Dissecting Regulatory Networks in Host-Pathogen Interaction Using ChIP-on-chip Technology

Cell Host and Microbe

Volumn 5, Issue 5, 2009, Pages 430-437

  Sala, Claudia ^a   Grainger, David C ^b   Cole, Stewart T ^a  

^a EPFL   (Switzerland)

^b UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RAC PROTEIN; RACA PROTEIN; RNA; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

BACTERIUM CULTURE; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME SEGREGATION; GENE MAPPING; GENE REGULATORY NETWORK; GENE SILENCING; HOST PATHOGEN INTERACTION; INTERMETHOD COMPARISON; NONHUMAN; PATHOGENESIS; PRIORITY JOURNAL; PROCESS DESIGN; PROTEIN DNA BINDING; PROTEIN EXPRESSION; PROTEIN MICROARRAY; PROTEIN RNA BINDING; PROTEIN TARGETING; REVIEW; SYSTEMS BIOLOGY; VALIDATION PROCESS;

ANIMALS; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; GENE REGULATORY NETWORKS; HOST-PATHOGEN INTERACTIONS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN BINDING; TRANSCRIPTION FACTORS;

BACTERIA (MICROORGANISMS);

EID: 65549122479     PISSN: 19313128     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chom.2009.04.007     Document Type: Review

References (85)

