A network of genes antagonistic to the LIN-35 retinoblastoma protein of Caenorhabditis elegans

Genetics

Volumn 191, Issue 4, 2012, Pages 1367-1380

  Polley, Stanley R G ^a   Fay, David S ^a  

^a UNIVERSITY OF WYOMING   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIN 35 RETINOBLASTOMA PROTEIN; PROHIBITIN; RETINOBLASTOMA PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BIOGENESIS; CAENORHABDITIS ELEGANS; CHROMATIN; EMBRYO; INTESTINE; LARVA; MOLECULAR EVOLUTION; MUTATION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; RIBOSOME; RNA INTERFERENCE; SCREENING; VULVA;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENOME-WIDE ASSOCIATION STUDY; MITOCHONDRIA; PHENOTYPE; REPRESSOR PROTEINS; RNA INTERFERENCE;

EID: 84865076490     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.140152     Document Type: Article

References (143)

1. Albanese, V., S. Reissmann, and J. Frydman, 2010 A ribosomeanchored chaperone network that facilitates eukaryotic ribosome biogenesis. J. Cell Biol. 189: 69-81.
2. Andersen, E. C., and H. R. Horvitz, 2007 Two C. elegans histone methyltransferases repress lin-3 EGF transcription to inhibit vulval development. Development 134: 2991-2999.
3. Andersen, E. C., X. Lu, and H. R. Horvitz, 2006 C. elegans ISWI and NURF301 antagonize an Rb-like pathway in the determination of multiple cell fates. Development 133: 2695-2704.
4. Artal-Sanz, M., and N. Tavernarakis, 2009a Prohibitin and mitochondrial biology. Trends Endocrinol. Metab. 20: 394-401.
5. Artal-Sanz, M., and N. Tavernarakis, 2009b Prohibitin couples diapause signalling to mitochondrial metabolism during ageing in C. elegans. Nature 461: 793-797.
6. Artal-Sanz, M., and N. Tavernarakis, 2010 Opposing function of mitochondrial prohibitin in aging. Aging (Albany NY) 2: 1004-1011.
7. Balciunaite, E., A. Spektor, N. H. Lents, H. Cam, H. Te Riele et al., 2005 Pocket protein complexes are recruited to distinct targets in quiescent and proliferating cells. Mol. Cell. Biol. 25: 8166-8178.
8. Bassler, J., P. Grandi, O. Gadal, T. Lessmann, E. Petfalski et al., 2001 Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol. Cell 8: 517-529.
9. Batsche, E., P. Moschopoulos, J. Desroches, S. Bilodeau, and J. Drouin, 2005 Retinoblastoma and the related pocket protein p107 act as coactivators of NeuroD1 to enhance gene transcription. J. Biol. Chem. 280: 16088-16095.
10. Beitel, G. J., E. J. Lambie, and H. R. Horvitz, 2000 The C. elegans gene lin-9, which acts in an Rb-related pathway, is required for gonadal sheath cell development and encodes a novel protein. Gene 254: 253-263.
11. Bell, O., C. Wirbelauer, M. Hild, A. N. Scharf, M. Schwaiger et al., 2007 Localized H3K36 methylation states define histone H4K16 acetylation during transcriptional elongation in Drosophila. EMBO J. 26: 4974-4984.
12. Bender, A. M., O. Wells, and D. S. Fay, 2004 lin-35/Rb and xnp-1/ ATR-X function redundantly to control somatic gonad development in C. elegans. Dev. Biol. 273: 335-349.
13. Bender, A. M., N. V. Kirienko, S. K. Olson, J. D. Esko, and D. S. Fay, 2007 lin-35/Rb and the CoREST ortholog spr-1 coordinately regulate vulval morphogenesis and gonad development in C. elegans. Dev. Biol. 302: 448-462.
14. Bender, L. B., J. Suh, C. R. Carroll, Y. Fong, I. M. Fingerman et al., 2006 MES-4: an autosome-associated histone methyltransferase that participates in silencing the X chromosomes in the C. elegans germ line. Development 133: 3907-3917.
15. Bernstein, B. E., J. K. Tong, and S. L. Schreiber, 2000 Genomewide studies of histone deacetylase function in yeast. Proc. Natl. Acad. Sci. USA 97: 13708-13713.
