Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast

Genomics

Volumn 96, Issue 6, 2010, Pages 352-361

  Su, Chien Hao ^a,b   Shih, Ching Hua ^a   Chang, Tien Hsien ^c,d   Tsai, Huai Kuang ^a,e  

^a INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

^b NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^c OHIO STATE UNIVERSITY   (United States)

^d GENOMICS RESEARCH CENTER   (Taiwan)

^e RESEARCH CENTER FOR INFORMATION TECHNOLOGY INNOVATION   (Taiwan)

Author keywords

Cis regulatory modules; Divergent gene pairs; Regulatory mechanisms; Transcription factor binding sites; Yeast

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CHROMOSOME PAIRING; COMPUTER MODEL; CONTROLLED STUDY; FUNGAL GENETICS; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; KNOCKOUT GENE; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM; SACCHAROMYCES CEREVISIAE;

BINDING SITES; COMPUTATIONAL BIOLOGY; ENHANCER ELEMENTS, GENETIC; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENOME, FUNGAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

SACCHAROMYCETALES;

EID: 78449262087     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.08.008     Document Type: Article

References (54)

1. Johnston M., Davis R.W. Sequences that regulate the divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol. Cell. Biol. 1984, 4:1440-1448.
2. Trinklein N.D., Aldred S.F., Hartman S.J., Schroeder D.I., Otillar R.P., Myers R.M. An abundance of bidirectional promoters in the human genome. Genome Res. 2004, 14:62-66.
3. Chen N., Stein L.D. Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. Genome Res. 2006, 16:606-617.
4. Engstrom P.G., Suzuki H., Ninomiya N., Akalin A., Sessa L., Lavorgna G., Brozzi A., Luzi L., Tan S.L., Yang L., Kunarso G., Ng E.L., Batalov S., Wahlestedt C., Kai C., Kawai J., Carninci P., Hayashizaki Y., Wells C., Bajic V.B., Orlando V., Reid J.F., Lenhard B., Lipovich L. Complex loci in human and mouse genomes. PLoS Genet. 2006, 2:e47.
5. Li Y.Y., Yu H., Guo Z.M., Guo T.Q., Tu K., Li Y.X. Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput. Biol. 2006, 2:e74.
6. Kruglyak S., Tang H. Regulation of adjacent yeast genes. Trends Genet. 2000, 16:109-111.
7. Thomas B. Gene clusters and polycistronic transcription in eukaryotes. BioEssays 1998, 20:480-487.
8. Travers M.T., Cambot M., Kennedy H.T., Lenoir G.M., Barber M.C., Joulin V. Asymmetric expression of transcripts derived from the shared promoter between the divergently oriented ACACA and TADA2L genes. Genomics 2005, 85:71-84.
9. Lin J.M., Collins P.J., Trinklein N.D., Fu Y., Xi H., Myers R.M., Weng Z. Transcription factor binding and modified histones in human bidirectional promoters. Genome Res. 2007, 17:818-827.
10. Zanotto E., Shah Z.H., Jacobs H.T. The bidirectional promoter of two genes for the mitochondrial translational apparatus in mouse is regulated by an array of CCAAT boxes interacting with the transcription factor NF-Y. Nucleic Acids Res. 2007, 35:664-677.
11. Cooper S.J., Trinklein N.D., Anton E.D., Nguyen L., Myers R.M. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res. 2006, 16:1-10.
12. Collins P.J., Kobayashi Y., Nguyen L., Trinklein N.D., Myers R.M. The ets-related transcription factor GABP directs bidirectional transcription. PLoS Genet. 2007, 3:e208.
13. Kensche P.R., Oti M., Dutilh B.E., Huynen M.A. Conservation of divergent transcription in fungi. Trends Genet. 2008, 24:207-211.
14. Hurst L.D., Williams E.J., Pal C. Natural selection promotes the conservation of linkage of co-expressed genes. Trends Genet. 2002, 18:604-606.
