Islands of co-expressed neighbouring genes in Arabidopsis thaliana suggest higher-order chromosome domains

Plant Journal

Volumn 45, Issue 3, 2006, Pages 347-357

  Zhan, Shuhua ^a   Horrocks, Julie ^a   Lukens, Lewis N ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

Arabidopsis thaliana; Chromatin domains; Gene regulation

Indexed keywords

CHROMOSOMES; PLANTS (BOTANY);

ARABIDOPSIS THALIANA; CHROMATIN DOMAINS; GENE REGULATION;

GENES;

ARABIDOPSIS; ARTICLE; DNA MICROARRAY; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; PLANT CHROMOSOME; SEQUENCE HOMOLOGY; ULTRASTRUCTURE;

ARABIDOPSIS; CHROMOSOMES, PLANT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY, NUCLEIC ACID;

GENES; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA;

EID: 33644871314     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2005.02619.x     Document Type: Article

References (44)

1. Allocco D.J. Kohane I.S. Butte A.J. 2004 Quantifying the relationship between co-expression, co-regulation, and gene function BMC Bioinformatics 5 18
2. Arnholdt-Schmitt B. 2004 Stress-induced cell reprogramming. A role for global genome regulation? Plant Physiol. 136 2579 2586
3. Bell A.C. Felsenfeld G. 2000 Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene Nature 405 482 485
4. Biehl A. Richly E. Noustos C. Salamani F. Leister D. 2005 Analysis of 101 nuclear transcriptomes reveals 23 distinct regulons and their relationships to metabolism, chromosomal distribution, and co-ordination of nuclear and plastid gene expression Gene 344 33 41
5. Birnbaum K. Shasha D.E. Wang J.Y. Jung J.W. Lambert G.M. Galbraith D.W. Benfey P.N. 2003 A gene expression map of the Arabidopsis root Science 302 1956 1960
6. Borevitz J.O. Ecker J.R. 2004 Plant genomics: the third wave Annu. Rev. Genomics Hum. Genet. 5 443 477
7. Caron H. van Schaik B. van der Mee M. et al. 2001 The human transcriptome map: clustering of highly expressed genes in chromosomal domains Science 291 1289 1292
8. Cohen B.A. Mitra R.D. Hughes J.F. Church G.M. 2000 A computational analysis of whole-genome expression data reveals chromosome domains of gene expression Nat. Genet. 26 183 186
9. Cook R.D. Weisberg S. 1999 Applied Regression Including Computing and Graphics Toronto, Canada John Wiley pp 56 78
10. Emerson B.M. 2002 Specificity of gene regulation Cell 109 267 270
11. Felsenfeld G. 1996 Chromatin unfolds Cell 86 13 19
12. Finnegan E.J. Sheldon C. Jardinaud F. Peacock W.J. Dennis E. 2004 A cluster of Arabidopsis genes with a coordinate response to an environmental stimulus Curr. Biol. 14 911 916
13. Fransz P. de Jong J.H. Lysak M. Castiglione M.R. Schubert I. 2002 Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate Proc. Natl Acad. Sci. USA 99 14584 14589
14. Fransz P. Soppe W. Schubert I. 2003 Heterochromatin in interphase nuclei of Arabidopsis thaliana Chromosome Res. 11 227 240
15. Freiman R. Albright S.R. Zheng S. Sha W. Hammer R. Tjian R. 2001 Requirement of tissue-selective TBP-associated factor TAFII105 in ovarian development Science 293 2084 2087
16. Gerasimova T.I. Byrd K. Corces V.G. 2000 A chromatin insulator determines the nuclear localization of DNA Mol. Cell 6 1025 1035
17. Grewal S.I.S. Moazed D. 2003 Heterochromatin and epigenetic control of gene expression Science 301 798 802
18. Hark A.T. Schoenherr C.J. Katz D.J. Ingram R.S. Levorse J.M. Tilghman S.M. 2000 CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus Nature 405 486 489
19. Hsieh T.-F. Fischer R.L. 2005 Biology of chromatin dynamics Annu. Rev. Plant. Biol. 56 327 351
20. Kraakman H.W. Mager L.S. Nieuwint K.T. Planta R.J. 1989 The divergently transcribed genes encoding yeast ribosomal proteins L46 and S24 are activated by shared RPG-boxes Nucleic Acids Res. 17 9693 9706
