A Network Model of the Molecular Organization of Chromatin in Drosophila

Molecular Cell

Volumn 49, Issue 4, 2013, Pages 759-771

  Van Bemmel, Joke G ^a,b   Filion, Guillaume J ^a,c   Rosado, Arantxa ^a   Talhout, Wendy ^a,d   De Haas, Marcel ^a   Van Welsem, Tibor ^a   Van Leeuwen, Fred ^a   Van Steensel, Bas ^a  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

^b ERASMUS MEDICAL CENTER   (Netherlands)

^c CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^d VSBN   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

HYBRID PROTEIN; INSECT PROTEIN; PROTEOME;

ARTICLE; BAYES THEOREM; CELL COMPARTMENTALIZATION; CHROMATIN; DNA REPAIR; DNA REPLICATION; DROSOPHILA MELANOGASTER; GENE ACTIVATION; GENE CONTROL; GENE REPRESSION; GENETIC ORGANIZATION; HISTONE MODIFICATION; NONHUMAN; NUCLEAR PORE; PROTEIN FUNCTION; PROTEIN INTERACTION;

ANIMALS; BAYES THEOREM; BINDING SITES; CELL LINE; CHROMATIN; CHROMOSOMES, INSECT; DNA REPAIR; DNA REPLICATION; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE ANNOTATION; NUCLEAR PROTEINS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 84874260828     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2013.01.040     Document Type: Article

References (56)

