Neighbourhood continuity is not required for correct testis gene expression in Drosophila

PLoS Biology

Volumn 8, Issue 11, 2010, Pages

  Meadows, Lisa A ^a,b   Chan, Yuk Sang ^a   Roote, John ^a   Russell, Steven ^a,b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME INVERSION; CHROMOSOME MAP; CONTROLLED STUDY; DROSOPHILA; GENE EXPRESSION PROFILING; GENE INTERACTION; GENE LOCATION; GENE SEQUENCE; GENETIC ORGANIZATION; HUMAN GENOME; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; QUANTITATIVE STUDY; REAL TIME POLYMERASE CHAIN REACTION; TESTIS; ANIMAL; DNA MICROARRAY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION REGULATION; GENETICS; MALE; METABOLISM; POLYMERASE CHAIN REACTION; SPERMATOCYTE;

EUKARYOTA;

ANIMALS; DROSOPHILA; GENE EXPRESSION REGULATION; IN SITU HYBRIDIZATION, FLUORESCENCE; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; SPERMATOCYTES; TESTIS;

EID: 78649931868     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.1000552     Document Type: Article

References (80)

1. Milot E, Strouboulis J, Trimborn T, Wijgerde M, de Boer E, et al. (1996) Heterochromatin effects on the frequency and duration of LCR-mediated gene transcription. Cell 87: 105-114.
2. Gierman HJ, Indemans MH, Koster J, Goetze S, Seppen J, et al. (2007) Domain-wide regulation of gene expression in the human genome. Genome Res 17: 1286-1295.
3. Csink AK, Bounoutas A, Griffith ML, Sabl JF, Sage BT (2002) Differential gene silencing by trans-heterochromatin in Drosophila melanogaster. Genetics 160: 257-269.
4. Cho RJ, Campbell MJ, Winzeler EA, Steinmetz L, Conway A, et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2: 65-73.
5. 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.
6. Kruglyak S, Tang H (2000) Regulation of adjacent yeast genes. Trends Genet 16: 109-111.
7. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, et al. (2003) A gene expression map of the Arabidopsis root. Science 302: 1956-1960.
8. Williams EJ, Bowles DJ (2004) Coexpression of neighboring genes in the genome of Arabidopsis thaliana. Genome Res 14: 1060-1067.
9. Blumenthal T (1998) Gene clusters and polycistronic transcription in eukaryotes. Bioessays 20: 480-487.
10. Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418: 975-979.
11. Lercher MJ, Blumenthal T, Hurst LD (2003) Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res 13: 238-243.
12. Chen N, Stein LD (2006) Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. Genome Res 16: 606-617.
13. Boutanaev AM, Kalmykova AI, Shevelyov YY, Nurminsky DI (2002) Large clusters of co-expressed genes in the Drosophila genome. Nature 420: 666-669.
14. Spellman PT, Rubin GM (2002) Evidence for large domains of similarly expressed genes in the Drosophila genome. J Biol 1: 5.
15. Thygesen HH, Zwinderman AH (2005) Modelling the correlation between the activities of adjacent genes in Drosophila. BMC Bioinformatics 6: 10.
16. Mezey JG, Nuzhdin SV, Ye F, Jones CD (2008) Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome. BMC Evol Biol 8: 2.
17. Ko MS, Threat TA, Wang X, Horton JH, Cui Y, et al. (1998) Genome-wide mapping of unselected transcripts from extraembryonic tissue of 7.5-day mouse embryos reveals enrichment in the t-complex and under-representation on the X chromosome. Hum Mol Genet 7: 1967-1978.
18. Li Q, Lee BT, Zhang L (2005) Genome-scale analysis of positional clustering of mouse testis-specific genes. BMC Genomics 6: 7.
19. Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science 291: 1289-1292.
20. Lercher MJ, Urrutia AO, Hurst LD (2002) Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet 31: 180-183.
21. Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, et al. (2003) The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res 13: 1998-2004.
22. Lee JM, Sonnhammer EL (2003) Genomic gene clustering analysis of pathways in eukaryotes. Genome Res 13: 875-882.
23. Parisi M, Nuttall R, Edwards P, Minor J, Naiman D, et al. (2004) A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. Genome Biol 5: R40.
