Schoenfelder S, Clay I, Fraser P. The transcriptional interactome: gene expression in 3D. Current Opinion in Genetics & Development 2010, 20(2):127-133.
4. Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, et al. Active genes dynamically colocalize to shared sites of ongoing transcription. Nature Genet 2004, 36(10):1065-1071. 10.1038/ng1423, 15361872.
5. Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nature Genet 2010, 42(1):53-U71. 10.1038/ng.496, 20010836.
6. Misteli T, Caceres JF, Spector DL. The dynamics of a pre-mRNA splicing factor in living cells. Nature 1997, 387(6632):523-527. 10.1038/387523a0, 9168118.
7. Lamond AI, Spector DL. Nuclear speckles: A model for nuclear organelles. Nat Rev Mol Cell Biol 2003, 4(8):605-612. 10.1038/nrm1172, 12923522.
8. Brown JM, Green J, das Neves RP, Wallace HAC, Smith AJH, Hughes J, Gray N, Taylor S, Wood WG, Higgs DR, et al. Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol 2008, 182(6):1083-1097. 10.1083/jcb.200803174, 2542471, 18809724.
9. Lawrence JB, Clemson CM. Gene associations: true romance or chance meeting in a nuclear neighborhood?. J Cell Biol 2008, 182(6):1035-1038. 10.1083/jcb.200808121, 2542465, 18809719.
10. 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.
11. Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K. COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res 2008, 36:D77-D82. 10.1093/nar/gkm840, 2238883, 17932064.
12. Batada NN, Urrutia AO, Hurst LD. Chromatin remodelling is a major source of coexpression of linked genes in yeast. Trends Genet 2007, 23(10):480-484. 10.1016/j.tig.2007.08.003, 17822800.
13. Zheng GY, Tu K, Yang Q, Xiong Y, Wei CC, Xie L, Zhu YY, Li YX. ITFP: an integrated platform of mammalian transcription factors. Bioinformatics 2008, 24(20):2416-2417. 10.1093/bioinformatics/btn439, 18713790.
14. Wang JZ, Du ZD, Payattakool R, Yu PS, Chen CF. A new method to measure the semantic similarity of GO terms. Bioinformatics 2007, 23(10):1274-1281. 10.1093/bioinformatics/btm087, 17344234.
15. Yu GC, Li F, Qin YD, Bo XC, Wu YB, Wang SQ. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 2010, 26(7):976-978. 10.1093/bioinformatics/btq064, 20179076.
16. Ragoczy T, Bender MA, Telling A, Byron R, Groudine M. The locus control region is required for association of the murine beta-globin locus with engaged transcription factories during erythroid maturation. Genes Dev 2006, 20(11):1447-1457. 10.1101/gad.1419506, 1475758, 16705039.
17. Chubb JR, Trcek T, Shenoy SM, Singer RH. Transcriptional pulsing of a developmental gene. Curr Biol 2006, 16(10):1018-1025. 10.1016/j.cub.2006.03.092, 16713960.
18. Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, van Steensel B, de Laat W. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nature Genet 2006, 38(11):1348-1354. 10.1038/ng1896, 17033623.
19. Cohen BA, Mitra RD, Hughes JD, Church GM. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nature Genet 2000, 26(2):183-186. 10.1038/79896, 11017073.