15. Cohen B.A., Mitra R.D., Hughes J.D., Church G.M. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet. 2000, 26:183-186.
16. Tsai H.K., Su C.P., Lu M.Y., Shih C.H., Wang D. Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system. BMC Genomics 2007, 8:352.
17. Yanai I., Hunter C.P. Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved. Genome Res. 2009, 19:2214-2220.
18. MacIsaac K.D., Wang T., Gordon D.B., Gifford D.K., Stormo G.D., Fraenkel E. An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinform. 2006, 7:113.
19. Harbison C.T., Gordon D.B., Lee T.I., Rinaldi N.J., Macisaac K.D., Danford T.W., Hannett N.M., Tagne J.B., Reynolds D.B., Yoo J., Jennings E.G., Zeitlinger J., Pokholok D.K., Kellis M., Rolfe P.A., Takusagawa K.T., Lander E.S., Gifford D.K., Fraenkel E., Young R.A. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431:99-104.
20. Tsai H.K., Chou M.Y., Shih C.H., Huang G.T., Chang T.H., Li W.H. MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Res. 2007, 35:W221-W226.
21. Dobi K.C., Winston F. Analysis of transcriptional activation at a distance in Saccharomyces cerevisiae. Mol. Cell. Biol. 2007, 27:5575-5586.
22. Hong E.L., Balakrishnan R., Dong Q., Christie K.R., Park J., Binkley G., Costanzo M.C., Dwight S.S., Engel S.R., Fisk D.G., Hirschman J.E., Hitz B.C., Krieger C.J., Livstone M.S., Miyasato S.R., Nash R.S., Oughtred R., Skrzypek M.S., Weng S., Wong E.D., Zhu K.K., Dolinski K., Botstein D., Cherry J.M. Gene ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res. 2008, 36:D577-D581.
23. Pilpel Y., Sudarsanam P., Church G.M. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet. 2001, 29:153-159.
24. Lapidot M., Pilpel Y. Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. Nucleic Acids Res. 2003, 31:3824-3828.
25. Storey J.D., Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 2003, 100:9440-9445.
26. Demeter J., Beauheim C., Gollub J., Hernandez-Boussard T., Jin H., Maier D., Matese J.C., Nitzberg M., Wymore F., Zachariah Z.K., Brown P.O., Sherlock G., Ball C.A. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res. 2007, 35:D766-D770.
27. Yoshimoto H., Saltsman K., Gasch A.P., Li H.X., Ogawa N., Botstein D., Brown P.O., Cyert M.S. Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J. Biol. Chem. 2002, 277:31079-31088.
28. Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 1998, 9:3273-3297.
29. Gasch A.P., Huang M., Metzner S., Botstein D., Elledge S.J., Brown P.O. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mec1p. Mol. Biol. Cell 2001, 12:2987-3003.
30. Ronen M., Botstein D. Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source. Proc. Natl. Acad. Sci. 2006, 103:389-394.
31. Carmel-Harel O., Stearman R., Gasch A.P., Botstein D., Brown P.O., Storz G. Role of thioredoxin reductase in the Yap1p-dependent response to oxidative stress in Saccharomyces cerevisiae. Mol. Microbiol. 2001, 39:595-605.
32. Shapira M., Segal E., Botstein D. Disruption of yeast forkhead-associated cell cycle transcription by oxidative stress. Mol. Biol. Cell 2004, 15:5659-5669.
33. Gasch A.P., Spellman P.T., Kao C.M., Carmel-Harel O., Eisen M.B., Storz G., Botstein D., Brown P.O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 2000, 11:4241-4257.
34. Quackenbush J. Microarray data normalization and transformation. Nat. Genet. 2002, 32(Suppl):496-501.
35. Bolstad B.M., Irizarry R.A., Astrand M., Speed T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
36. Hu Z., Killion P.J., Iyer V.R. Genetic reconstruction of a functional transcriptional regulatory network. Nat. Genet. 2007, 39:683-687.