24. Parisi M, Nuttall R, Naiman D, Bouffard G, Malley J, et al. (2003) Paucity of genes on the Drosophila X chromosome showing male-biased expression. Science 299: 697-700.
25. Zhang Y, Sturgill D, Parisi M, Kumar S, Oliver B (2007) Constraint and turnover in sex-biased gene expression in the genus Drosophila. Nature 450: 233-238.
26. Jin W, Riley R, Wolfinger R, White K, Passador-Gurgel G, et al. (2001) The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nature Genetics 29: 389-395.
27. Baker DA, Meadows LA, Wang J, Dow JA, Russell S (2007) Variable sexually dimorphic gene expression in laboratory strains of Drosophila melanogaster. BMC Genomics 8: 454.
28. Innocenti P, Morrow E (2010) The sexually antogonistic genes of Drosophila melanogaster. PLoS Biology 8: e1000335. doi:10.1371/journal.pbio.1000335.
29. Hurst LD, Williams EJ, Pal C (2002) Natural selection promotes the conservation of linkage of co-expressed genes. Trends Genet 18: 604-606.
30. Ranz JM, Maurin D, Chan YS, von Grotthuss M, Hillier LW, et al. (2007) Principles of genome evolution in the Drosophila melanogaster species group. PLoS Biol 5: e152. doi:10.1371/journal.pbio.0050152.
31. Singer GA, Lloyd AT, Huminiecki LB, Wolfe KH (2005) Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. Mol Biol Evol 22: 767-775.
32. Semon M, Duret L (2006) Evolutionary origin and maintenance of coexpressed gene clusters in mammals. Mol Biol Evol 23: 1715-1723.
33. Nie H, Crooijmans RP, Bastiaansen JW, Megens HJ, Groenen MA (2010) Regional regulation of transcription in the chicken genome. BMC Genomics 11: 28.
34. Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, et al. (2004) A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306: 655-660.
35. Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, et al. (2008) Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes. Genetics 179: 1657-1680.
36. Oliver B, Parisi M, Clark D (2002) Gene expression neighborhoods. J Biol 1: 4.
37. Hurst LD, Pal C, Lercher MJ (2004) The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet 5: 299-310.
38. Kosak ST, Groudine M (2004) Gene order and dynamic domains. Science 306: 644-647.
39. Oliver B, Misteli T (2005) A non-random walk through the genome. Genome Biol 6: 214.
40. Purmann A, Toedling J, Schueler M, Carninci P, Lehrach H, et al. (2007) Genomic organization of transcriptomes in mammals: coregulation and cofunctionality. Genomics 89: 580-587.
41. Meiklejohn CD, Parsch J, Ranz JM, Hartl DL (2003) Rapid evolution of male-biased gene expression in Drosophila. Proc Natl Acad Sci USA 100: 9894-9899.
42. Chintapalli VR, Wang J, Dow JA (2007) Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet 39: 715-720.
43. Ryder E, Ashburner M, Bautista-Llacer R, Drummond J, Webster J, et al. (2007) The DrosDel deletion collection: a Drosophila genomewide chromosomal deficiency resource. Genetics 177: 615-629.
44. Ryder E, Blows F, Ashburner M, Bautista-Llacer R, Coulson D, et al. (2004) The DrosDel collection: a set of P-element insertions for generating custom chromosomal aberrations in Drosophila melanogaster. Genetics 167: 797-813.
45. Ashburner M, Golic KC, Hawley RS (2005) Drosophila: a laboratory handbook. New York: Cold Spring Harbor Laboratory Press.
46. Zeitouni B, Senatore S, Severac D, Aknin C, Semeriva M, et al. (2007) Signalling pathways involved in adult heart formation revealed by gene expression profiling in Drosophila. PLoS Genet 3: 1907-1921. doi:10.1371/ journal.pgen.0030174.
47. Lee TI, Young RA (2000) Transcription of eukaryotic protein-coding genes. Annu Rev Genet 34: 77-137.
48. van Driel R, Fransz PF, Verschure PJ (2003) The eukaryotic genome: a system regulated at different hierarchical levels. J Cell Sci 116: 4067-4075.
49. Jiang Y, Bressler J, Beaudet A (2004) Epigenetics and human disease. Annu Rev Genomics Hum Genet 5: 479-510.
50. Babu M, Janga S, de Santiago I, Pombo A (2008) Eukaryotic gene regulation in three dimensions and its impact on genome evolution. Curr Opin Genet Dev 18: 571-582.