1. Aoyagi N., Wassarman D.A. Genes encoding Drosophila melanogaster RNA polymerase II general transcription factors: diversity in TFIIA and TFIID components contributes to gene-specific transcriptional regulation. J. Cell Biol. 2000, 150:F45-F50.
2. Bannister A.J., Zegerman P., Partridge J.F., Miska E.A., Thomas J.O., Allshire R.C., Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 2001, 410:120-124.
3. Brachmann C.B., Davies A., Cost G.J., Caputo E., Li J., Hieter P., Boeke J.D. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 1998, 14:115-132.
4. Braunschweig U., Hogan G.J., Pagie L., van Steensel B. Histone H1 binding is inhibited by histone variant H3.3. EMBO J. 2009, 28:3635-3645.
5. Chamovitz D.A. Revisiting the COP9 signalosome as a transcriptional regulator. EMBO Rep. 2009, 10:352-358.
6. Chintapalli V.R., Wang J., Dow J.A. Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat. Genet. 2007, 39:715-720.
7. Cooper G.F., Herskovits E. A Bayesian method for the induction of probabilistic networks from data. Machine Learning 1992, 9:309-347.
8. Cui X.J., Li H., Liu G.Q. Combinatorial patterns of histone modifications in Saccharomyces cerevisiae. Yeast 2011, 28:683-691.
9. Delattre M., Spierer A., Tonka C.H., Spierer P. The genomic silencing of position-effect variegation in Drosophila melanogaster: interaction between the heterochromatin-associated proteins Su(var)3-7 and HP1. J. Cell Sci. 2000, 113:4253-4261.
10. Drysdale R. FlyBase: a database for the Drosophila research community. Methods Mol. Biol. 2008, 420:45-59. FlyBase Consortium.
11. Dunham I., Kundaje A., Aldred S.F., Collins P.J., Davis C.A., Doyle F., Epstein C.B., Frietze S., Harrow J., Kaul R., et al. An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. ENCODE Project Consortium.
12. Eaton M.L., Prinz J.A., MacAlpine H.K., Tretyakov G., Kharchenko P.V., MacAlpine D.M. Chromatin signatures of the Drosophila replication program. Genome Res. 2011, 21:164-174.
13. Ernst J., Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol. 2010, 28:817-825.
14. Ernst J., Kheradpour P., Mikkelsen T.S., Shoresh N., Ward L.D., Epstein C.B., Zhang X., Wang L., Issner R., Coyne M., et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473:43-49.
15. Filion G.J., van Bemmel J.G., Braunschweig U., Talhout W., Kind J., Ward L.D., Brugman W., de Castro I.J., Kerkhoven R.M., Bussemaker H.J., van Steensel B. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 2010, 143:212-224.
16. Friedman N. Inferring cellular networks using probabilistic graphical models. Science 2004, 303:799-805.
17. Friedman N., Linial M., Nachman I., Pe'er D. Using Bayesian networks to analyze expression data. J. Comput. Biol. 2000, 7:601-620.
18. Gietz R.D. Yeast two-hybrid system screening. Methods Mol. Biol. 2006, 313:345-371.
19. Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., Hao Y.L., Ooi C.E., Godwin B., Vitols E., et al. A protein interaction map of Drosophila melanogaster. Science 2003, 302:1727-1736.
20. Greil F., de Wit E., Bussemaker H.J., van Steensel B. HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila. EMBO J. 2007, 26:741-751.
21. Greil F., Moorman C., van Steensel B. DamID: mapping of in vivo protein-genome interactions using tethered DNA adenine methyltransferase. Methods Enzymol. 2006, 410:342-359.
22. Greil F., van der Kraan I., Delrow J., Smothers J.F., de Wit E., Bussemaker H.J., van Driel R., Henikoff S., van Steensel B. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev. 2003, 17:2825-2838.
23. Groth A., Ray-Gallet D., Quivy J.P., Lukas J., Bartek J., Almouzni G. Human Asf1 regulates the flow of S phase histones during replicational stress. Mol. Cell 2005, 17:301-311.
24. Henderson D.S., Banga S.S., Grigliatti T.A., Boyd J.B. Mutagen sensitivity and suppression of position-effect variegation result from mutations in mus209, the Drosophila gene encoding PCNA. EMBO J. 1994, 13:1450-1459.
25. Jaskulski D., deRiel J.K., Mercer W.E., Calabretta B., Baserga R. Inhibition of cellular proliferation by antisense oligodeoxynucleotides to PCNA cyclin. Science 1988, 240:1544-1546.
26. Kalverda B., Pickersgill H., Shloma V.V., Fornerod M. Nucleoporins directly stimulate expression of developmental and cell-cycle genes inside the nucleoplasm. Cell 2010, 140:360-371.
27. Kharchenko P.V., Alekseyenko A.A., Schwartz Y.B., Minoda A., Riddle N.C., Ernst J., Sabo P.J., Larschan E., Gorchakov A.A., Gu T., et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 2011, 471:480-485.
28. Kuo M.H., Allis C.D. Roles of histone acetyltransferases and deacetylases in gene regulation. BioEssays 1998, 20:615-626.
29. Kusch T., Florens L., Macdonald W.H., Swanson S.K., Glaser R.L., Yates J.R., Abmayr S.M., Washburn M.P., Workman J.L. Acetylation by Tip60 is required for selective histone variant exchange at DNA lesions. Science 2004, 306:2084-2087.