37. Tsai H.K., Lu H.H., Li W.H. Statistical methods for identifying yeast cell cycle transcription factors. Proc. Natl. Acad. Sci. USA 2005, 102:13532-13537.
38. Simon I., Barnett J., Hannett N., Harbison C.T., Rinaldi N.J., Volkert T.L., Wyrick J.J., Zeitlinger J., Gifford D.K., Jaakkola T.S., Young R.A. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 2001, 106:697-708.
39. Koch C., Moll T., Neuberg M., Ahorn H., Nasmyth K. A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 1993, 261:1551-1557.
40. Iyer V.R., Horak C.E., Scafe C.S., Botstein D., Snyder M., Brown P.O. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409:533-538.
41. Mewes H.W., Heumann K., Kaps A., Mayer K., Pfeiffer F., Stocker S., Frishman D. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 1999, 27:44-48.
42. Chiang D.Y., Nix D.A., Shultzaberger R.K., Gasch A.P., Eisen M.B. Flexible promoter architecture requirements for coactivator recruitment. BMC Mol. Biol. 2006, 7:16.
43. Hollenhorst P.C., Pietz G., Fox C.A. Mechanisms controlling differential promoter-occupancy by the yeast forkhead proteins Fkh1p and Fkh2p: implications for regulating the cell cycle and differentiation. Genes Dev. 2001, 15:2445-2456.
44. Hoppen J., Repenning A., Albrecht A., Geburtig S., Schuller H.J. Comparative analysis of promoter regions containing binding sites of the heterodimeric transcription factor Ino2/Ino4 involved in yeast phospholipid biosynthesis. Yeast 2005, 22:601-613.
45. Ruepp A., Zollner A., Maier D., Albermann K., Hani J., Mokrejs M., Tetko I., Guldener U., Mannhaupt G., Munsterkotter M., Mewes H.W. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 2004, 32:5539-5545.
46. Jelinsky S.A., Estep P., Church G.M., Samson L.D. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol. Cell. Biol. 2000, 20:8157-8167.
47. Matsumoto R., Akama K., Rakwal R., Iwahashi H. The stress response against denatured proteins in the deletion of cytosolic chaperones SSA1/2 is different from heat-shock response in Saccharomyces cerevisiae. BMC Genomics 2005, 6:141.
48. Xu R.M., Koch C., Liu Y., Horton J.R., Knapp D., Nasmyth K., Cheng X. Crystal structure of the DNA-binding domain of Mbp1, a transcription factor important in cell-cycle control of DNA synthesis. Structure 1997, 5:349-358.
49. Chen L., Cai L., Skogerbo G., Zhao Y., Chen R. Assessing TF regulatory relationships of divergently transcribed genes. Genomics 2008, 92:316-321.
50. Teixeira M.C., Monteiro P., Jain P., Tenreiro S., Fernandes A.R., Mira N.P., Alenquer M., Freitas A.T., Oliveira A.L., Sa-Correia I. The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 2006, 34:D446-D451.
51. Badis G., Chan E.T., van Bakel H., Pena-Castillo L., Tillo D., Tsui K., Carlson C.D., Gossett A.J., Hasinoff M.J., Warren C.L., Gebbia M., Talukder S., Yang A., Mnaimneh S., Terterov D., Coburn D., Li Yeo A., Yeo Z.X., Clarke N.D., Lieb J.D., Ansari A.Z., Nislow C., Hughes T.R. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol. Cell 2008, 32:878-887.
52. Granek J.A., Clarke N.D. Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome Biol. 2005, 6:R87.
53. Erb I., van Nimwegen E. Statistical features of yeast's transcriptional regulatory code. IEEE Proceedings of the first International Conference on Computational Systems Biology (ICCSB) 2006, 111-118.
54. Yarragudi A., Miyake T., Li R., Morse R.H. Comparison of ABF1 and RAP1 in chromatin opening and transactivator potentiation in the budding yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 2004, 24:9152-9164.