16. Black, E. P., E. Huang, H. Dressman, R. Rempel, N. Laakso et al., 2003 Distinct gene expression phenotypes of cells lacking Rb and Rb family members. Cancer Res. 63: 3716-3723.
17. Bousquet-Antonelli, C., E. Vanrobays, J. P. Gelugne, M. Caizergues-Ferrer, and Y. Henry, 2000 Rrp8p is a yeast nucleolar protein functionally linked to Gar1p and involved in pre-rRNA cleavage at site A2. RNA 6: 826-843.
18. Cai, Y., J. Jin, C. Tomomori-Sato, S. Sato, I. Sorokina et al., 2003 Identification of new subunits of the multiprotein mammalian TRRAP/TIP60-containing histone acetyltransferase complex. J. Biol. Chem. 278: 42733-42736.
19. Calo, E., J. A. Quintero-Estades, P. S. Danielian, S. Nedelcu, S. D. Berman et al., 2010 Rb regulates fate choice and lineage commitment in vivo. Nature 466: 1110-1114.
20. Cao, L., B. Peng, L. Yao, X. Zhang, K. Sun et al., 2010 The ancient function of RB-E2F pathway: insights from its evolutionary history. Biol. Direct 5: 55.
21. Ceol, C. J., and H. R. Horvitz, 2001 dpl-1 DP and efl-1 E2F act with lin-35 Rb to antagonize Ras signaling in C. elegans vulval development. Mol. Cell 7: 461-473.
22. Ceol, C. J., and H. R. Horvitz, 2004 A new class of C. elegans synMuv genes implicates a Tip60/NuA4-like HAT complex as a negative regulator of Ras signaling. Dev. Cell 6: 563-576.
23. Ceron, J., J. F. Rual, A. Chandra, D. Dupuy, M. Vidal et al., 2007 Large-scale RNAi screens identify novel genes that interact with the C. elegans retinoblastoma pathway as well as splicingrelated components with synMuv B activity. BMC Dev. Biol. 7: 30.
24. Checchi, P. M., and W. G. Kelly, 2006 emb-4 is a conserved gene required for efficient germline-specific chromatin remodeling during Caenorhabditis elegans embryogenesis. Genetics 174: 1895-1906.
25. Chen, D., R. Opavsky, M. Pacal, N. Tanimoto, P. Wenzel et al., 2007 Rb-mediated neuronal differentiation through cell-cycle-independent regulation of E2f3a. PLoS Biol. 5: e179.
26. Chi, W., and V. Reinke, 2006 Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1 (E2F) does not require LIN-35 (pRB). Development 133: 3147-3157.
27. Chinnam, M., and D. W. Goodrich, 2011 RB1, development, and cancer. Curr. Top. Dev. Biol. 94: 129-169.
28. Cui, M., D. S. Fay, and M. Han, 2004 lin-35/Rb cooperates with the SWI/SNF complex to control Caenorhabditis elegans larval development. Genetics 167: 1177-1185.
29. Cui, M., E. B. Kim, and M. Han, 2006 Diverse chromatin remodeling genes antagonize the Rb-involved SynMuv pathways in C. elegans. PLoS Genet. 2: e74.
30. David, A. E., 1976 Control of vesicular stomatitis virus protein synthesis. Virology 71: 217-229.
31. De Falco, G., F. Comes, and C. Simone, 2006 pRb: master of differentiation. Coupling irreversible cell cycle withdrawal with induction of muscle-specific transcription. Oncogene 25: 5244-5249.
32. Dehe, P. M., and V. Geli, 2006 The multiple faces of Set1. Biochem. Cell Biol. 84: 536-548.
33. Dejosez, M., S. S. Levine, G. M. Frampton, W. A. Whyte, S. A. Stratton et al., 2010 Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells. Genes Dev. 24: 1479-1484.
34. de la Cruz, J., E. Sanz-Martinez, and M. Remacha, 2005 The essential WD-repeat protein Rsa4p is required for rRNA processing and intra-nuclear transport of 60S ribosomal subunits. Nucleic Acids Res. 33: 5728-5739.
35. Delehouzee, S., T. Yoshikawa, C. Sawa, J. Sawada, T. Ito et al., 2005 GABP, HCF-1 and YY1 are involved in Rb gene expression during myogenesis. Genes Cells 10: 717-731.