30. Lachner M., O'Carroll D., Rea S., Mechtler K., Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 2001, 410:116-120.
31. Lasko P. The drosophila melanogaster genome: translation factors and RNA binding proteins. J. Cell Biol. 2000, 150:F51-F56.
32. Liu T., Rechtsteiner A., Egelhofer T.A., Vielle A., Latorre I., Cheung M.S., Ercan S., Ikegami K., Jensen M., Kolasinska-Zwierz P., et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res. 2011, 21:227-236.
33. Liu Y.C., Marraccino R.L., Keng P.C., Bambara R.A., Lord E.M., Chou W.G., Zain S.B. Requirement for proliferating cell nuclear antigen expression during stages of the Chinese hamster ovary cell cycle. Biochemistry 1989, 28:2967-2974.
34. Llano M., Saenz D.T., Meehan A., Wongthida P., Peretz M., Walker W.H., Teo W., Poeschla E.M. An essential role for LEDGF/p75 in HIV integration. Science 2006, 314:461-464.
35. Loo L.W., Secombe J., Little J.T., Carlos L.S., Yost C., Cheng P.F., Flynn E.M., Edgar B.A., Eisenman R.N. The transcriptional repressor dMnt is a regulator of growth in Drosophila melanogaster. Mol. Cell. Biol. 2005, 25:7078-7091.
36. Lv J., Qiao H., Liu H., Wu X., Zhu J., Su J., Wang F., Cui Y., Zhang Y. Discovering cooperative relationships of chromatin modifications in human T cells based on a proposed closeness measure. PLoS ONE 2010, 5:e14219.
37. Murali T., Pacifico S., Yu J., Guest S., Roberts G.G., Finley R.L. DroID 2011: a comprehensive, integrated resource for protein, transcription factor, RNA and gene interactions for Drosophila. Nucleic Acids Res. 2011, 39(Database issue):D736-D743.
38. Pauli A., van Bemmel J.G., Oliveira R.A., Itoh T., Shirahige K., van Steensel B., Nasmyth K. A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. Current Biol. 2010, 20:1787-1798.
39. Pe'er D. Bayesian network analysis of signaling networks: a primer. Sci. STKE 2005, 2005:pl4.
40. Pearl J. Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference 1988, Morgan Kaufmann, San Francisco.
41. Pradeepa M.M., Sutherland H.G., Ule J., Grimes G.R., Bickmore W.A. Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet. 2012, 8:e1002717.
42. Ravi D., Wiles A.M., Bhavani S., Ruan J., Leder P., Bishop A.J. A network of conserved damage survival pathways revealed by a genomic RNAi screen. PLoS Genet. 2009, 5:e1000527.
43. Roudier F., Ahmed I., Bérard C., Sarazin A., Mary-Huard T., Cortijo S., Bouyer D., Caillieux E., Duvernois-Berthet E., Al-Shikhley L., et al. Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J. 2011, 30:1928-1938.
44. Roy S., Ernst J., Kharchenko P.V., Kheradpour P., Negre N., Eaton M.L., Landolin J.M., Bristow C.A., Ma L., Lin M.F., et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 2010, 330:1787-1797. modENCODE Consortium.
45. Schotta G., Ebert A., Krauss V., Fischer A., Hoffmann J., Rea S., Jenuwein T., Dorn R., Reuter G. Central role of Drosophila SU(VAR)3-9 in histone H3-K9 methylation and heterochromatic gene silencing. EMBO J. 2002, 21:1121-1131.
46. Schulz L.L., Tyler J.K. The histone chaperone ASF1 localizes to active DNA replication forks to mediate efficient DNA replication. FASEB J. 2006, 20:488-490.
47. Stark C., Breitkreutz B.J., Chatr-Aryamontri A., Boucher L., Oughtred R., Livstone M.S., Nixon J., Van Auken K., Wang X., Shi X., et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011, 39(Database issue):D698-D704.
48. Suntharalingam M., Wente S.R. Peering through the pore: nuclear pore complex structure, assembly, and function. Dev. Cell 2003, 4:775-789.
49. Taniue K., Nishida A., Hamada F., Sugie A., Oda T., Ui-Tei K., Tabata T., Akiyama T. Sunspot, a link between Wingless signaling and endoreplication in Drosophila. Development 2010, 137:1755-1764.
50. van Leeuwen F., Gottschling D.E. Assays for gene silencing in yeast. Methods Enzymol. 2002, 350:165-186.
51. van Steensel B., Braunschweig U., Filion G.J., Chen M., van Bemmel J.G., Ideker T. Bayesian network analysis of targeting interactions in chromatin. Genome Res. 2010, 20:190-200.
52. van Steensel B., Delrow J., Henikoff S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 2001, 27:304-308.
53. van Steensel B., Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat. Biotechnol. 2000, 18:424-428.
54. Vidal M., Brachmann R.K., Fattaey A., Harlow E., Boeke J.D. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. USA 1996, 93:10315-10320.
55. Wang Z., Buratowski S., Svejstrup J.Q., Feaver W.J., Wu X., Kornberg R.D., Donahue T.F., Friedberg E.C. The yeast TFB1 and SSL1 genes, which encode subunits of transcription factor IIH, are required for nucleotide excision repair and RNA polymerase II transcription. Mol. Cell. Biol. 1995, 15:2288-2293.
56. Yu H., Zhu S., Zhou B., Xue H., Han J.D. Inferring causal relationships among different histone modifications and gene expression. Genome Res. 2008, 18:1314-1324.