1. Alcorlo M., Salas M., and Hermoso J.M. In vivo DNA binding of bacteriophage GA-1 protein p6. J. Bacteriol. 189 (2007) 8024-8033
2. Bar-Joseph Z., Gerber G.K., Lee T.I., Rinaldi N.J., Yoo J.Y., Robert F., Gordon D.B., Fraenkel E., Jaakkola T.S., Young R.A., et al. Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 21 (2003) 1337-1342
3. Ben-Yehuda S., Fujita M., Liu X.S., Gorbatyuk B., Skoko D., Yan J., Marko J.F., Liu J.S., Eichenberger P., Rudner D.Z., et al. Defining a centromere-like element in Bacillus subtilis by Identifying the binding sites for the chromosome-anchoring protein RacA. Mol. Cell 17 (2005) 773-782
4. Betts J.C., Lukey P.T., Robb L.C., McAdam R.A., and Duncan K. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol. Microbiol. 43 (2002) 717-731
5. Blanco L., Gutierrez J., Lazaro J.M., Bernad A., and Salas M. Replication of phage phi 29 DNA in vitro: role of the viral protein p6 in initiation and elongation. Nucleic Acids Res. 14 (1986) 4923-4937
6. Boshoff H.I., and Barry III C.E. Tuberculosis - metabolism and respiration in the absence of growth. Nat. Rev. Microbiol. 3 (2005) 70-80
7. Boshoff H.I., Myers T.G., Copp B.R., McNeil M.R., Wilson M.A., and Barry III C.E. The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J. Biol. Chem. 279 (2004) 40174-40184
8. Boyer L.A., Lee T.I., Cole M.F., Johnstone S.E., Levine S.S., Zucker J.P., Guenther M.G., Kumar R.M., Murray H.L., Jenner R.G., et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122 (2005) 947-956
9. Breier A.M., and Grossman A.D. Whole-genome analysis of the chromosome partitioning and sporulation protein Spo0J (ParB) reveals spreading and origin-distal sites on the Bacillus subtilis chromosome. Mol. Microbiol. 64 (2007) 703-718
10. Bulyk M.L. DNA microarray technologies for measuring protein-DNA interactions. Curr. Opin. Biotechnol. 17 (2006) 422-430
11. Camacho A., and Salas M. Repression of bacteriophage phi 29 early promoter C2 by viral protein p6 is due to impairment of closed complex. J. Biol. Chem. 276 (2001) 28927-28932
12. Campbell E.A., Korzheva N., Mustaev A., Murakami K., Nair S., Goldfarb A., and Darst S.A. Structural mechanism for rifampicin inhibition of bacterial rna polymerase. Cell 104 (2001) 901-912
13. Cardinale C.J., Washburn R.S., Tadigotla V.R., Brown L.M., Gottesman M.E., and Nudler E. Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science 320 (2008) 935-938
14. Cawley S., Bekiranov S., Ng H.H., Kapranov P., Sekinger E.A., Kampa D., Piccolboni A., Sementchenko V., Cheng J., Williams A.J., et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116 (2004) 499-509
15. Chang Y.J., Wu M.S., Lin J.T., Pestell R.G., Blaser M.J., and Chen C.C. Mechanisms for Helicobacter pylori CagA-induced cyclin D1 expression that affect cell cycle. Cell. Microbiol. 8 (2006) 1740-1752
16. Cooper A.M., Dalton D.K., Stewart T.A., Griffin J.P., Russell D.G., and Orme I.M. Disseminated tuberculosis in interferon gamma gene-disrupted mice. J. Exp. Med. 178 (1993) 2243-2247
17. Danielli A., Roncarati D., Delany I., Chiarini V., Rappuoli R., and Scarlato V. In vivo dissection of the Helicobacter pylori Fur regulatory circuit by genome-wide location analysis. J. Bacteriol. 188 (2006) 4654-4662
18. de Folter S., Urbanus S.L., van Zuijlen L.G., Kaufmann K., and Angenent G.C. Tagging of MADS domain proteins for chromatin immunoprecipitation. BMC Plant Biol. 7 (2007) 47
19. Dorman C.J. H-NS: a universal regulator for a dynamic genome. Nat. Rev. Microbiol. 2 (2004) 391-400
20. Eichenberger P., Fujita M., Jensen S.T., Conlon E.M., Rudner D.Z., Wang S.T., Ferguson C., Haga K., Sato T., Liu J.S., et al. The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis. PLoS Biol. 2 (2004) e328
21. Fang F.C., and Rimsky S. New insights into transcriptional regulation by H-NS. Curr. Opin. Microbiol. 11 (2008) 113-120
22. Fejes A.P., Robertson G., Bilenky M., Varhol R., Bainbridge M., and Jones S.J. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24 (2008) 1729-1730
23. Flynn J.L., Chan J., Triebold K.J., Dalton D.K., Stewart T.A., and Bloom B.R. An essential role for interferon gamma in resistance to Mycobacterium tuberculosis infection. J. Exp. Med. 178 (1993) 2249-2254
24. Frigui W., Bottai D., Majlessi L., Monot M., Josselin E., Brodin P., Garnier T., Gicquel B., Martin C., Leclerc C., et al. Control of M. tuberculosis ESAT-6 secretion and specific T cell recognition by PhoP. PLoS Pathog. 4 (2008) e33
25. Fujita N., and Wade P.A. Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes. Methods 33 (2004) 81-85
26. Gonzalez-Huici V., Salas M., and Hermoso J.M. Genome wide, supercoiling-dependent in vivo binding of a viral protein involved in DNA replication and transcriptional control. Nucleic Acids Res. 32 (2004) 2306-2314
27. Gonzalo-Asensio J., Mostowy S., Harders-Westerveen J., Huygen K., Hernandez-Pando R., Thole J., Behr M., Gicquel B., and Martin C. PhoP: a missing piece in the intricate puzzle of Mycobacterium tuberculosis virulence. PLoS ONE 3 (2008) e3496