36. Eisen, A., R. T. Utley, A. Nourani, S. Allard, P. Schmidt et al., 2001 The yeast NuA4 and Drosophila MSL complexes contain homologous subunits important for transcription regulation. J. Biol. Chem. 276: 3484-3491.
37. Fay, D. S., and J. Yochem, 2007 The SynMuv genes of Caenorhabditis elegans in vulval development and beyond. Dev. Biol. 306: 1-9.
38. Fay, D. S., S. Keenan, and M. Han, 2002 fzr-1 and lin-35/Rb function redundantly to control cell proliferation in C. elegans as revealed by a nonbiased synthetic screen. Genes Dev. 16: 503-517.
39. Fay, D. S., E. Large, M. Han, and M. Darland, 2003 lin-35/Rb and ubc-18, an E2 ubiquitin-conjugating enzyme, function redundantly to control pharyngeal morphogenesis in C. elegans. Development 130: 3319-3330.
40. Fay, D. S., X. Qiu, E. Large, C. P. Smith, S. Mango et al., 2004 The coordinate regulation of pharyngeal development in C. elegans by lin-35/Rb, pha-1, and ubc-18. Dev. Biol. 271: 11-25.
41. Ferguson, E. L., and H. R. Horvitz, 1989 The multivulva phenotype of certain Caenorhabditis elegans mutants results from defects in two functionally redundant pathways. Genetics 123: 109-121.
42. Fisher, K., S. M. Southall, J. R. Wilson, and G. B. Poulin, 2010 Methylation and demethylation activities of a C. elegans MLL-like complex attenuate RAS signalling. Dev. Biol. 341: 142-153.
43. Fukushige, T., M. G. Hawkins, and J. D. McGhee, 1998 The GATAfactor elt-2 is essential for formation of the Caenorhabditis elegans intestine. Dev. Biol. 198: 286-302.
44. Fukuyama, M., A. E. Rougvie, and J. H. Rothman, 2006 C. elegans DAF-18/PTEN mediates nutrient-dependent arrest of cell cycle and growth in the germline. Curr. Biol. 16: 773-779.
45. Furuhashi, H., T. Takasaki, A. Rechtsteiner, T. Li, H. Kimura et al., 2010 Trans-generational epigenetic regulation of C. elegans primordial germ cells. Epigenetics Chromatin 3: 15.
46. Fusaro, G., S. Wang, and S. Chellappan, 2002 Differential regulation of Rb family proteins and prohibitin during camptothecininduced apoptosis. Oncogene 21: 4539-4548.
47. Galani, K., T. A. Nissan, E. Petfalski, D. Tollervey, and E. Hurt, 2004 Rea1, a dynein-related nuclear AAA-ATPase, is involved in late rRNA processing and nuclear export of 60 S subunits. J. Biol. Chem. 279: 55411-55418.
48. Gery, S., A.F. Gombart, Y.K. Fung, andH.P. Koeffler,2004 C/EBPepsilon interactswithretinoblastomaandE2F1duringgranulopoiesis. Blood 103: 828-835.
49. Gu, T., S. Orita, and M. Han, 1998 Caenorhabditis elegans SUR-5, a novel but conserved protein, negatively regulates LET-60 Ras activity during vulval induction. Mol. Cell. Biol. 18: 4556-4564.
50. Halbach, A., H. Zhang, A. Wengi, Z. Jablonska, I. M. Gruber et al., 2009 Cotranslational assembly of the yeast SET1C histone methyltransferase complex. EMBO J. 28: 2959-2970.
51. Hanazawa, M., I. Kawasaki, H. Kunitomo, K. Gengyo-Ando, K. L. Bennett et al., 2004 The Caenorhabditis elegans eukaryotic initiation factor 5A homologue, IFF-1, is required for germ cell proliferation, gametogenesis and localization of the P-granule component PGL-1. Mech. Dev. 121: 213-224.
52. Hang, M., and M. M. Smith, 2011 Genetic analysis implicates the Set3/Hos2 histone deacetylase in the deposition and remodeling of nucleosomes containing H2A.Z. Genetics 187: 1053-1066.
