Chromosomal clustering of a human transcriptome reveals regulatory background

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Vogel, Jan H ^a   von Heydebreck, Anja ^a   Purmann, Antje ^a   Sperling, Silke ^a  

^a MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; BIOLOGICAL IMPLICATIONS; FUNCTIONAL CLASSIFICATION; GENOMIC ORGANIZATION; LINEAR ARRANGEMENTS; NUCLEAR ORGANIZATION; SMALL CLUSTERS; TRANSCRIPTIONAL REGULATION;

TRANSCRIPTION FACTORS;

GENES;

GENE PRODUCT; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ARTICLE; CELL NUCLEUS; CHROMOSOME ANALYSIS; CLUSTER ANALYSIS; CONTROLLED STUDY; DNA STRUCTURE; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENETIC ANALYSIS; GENOME; HEART; HOUSEKEEPING GENE; HUMAN; TRANSCRIPTION REGULATION; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; CHROMOSOME MAP; GENE ORDER; GENETICS; HEART MUSCLE; METABOLISM; MULTIGENE FAMILY; PHYSIOLOGY;

EUKARYOTA;

BINDING SITES; CHROMOSOME MAPPING; GENE EXPRESSION; GENE ORDER; HUMANS; MODELS, BIOLOGICAL; MULTIGENE FAMILY; MYOCARDIUM; TRANSCRIPTION FACTORS;

EID: 25444516785     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-230     Document Type: Article

References (31)

1. van Driel R, Fransz PF, Verschure PJ: The eukaryotic genome: a system regulated at different hierarchical levels. J Cell Sci 2003, 116(Pt 20):4067-4075.
2. Hurst LD, Pal C, Lercher MJ: The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 2004, 5(4):299-310.
3. Hershberg R, Yeger-Lotem E, Margalit H: Chromosomal organization is shaped by the transcription regulatory network. Trends Genet 2005, 21(3):138-142.
4. Grewal SI, Moazed D: Heterochromatin and epigenetic control of gene expression. Science 2003, 301(5634):798-802.
5. Brown KE: Chromatin folding and gene expression: new tools to reveal the spatial organization of genes. Chromosome Res 2003, 11(5):423-433.
6. Stein GS, Lian JB, Montecino M, Stein JL, van Wijnen AJ, Javed A, Pratap J, Choi J, Zaidi SK, Gutierrez S, Harrington K, Shen J, Young D, Pockwinse S: Nuclear microenvironments support physiological control of gene expression. Chromosome Res 2003, 11(5):527-536.
7. Lawrence JG: Shared strategies in gene organization among prokaryotes and eukaryotes. Cell 2002, 110(4):407-413.
8. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, Wodicka L, Wolfsberg TG, Gabrielian AE, Landsman D, Lockhart DJ, Davis RW: A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 1998, 2(1):65-73.
9. Cohen BA, Mitra RD, Hughes JD, Church GM: A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet 2000, 26(2):183-186.
10. Roy PJ, Stuart JM, Lund J, Kim SK: Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 2002, 418(6901):975-979.
11. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI: Large clusters of co-expressed genes in the Drosophila genome. Nature 2002, 420(6916):666-669.
12. Spellman PT, Rubin GM: Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 2002, 1(1):5.
13. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A, Versteeg R: The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 2001, 291(5507):1289-1292.
14. Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 2002, 31(2):180-183.
15. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB: A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 2004, 101(16):6062-6067.
16. Schubeler D, Francastel C, Cimbora DM, Reik A, Martin DI, Groudine M: Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human beta-globin locus. Genes Dev 2000, 14(8):940-950.
17. Yamashita M, Ukai-Tadenuma M, Kimura M, Omori M, Inami M, Taniguchi M, Nakayama T: Identification of a conserved GATA3 response element upstream proximal from the interleukin-13 gene locus. J Biol Chem 2002, 277(44):42399-42408.
18. Choudhary SK, Wykes SM, Kramer JA, Mohamed AN, Koppitch F, Nelson JE, Krawetz SA: A haploid expressed gene cluster exists as a single chromatin domain in human sperm. J Biol Chem 1995, 270(15):8755-8762.
19. Kalmykova AI, Nurminsky DI, Ryzhov DV, Shevelyov YY: Regulated chromatin domain comprising cluster of co-expressed genes in Drosophila melanogaster. Nucleic Acids Res 2005, 33(5):1435-1444.
20. Lawson GM, Knoll BJ, March CJ, Woo SL, Tsai MJ, O'Malley BW: Definition of 5′ and 3′ structural boundaries of the chromatin domain containing the ovalbumin multigene family. J Biol Chem 1982, 257(3):1501-1507.
21. Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P: Coexpression analysis of human genes across many microarray data sets. Genome Res 2004, 14(6):1085-1094.
22. Kaynak B, von Heydebreck A, Mebus S, Seelow D, Hennig S, Vogel J, Sperling HP, Pregla R, Alexi-Meskishvili V, Hetzer R, Lange PE, Vingron M, Lehrach H, Sperling S: Genome-wide array analysis of normal and malformed human hearts. Circulation 2003, 107(19):2467-2474.
23. Dieterich C, Wang H, Rateitschak K, Luz H, Vingron M: CORG: a database for COmparative Regulatory Genomics. Nucleic Acids Res 2003, 31(1):55-57.
24. DeKoter RP, Singh H: Regulation of B lymphocyte and macrophage development by graded expression of PU.1. Science 2000, 288(5470):1439-1441.
25. Lundgren M, Chow CM, Sabbattini P, Georgiou A, Minaee S, Dillon N: Transcription factor dosage affects changes in higher order chromatin structure associated with activation of a heterochromatic gene. Cell 2000, 103(5):733-743.
26. Wallin JJ, Gackstetter ER, Koshland ME: Dependence of BSAP repressor and activator functions on BSAP concentration. Science 1998, 279(5358):1961-1964.
27. Bortoluzzi S, Rampoldi L, Simionati B, Zimbello R, Barbon A, d'Alessi F, Tiso N, Pallavicini A, Toppo S, Cannata N, Valle G, Lanfranchi G, Danieli GA: A comprehensive, high-resolution genomic transcript map of human skeletal muscle. Genome Res 1998, 8(8):817-825.
28. Gabrielsson BL, Carlsson B, Carlsson LM: Partial genome scale analysis of gene expression in human adipose tissue using DNA array. Obes Res 2000, 8(5):374-384.
29. Barrans JD, Ip J, Lam CW, Hwang IL, Dzau VJ, Liew CC: Chromosomal distribution of the human cardiovascular transcriptome. Genomics 2003, 81(5):519-524.
30. Dempsey AA, Pabalan N, Tang HC, Liew CC: Organization of human cardiovascular-expressed genes on chromosomes 21 and 22. J Mol Cell Cardiol 2001, 33(3):587-591.
31. Kluger Y, Yu H, Qian J, Gerstein M: Relationship between gene co-expression and probe localization on microarray slides. BMC Genomics 2003, 4(1):49.