28. Grainger D.C., Overton T.W., Reppas N., Wade J.T., Tamai E., Hobman J.L., Constantinidou C., Struhl K., Church G., and Busby S.J. Genomic studies with Escherichia coli MelR protein: applications of chromatin immunoprecipitation and microarrays. J. Bacteriol. 186 (2004) 6938-6943
29. Grainger D.C., Hurd D., Harrison M., Holdstock J., and Busby S.J. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc. Natl. Acad. Sci. USA 102 (2005) 17693-17698
30. Grainger D.C., Hurd D., Goldberg M.D., and Busby S.J. Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res. 34 (2006) 4642-4652
31. Grainger D.C., Aiba H., Hurd D., Browning D.F., and Busby S.J. Transcription factor distribution in Escherichia coli: studies with FNR protein. Nucleic Acids Res. 35 (2007) 269-278
32. Grifantini R., Bartolini E., Muzzi A., Draghi M., Frigimelica E., Berger J., Randazzo F., and Grandi G. Gene expression profile in Neisseria meningitidis and Neisseria lactamica upon host-cell contact: from basic research to vaccine development. Ann. N Y Acad. Sci. 975 (2002) 202-216
33. Grifantini R., Sebastian S., Frigimelica E., Draghi M., Bartolini E., Muzzi A., Rappuoli R., Grandi G., and Genco C.A. Identification of iron-activated and -repressed Fur-dependent genes by transcriptome analysis of Neisseria meningitidis group B. Proc. Natl. Acad. Sci. USA 100 (2003) 9542-9547
34. Groisman E.A., and Mouslim C. Sensing by bacterial regulatory systems in host and non-host environments. Nat. Rev. Microbiol. 4 (2006) 705-709
35. Guinn K.M., Hickey M.J., Mathur S.K., Zakel K.L., Grotzke J.E., Lewinsohn D.M., Smith S., and Sherman D.R. Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis. Mol. Microbiol. 51 (2004) 359-370
36. 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., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431 (2004) 99-104
37. Jang M.K., Kwon D., and McBride A.A. Papillomavirus E2 Proteins and the Host Brd4 Protein Associate with Transcriptionally Active Cellular Chromatin. J. Virol. 83 (2009) 2592-2600
38. Jensen S.T., and Liu J.S. BioOptimizer: a Bayesian scoring function approach to motif discovery. Bioinformatics 20 (2004) 1557-1564
39. Johnson D.S., Mortazavi A., Myers R.M., and Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007) 1497-1502
40. Kay S., Hahn S., Marois E., Hause G., and Bonas U. A bacterial effector acts as a plant transcription factor and induces a cell size regulator. Science 318 (2007) 648-651
41. Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12 (2002) 656-664
42. Kim M.H., Yoo H.S., Kim M.Y., Jang H.J., Baek M.K., Kim H.R., Kim K.K., Shin B.A., Ahn B.W., and Jung Y.D. Helicobacter pylori stimulates urokinase plasminogen activator receptor expression and cell invasiveness through reactive oxygen species and NF-kappaB signaling in human gastric carcinoma cells. Int. J. Mol. Med. 19 (2007) 689-697
43. Kolodziej K.E., Pourfarzad F., de Boer E., Krpic S., Grosveld F., and Strouboulis J. Optimal use of tandem biotin and V5 tags in ChIP assays. BMC Mol. Biol. 10 (2009) 6
44. Laub M.T., Chen S.L., Shapiro L., and McAdams H.H. Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle. Proc. Natl. Acad. Sci. USA 99 (2002) 4632-4637
45. Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
46. Lee T.I., Johnstone S.E., and Young R.A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nat. Protocols 1 (2006) 729-748
47. Lee J.S., Krause R., Schreiber J., Mollenkopf H.J., Kowall J., Stein R., Jeon B.Y., Kwak J.Y., Song M.K., Patron J.P., et al. Mutation in the transcriptional regulator PhoP contributes to avirulence of Mycobacterium tuberculosis H37Ra strain. Cell Host Microbe 3 (2008) 97-103
48. Leng J., Butcher B.A., Egan C.E., Abdallah D.S., and Denkers E.Y. Toxoplasma gondii prevents chromatin remodeling initiated by TLR-triggered macrophage activation. J. Immunol. 182 (2009) 489-497
49. Li H., Ruan J., and Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18 (2008) 1851-1858
50. Li R., Li Y., Kristiansen K., and Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 24 (2008) 713-714
51. Liu Y., Wei L., Batzoglou S., Brutlag D.L., Liu J.S., and Liu X.S. A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res. 32 (2004) 204-207
52. Lucchini S., Rowley G., Goldberg M.D., Hurd D., Harrison M., and Hinton J.C. H-NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog. 2 (2006) e81
53. Molle V., Fujita M., Jensen S.T., Eichenberger P., Gonzalez-Pastor J.E., Liu J.S., and Losick R. The Spo0A regulon of Bacillus subtilis. Mol. Microbiol. 50 (2003) 1683-1701
54. Molle V., Nakaura Y., Shivers R.P., Yamaguchi H., Losick R., Fujita Y., and Sonenshein A.L. Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J. Bacteriol. 185 (2003) 1911-1922
55. Mooney R.A., Davis S.E., Peters J.M., Rowland J.L., Ansari A.Z., and Landick R. Regulator trafficking on bacterial transcription units in vivo. Mol. Cell 33 (2009) 97-108
56. Morozova O., and Marra M.A. Applications of next-generation sequencing technologies in functional genomics. Genomics 92 (2008) 255-264
