A systems-level approach to mapping the telomere length maintenance gene circuitry

Molecular Systems Biology

Volumn 4, Issue , 2008, Pages

  Shachar, Rafi ^a   Ungar, Lior ^a   Kupiec, Martin ^a   Ruppin, Eytan ^a   Sharan, Roded ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

Network inference; Telomere

Indexed keywords

NUCLEOPROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; TELOMERE BINDING PROTEIN;

ARTICLE; CHROMOSOMAL INSTABILITY; CONTROLLED STUDY; GENE DELETION; GENE LOCATION; GENE MAPPING; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; TELOMERE; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENETICS; GENOME; METABOLISM; MUTATION; PHENOTYPE; PHYSIOLOGY; PROBABILITY; STATISTICAL MODEL; SYSTEMS BIOLOGY; ULTRASTRUCTURE;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

GENE EXPRESSION REGULATION, FUNGAL; GENOME; GENOME, FUNGAL; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; PHENOTYPE; PROBABILITY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SYSTEMS BIOLOGY; TELOMERE; TELOMERE-BINDING PROTEINS;

EID: 42949168427     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2008.13     Document Type: Article

References (31)

1. Askree SH, Yehuda T, Smolikov S, Gurevich R, Hawk J, Coker C, Krauskopf A, Kupiec M, McEachern MJ (2004) A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length. Proc Natl Acad Sci USA 101: 8658-8663
2. Begley TJ, Rosenbach AS, Ideker T, Samson LD (2002) Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping. Mol Cancer Res 1: 103-112
3. Begley TJ, Rosenbach AS, Ideker T, Samson LD (2004) Hot spots for modulating toxicity identified by genomic phenotyping and localization mapping. Mol Cell 16: 117-125
4. Blackburn EH (2000) Telomere states and cell fates. Nature 408: 53-56
5. Blackburn EH, Chan S, Chang J, Fulton TB, Krauskopf A, McEachern M, Prescott J, Roy J, Smith C, Wang H (2000) Molecular manifestations and molecular determinants of telomere capping. Cold Spring Harb Symp Quant Biol 65: 253-263
6. Brandes U (2001) A faster algorithm for betweenness centrality. J Math Sociol 25: 163-177
7. Calvano SE, Xiao W, Richards DR, Felciano RM, Baker HV, Cho RJ, Chen RO, Brownstein BH, Cobb JP, Tschoeke SK, Miller-Graziano C, Moldawer LL, Mindrinos MN, Davis RW, Tompkins RG, Lowry SF (2005) A network-based analysis of systemic inflammation in humans. Nature 437: 1032-1037
8. de Lange T (2005) Shelterin: the protein complex that shapes and safeguards human telomeres. Genes Dev 19: 2100-2110
9. Dover J, Schneider J, Tawiah-Boateng MA, Wood A, Dean K, Johnston M, Shilatifard A (2002) Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem 277: 28368-28371
10. Downey M, Houlsworth R, Maringele L, Rollie A, Brehme M, Galicia S, Guillard S, Partington M, Zubko MK, Krogan NJ, Emili A, Greenblatt JF, Harrington L, Lydall D, Durocher D (2006) A genome-wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator. Cell 124: 1155-1168
11. Freeman L (1977) A set of measures of centrality based on betweenness. Sociometry 40: 35-41
12. Gatbonton T, Imbesi M, Nelson M, Akey JM, Ruderfer DM, Kruglyak L, Simon JA, Bedalov A (2006) Telomere length as a quantitative trait: genome-wide survey and genetic mapping of telomere length-control genes in yeast. PLoS Genet 2: e35
13. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M et al (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636
14. Kisseleva-Romanova E, Lopreiato R, Baudin-Baillieu A, Rousselle JC, Ilan L, Hofmann K, Namane A, Mann C, Libri D (2006) Yeast homolog of a cancer-testis antigen defines a new transcription complex. EMBO J 25: 3576-3585
15. Klein P, Ravi R (1995) A nearly best-possible approximation algorithm for node-weighted Steiner trees. J Algorithms 19: 104-115
16. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B et al (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643
17. Krogan NJ, Dover J, Khorrami S, Greenblatt JF, Schneider J, Johnston M, Shilatifard A (2002) COMPASS, a histone H3 (lysine 4) methyltransferase required for telomeric silencing of gene expression. J Biol Chem 277: 10753-10755
18. Krylov DM, Wolf YI, Rogozin IB, Koonin EV (2003) Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 13: 2229-2235
19. Mewes HW, Frishman D, Mayer KF, Munsterkotter M, Noubibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stumpflen V (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 34: D169-D172
20. Ourfali O, Shlomi T, Ideker T, Ruppin E, Sharan R (2007) SPINE: a framework for signaling-regulatory pathway inference from cause-effect experiments. Bioinformatics 23: i359-i366
21. Rog O, Smolikov S, Krauskopf A, Kupiec M (2005) The yeast VPS genes affect telomere length regulation. Curr Genet 47: 18-28
22. Said MR, Begley TJ, Oppenheim AV, Lauffenburger DA, Samson LD (2004) Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 101: 18006-18011
23. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res 32: D449-D451
24. Sharan R, Ideker T, Kelley B, Shamir R, Karp RM (2005a) Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol 12: 835-846
25. Sharan R, Suthram S, Kelley RM, Kuhn T, McCuine S, Uetz P, Sittler T, Karp RM, Ideker T (2005b) Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 102: 1974-1979
26. Shlomi T, Segal D, Ruppin E, Sharan R (2006) QPath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics 7: 199
27. Tegner J, Bjorkegren J (2007) Perturbations to uncover gene networks. Trends Genet 23: 34-41
28. Verdun RE, Karlseder J (2007) Replication and protection of telomeres. Nature 447: 924-931
29. Wood A, Krogan NJ, Dover J, Schneider J, Heidt J, Boateng MA, Dean K, Golshani A, Zhang Y, Greenblatt JF, Johnston M, Shilatifard A (2003) Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol Cell 11: 267-274
30. Yeang CH, Ideker T, Jaakkola T (2004) Physical network models. J Comput Biol 11: 243-262
31. Yeang CH, Vingron M (2006) A joint model of regulatory and metabolic networks. BMC Bioinformatics 7: 332