51. Branco M, Pombo A (2007) Chromosome organization: new facts, new models. Trends Cell Biol 17: 127-134.
52. De S, Babu M (2010) Genomic neighbourhood and the regulation of gene expression. Curr Opin Cell Biol 22: 326-333.
53. Cajiao I, Zhang A, Yoo EJ, Cooke NE, Liebhaber SA (2004) Bystander gene activation by a locus control region. EMBO J 23: 3854-3863.
54. Ebisuya M, Yamamoto T, Nakajima M, Nishida E (2008) Ripples from neighbouring transcription. Nat Cell Biol 10: 1106-1113.
55. 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.
56. Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl 1: S96-S104.
57. Sproul D, Gilbert N, Bickmore WA (2005) The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet 6: 775-781.
58. Kouzarides T (2007) Chromatin modifications and their function. Cell 128: 693-705.
59. Rando OJ, Chang HY (2009) Genome-wide views of chromatin structure. Annu Rev Biochem 78: 245-271.
60. Wei GH, Liu DP, Liang CC (2005) Chromatin domain boundaries: insulators and beyond. Cell Res 15: 292-300.
61. Negre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, et al. (2010) A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet 6: e1000814. doi:10.1371/journal.pgen.1000814.
62. Fraser P, Bickmore W (2007) Nuclear organization of the genome and the potential for gene regulation. Nature 447: 413-417.
63. Kumaran RI, Thakar R, Spector DL (2008) Chromatin dynamics and gene positioning. Cell 132: 929-934.
64. Brown JM, Leach J, Reittie JE, Atzberger A, Lee-Prudhoe J, et al. (2006) Coregulated human globin genes are frequently in spatial proximity when active. J Cell Biol 172: 177-187.
65. Brown JM, Green J, das Neves RP, Wallace HA, Smith AJ, et al. (2008) Association between active genes occurs at nuclear speckles and is modulated by chromatin environment. J Cell Biol 182: 1083-1097.
66. Kuroda M, Tanabe H, Yoshida K, Oikawa K, Saito A, et al. (2004) Alteration of chromosome positioning during adipocyte differentiation. J Cell Sci 117: 5897-5903.
67. Pai DA, Engelke DR (2010) Spatial organization of genes as a component of regulated expression. Chromosoma 119: 13-25.
68. Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, et al. (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36: 1065-1071.
69. Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, et al. (2007) Myc dynamically and preferentially relocates to a transcription factory occupied by Igh. PLoS Biol 5: e192. doi:10.1371/journal.pbio.0050192.
70. Janssen S, Cuvier O, Muller M, Laemmli UK (2000) Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster. Mol Cell 6: 1013-1024.
71. Liu X, Wu B, Szary J, Kofoed EM, Schaufele F (2007) Functional sequestration of transcription factor activity by repetitive DNA. J Biol Chem 282: 20868-20876.
72. Chen X, Hiller M, Sancak Y, Fuller M (2005) Tissue-specific TAFs counteract polycomb to turn on terminal differentiation. Science 310: 869-872.
73. Hiller M, Chen X, Pringle M, Suchorolski M, Sancak Y, et al. (2004) Testis-specific TAF homologs collaborate to control a tissue-specific transcription program. Development 131: 5297-5308.
74. White-Cooper H (2010) Molecular mechanisms of gene regulation during Drosophila spermatogenesis. Reproduction 139: 11-21.
75. Hammoud S, Nix D, Zhang H, Purwar J, Carrell D, et al. (2009) Distinctive chromatin in human sperm packages genes for embryo development. Nature 460: 473-479.
76. Kolthur-Seetharam U, Martianov I, Davidson I (2008) Specialization of the general transcriptional machinery in male germ cells. Cell Cycle 7: 3493-3498.
77. Buhler J, Ideker T, Haynor D (2000) Dapple: improved techniques for finding spots on DNA microarrays. UW CSE Technical Report UWTR 2000-08-05.
78. Baldi P, Long AD (2001) A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 17: 509-519.
79. Lyne R, Smith R, Rutherford K, Wakeling M, Varley A, et al. (2007) FlyMine: an integrated database for Drosophila and Anopheles genomics. Genome Biol 8: R129.
80. Bantignies F, Grimaud C, Lavrov S, Gabut M, Cavalli G (2003) Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev 17: 2406-2420.