57. Navarre W.W., Halsey T.A., Walthers D., Frye J., McClelland M., Potter J.L., Kenney L.J., Gunn J.S., Fang F.C., and Libby S.J. Co-regulation of Salmonella enterica genes required for virulence and resistance to antimicrobial peptides by SlyA and PhoP/PhoQ. Mol. Microbiol. 56 (2005) 492-508
58. Navarre W.W., Porwollik S., Wang Y., McClelland M., Rosen H., Libby S.J., and Fang F.C. Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella. Science 313 (2006) 236-238
59. Navarre W.W., McClelland M., Libby S.J., and Fang F.C. Silencing of xenogeneic DNA by H-NS-facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev. 21 (2007) 1456-1471
60. Ning Z., Cox A.J., and Mullikin J.C. SSAHA: a fast search method for large DNA databases. Genome Res. 11 (2001) 1725-1729
61. Oshima T., Ishikawa S., Kurokawa K., Aiba H., and Ogasawara N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res. 13 (2006) 141-153
62. Pecenkova T., and Paces V. Molecular phylogeny of phi29-like phages and their evolutionary relatedness to other protein-primed replicating phages and other phages hosted by gram-positive bacteria. J. Mol. Evol. 48 (1999) 197-208
63. Raghavan S., Manzanillo P., Chan K., Dovey C., and Cox J.S. Secreted transcription factor controls Mycobacterium tuberculosis virulence. Nature 454 (2008) 717-721
64. Rodrigue S., Brodeur J., Jacques P.E., Gervais A.L., Brzezinski R., and Gaudreau L. Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays. J. Bacteriol. 189 (2007) 1505-1513
65. Rohde K., Yates R.M., Purdy G.E., and Russell D.G. Mycobacterium tuberculosis and the environment within the phagosome. Immunol. Rev. 219 (2007) 37-54
66. Rohde K.H., Abramovitch R.B., and Russell D.G. Mycobacterium tuberculosis invasion of macrophages: linking bacterial gene expression to environmental cues. Cell Host Microbe 2 (2007) 352-364
67. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A., and Barrell B. Artemis: sequence visualization and annotation. Bioinformatics 16 (2000) 944-945
68. Ryndak M., Wang S., and Smith I. PhoP, a key player in Mycobacterium tuberculosis virulence. Trends Microbiol. 16 (2008) 528-534
69. Sala C., Haouz A., Saul F.A., Miras I., Rosenkrands I., Alzari P.M., and Cole S.T. Genome-wide regulon and crystal structure of BlaI (Rv1846c) from Mycobacterium tuberculosis. Mol. Microbiol. 71 (2009) 1102-1116
70. Samten B., Howard S.T., Weis S.E., Wu S., Shams H., Townsend J.C., Safi H., and Barnes P.F. Cyclic AMP response element-binding protein positively regulates production of IFN-gamma by T cells in response to a microbial pathogen. J. Immunol. 174 (2005) 6357-6363
71. Sanchez-Elsner T., Gou D., Kremmer E., and Sauer F. Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 311 (2006) 1118-1123
72. Schnappinger D., Ehrt S., Voskuil M.I., Liu Y., Mangan J.A., Monahan I.M., Dolganov G., Efron B., Butcher P.D., Nathan C., et al. Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment. J. Exp. Med. 198 (2003) 693-704
73. Shen X., Collier J., Dill D., Shapiro L., Horowitz M., and McAdams H.H. Architecture and inherent robustness of a bacterial cell-cycle control system. Proc. Natl. Acad. Sci. USA 105 (2008) 11340-11345
74. Shimada T., Ishihama A., Busby S.J., and Grainger D.C. The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Res. 36 (2008) 3950-3955
75. Talaat A.M., Lyons R., Howard S.T., and Johnston S.A. The temporal expression profile of Mycobacterium tuberculosis infection in mice. Proc. Natl. Acad. Sci. USA 101 (2004) 4602-4607
76. Ule J., Jensen K.B., Ruggiu M., Mele A., Ule A., and Darnell R.B. CLIP identifies Nova-regulated RNA networks in the brain. Science 302 (2003) 1212-1215
77. Valouev A., Johnson D.S., Sundquist A., Medina C., Anton E., Batzoglou S., Myers R.M., and Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5 (2008) 829-834
78. Venza I., Cucinotta M., Visalli M., De Grazia G., Oliva S., and Teti D. Pseudomonas aeruginosa induces IL-8 gene expression in human conjunctiva through the recruitment of both RelA and C/EBPbeta to the IL-8 promoter. J. Biol. Chem. 284 (2008) 4191-4199
79. Voskuil M.I. Mycobacterium tuberculosis gene expression during environmental conditions associated with latency. Tuberculosis (Edinb.) 84 (2004) 138-143
80. Voskuil M.I., Visconti K.C., and Schoolnik G.K. Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Tuberculosis (Edinb.) 84 (2004) 218-227
81. Wade J.T., Reppas N.B., Church G.M., and Struhl K. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 19 (2005) 2619-2630
82. Wade J.T., Roa D.C., Grainger D.C., Hurd D., Busby S.J., Struhl K., and Nudler E. Extensive functional overlap between sigma factors in Escherichia coli. Nat. Struct. Mol. Biol. 13 (2006) 806-814
83. Wade J.T., Struhl K., Busby S.J., and Grainger D.C. Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization. Mol. Microbiol. 65 (2007) 21-26
84. Walters S.B., Dubnau E., Kolesnikova I., Laval F., Daffe M., and Smith I. The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. Mol. Microbiol. 60 (2006) 312-330
85. Wayne L.G., and Sohaskey C.D. Nonreplicating persistence of mycobacterium tuberculosis. Annu. Rev. Microbiol. 55 (2001) 139-163