53. Harrison, M. M., C. J. Ceol, X. Lu, and H. R. Horvitz, 2006 Some C. elegans class B synthetic multivulva proteins encode a conserved LIN-35 Rb-containing complex distinct from a NuRD-like complex. Proc. Natl. Acad. Sci. USA 103: 16782-16787.
54. Hsieh, J., J. Liu, S. A. Kostas, C. Chang, P. W. Sternberg et al., 1999 The RING finger/B-box factor TAM-1 and a retinoblastoma-like protein LIN-35 modulate context-dependent gene silencing in Caenorhabditis elegans. Genes Dev. 13: 2958-2970.
55. Hua, H., and N. Sarvetnick, 2007 Expression of Id1 in adult, regenerating and developing pancreas. Endocrine 32: 280-286.
56. Jen, G., C. H. Birge, and R. E. Thach, 1978 Comparison of initiation rates of encephalomyocarditis virus and host protein synthesis in infected cells. J. Virol. 27: 640-647.
57. Ji, Y., and G. P. Studzinski, 2004 Retinoblastoma protein and CCAAT/enhancer-binding protein beta are required for 1,25-dihydroxyvitamin D3-induced monocytic differentiation of HL60 cells. Cancer Res. 64: 370-377.
58. Kamath, R. S., A. G. Fraser, Y. Dong, G. Poulin, R. Durbin et al., 2003 Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421: 231-237.
59. Killian, D. J., and E. J. Hubbard, 2004 C. elegans pro-1 activity is required for soma/germline interactions that influence proliferation and differentiation in the germ line. Development 131: 1267-1278.
60. Kim, J. K., H. W. Gabel, R. S. Kamath, M. Tewari, A. Pasquinelli et al., 2005 Functional genomic analysis of RNA interference in C. elegans. Science 308: 1164-1167.
61. Kim, Y. C., S. Y. Kim, J. M. Mellado-Gil, H. Yadav, W. Neidermyer et al., 2011 RB regulates pancreas development by stabilizing Pdx1. EMBO J. 30: 1563-1576.
62. Kirienko, N. V., and D. S. Fay, 2007 Transcriptome profiling of the C. elegans Rb ortholog reveals diverse developmental roles. Dev. Biol. 305: 674-684.
63. Kirienko, N. V., J. D. McEnerney, and D. S. Fay, 2008 Coordinated regulation of intestinal functions in C. elegans by LIN-35/Rb and SLR-2. PLoS Genet. 4: e1000059.
64. Kirienko, N. V., K. Mani, and D. S. Fay, 2010 Cancer models in Caenorhabditis elegans. Dev. Dyn. 239: 1413-1448.
65. Kleivi, K., G. E. Lind, C. B. Diep, G. I. Meling, L. T. Brandal et al., 2007 Gene expression profiles of primary colorectal carcinomas, liver metastases, and carcinomatoses. Mol. Cancer 6: 2.
66. Knudsen, E. S., and K. E. Knudsen, 2006 Retinoblastoma tumor suppressor: where cancer meets the cell cycle. Exp. Biol. Med. (Maywood) 231: 1271-1281.
67. Knudson, A. G. Jr. 1971 Mutation and cancer: statistical study of retinoblastoma. Proc. Natl. Acad. Sci. USA 68: 820-823.
68. Komatsu, H., M. Y. Chao, J. Larkins-Ford, M. E. Corkins, G. A. Somers et al., 2008 OSM-11 facilitates LIN-12 Notch signaling during Caenorhabditis elegans vulval development. PLoS Biol. 6: e196.
69. Krogan, N. J., W. T. Peng, G. Cagney, M. D. Robinson, R. Haw et al., 2004 High-definition macromolecular composition of yeast RNA-processing complexes. Mol. Cell 13: 225-239.
70. Lasorella, A., M. Noseda, M. Beyna, Y. Yokota, and A. Iavarone, 2000 Id2 is a retinoblastoma protein target and mediates signalling by Myc oncoproteins. Nature 407: 592-598.
71. Lasorella, A., G. Rothschild, Y. Yokota, R. G. Russell, and A. Iavarone, 2005 Id2 mediates tumor initiation, proliferation, and angiogenesis in Rb mutant mice. Mol. Cell. Biol. 25: 3563-3574.