21. Lercher M.J. Urrutia A.O. Hurst L.D. 2002 Clustering of house keeping genes provides a unified model of gene order in the human genome Nat. Genet. 31 180 183
22. Lercher M.J. Blumenthal T. Hurst L.D. 2003 Co-expression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes Genome Res. 13 238 243
23. Litt M.D. Simpson M. Gaszner M. Allis C.D. Felsenfeld G. 2001 Correlation between histone lysine methylation and developmental changes at the chicken β-globin locus Science 293 2453 2455
24. Ma L. Sun N. Liu X. Jiao Y. Zhao H. Deng X.W. 2005 Organ-specific expression of the Arabidopsis genome during development Plant Physiol. 138 80 91
25. Mutskov V.J. Farrell C.M. Wade P.A. Wolffe A.P. Felsenfeld G. 2002 The barrier function of an insulator couples high histone acetylation levels with specific protection of promoter DNA from methylation Genes Dev. 16 1540 1554
26. Noma K. Allis C.D. Grewal S.I.S. 2001 Transitions in distinct histone H3 patterns at the heterochromatin domain boundaries Science 293 1150 1155
27. R Development Core Team 2004 r : A language and environment for statistical computing Vienna, Austria R Foundation for Statistical Computing
28. Redman J. Haas B. Tanimoto G. Town C.D. 2004 Development and evaluation of an Arabidopsis whole genome Affymetrix probe array Plant J. 38 545 561
29. Ren X. Fiers M. Stiekema W. Nap J. 2005 Local coexpression domains of two to four genes in the genome of Arabidopsis Plant Physiol. 138 923 934
30. Roy P.J. Stuart J.M. Lund J. Kim S.K. 2002 Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans Nature 418 975 979
31. Schmid M. Davison T. Henz S. Pape U. Demar M. Vingron M. Scholkopf B. Weigel D. Lohmann J. 2005 A gene expression map of Arabidopsis thaliana development Nat. Genet. 37 501 506
32. Shin R. Kim M.J. Paek K.-H. 2003 The CaTin1 (Capsicum annuum TMV-induced Clone 1) and CaTin1-2 genes are linked head-to-head and share a bidirectional promoter Plant Cell Physiol. 44 549 554
33. Soppe W.J.J. Jasencakova Z. Houben A. Kakutani T. Meister A. Huang M.S. Jacobsen S.E. Schubert I. Fransz P.F. 2002 DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis EMBO J. 21 6549 6559
34. Spellman P.T. Rubin G.M. 2002 Evidence for large domains of similarly expressed genes in the Drosophila genome J. Biol. 1 5.1 5.8
35. Stolc V. Gauhar Z. Mason C. et al. 2004 A gene expression map for the euchromatic genome of Drosophila melanogaster Science 306 655 660
36. Su R.-C. Brown K.E. Saaber S. Fisher A.G. Merkenschlager M. Smale S.T. 2004 Dynamic assembly of silent chromatin during thymocyte maturation Nat. Genet. 36 502 506
37. Udvardy A. Maine E. Schedl P. 1985 The 87A7 chromomere identification of novel chromatin structures flanking the heat shock locus that may define the boundaries of higher order domains J. Mol. Biol. 185 341 358
38. Vermaak D. Ahmad K. Henikoff S. 2003 Maintenance of chromatin states: an open-and-shut case opinion Curr. Opin. Cell Biol. 15 266 274
39. Volpi E.V. Chevret E. Jones T. et al. 2000 Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response interferon in interphase nuclei J. Cell Sci. 113 1565 1567
40. Weisbrod S. 1982 Active chromatin Nature 297 289 295
41. Williams E.J.B. Bowles D.J. 2004 Co-expression of neighboring genes in the genome of Arabidopsis thaliana Genome Res. 14 1060 1067
42. Xie M. He Y. Gan S. 2001 Bidirectionalization of polar promoters in plants Nat. Biotechnol. 19 677 679
43. Xu W. Chen H. Du K. Asahara H. Tini M. Emerson B. Montminy M. Evans R.M. 2001 A transcriptional switch mediated by cofactor methylation Science 294 2507 2510
44. Yasui D. Miyano S. Cai S. Varga-Weisz P. Kohwi-Shigematsu T. 2002 SATB1 targets chromatin remodelling to regulate genes over long distances Nature 419 641 645