72. Lehner, B., A. Calixto, C. Crombie, J. Tischler, A. Fortunato et al., 2006 Loss of LIN-35, the Caenorhabditis elegans ortholog of the tumor suppressor p105Rb, results in enhanced RNA interference. Genome Biol. 7: R4.
73. Leung, J. K., N. Berube, S. Venable, S. Ahmed, N. Timchenko et al., 2001 MRG15 activates the B-myb promoter through formation of a nuclear complex with the retinoblastoma protein and the novel protein PAM14. J. Biol. Chem. 276: 39171-39178.
74. Li, S., J. A. Dent, and R. Roy, 2003 Regulation of intermuscular electrical coupling by the Caenorhabditis elegans innexin inx-6. Mol. Biol. Cell 14: 2630-2644.
75. Li, S., C. M. Armstrong, N. Bertin, H. Ge, S. Milstein et al., 2004 A map of the interactome network of the metazoan C. elegans. Science 303: 540-543.
76. Li, T., and W. G. Kelly, 2011 A role for Set1/MLL-related components in epigenetic regulation of the Caenorhabditis elegans germ line. PLoS Genet. 7: e1001349.
77. Lo, K. Y., Z. Li, C. Bussiere, S. Bresson, E. M. Marcotte et al., 2010 Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit. Mol. Cell 39: 196-208.
78. Lu, X., and H. R. Horvitz, 1998 lin-35 and lin-53, two genes that antagonize a C. elegans Ras pathway, encode proteins similar to Rb and its binding protein RbAp48. Cell 95: 981-991.
79. Mani, K., and D. S. Fay, 2009 A mechanistic basis for the coordinated regulation of pharyngeal morphogenesis in Caenorhabditis elegans by LIN-35/Rb and UBC-18-ARI-1. PLoS Genet. 5: e1000510.
80. Markey, M. P., S. P. Angus, M. W. Strobeck, S. L. Williams, R. W. Gunawardena et al., 2002 Unbiased analysis of RB-mediated transcriptional repression identifies novel targets and distinctions from E2F action. Cancer Res. 62: 6587-6597.
81. Mello, C. C., J. M. Kramer, D. Stinchcomb, and V. Ambros, 1991 Efficient gene transfer in C. elegans: extrachromosomal maintenance and integration of transforming sequences. EMBO J. 10: 3959-3970.
82. Milkereit, P., O. Gadal, A. Podtelejnikov, S. Trumtel, N. Gas et al., 2001 Maturation and intranuclear transport of pre-ribosomes requires Noc proteins. Cell 105: 499-509.
83. Mishra, S., S. R. Ande, and B. L. Nyomba, 2010 The role of prohibitin in cell signaling. FEBS J. 277: 3937-3946.
84. Mohan, M., H. M. Herz, E. R. Smith, Y. Zhang, J. Jackson et al., 2011 The COMPASS family of H3K4 methylases in Drosophila. Mol. Cell. Biol. 31: 4310-4318.
85. Morris, E. J., and N. J. Dyson, 2001 Retinoblastoma protein partners. Adv. Cancer Res. 82: 1-54.
86. Muller, H., A. P. Bracken, R. Vernell, M. C. Moroni, F. Christians et al., 2001 E2Fs regulate the expression of genes involved in differentiation, development, proliferation, and apoptosis. Genes Dev. 15: 267-285.
87. Murton, B. L., W. L. Chin, C. P. Ponting, and L. S. Itzhaki, 2010 Characterising the binding specificities of the subunits associated with the KMT2/Set1 histone lysine methyltransferase. J. Mol. Biol. 398: 481-488.
88. Nimura, K., K. Ura, H. Shiratori, M. Ikawa, M. Okabe et al., 2009 A histone H3 lysine 36 trimethyltransferase links Nkx2-5 to Wolf-Hirschhorn syndrome. Nature 460: 287-291.
89. O'Rourke, E. J., A. A. Soukas, C. E. Carr, and G. Ruvkun, 2009 C. elegans major fats are stored in vesicles distinct from lysosomerelated organelles. Cell Metab. 10: 430-435.
90. Osman, C., C. Merkwirth, and T. Langer, 2009 Prohibitins and the functional compartmentalization of mitochondrial membranes. J. Cell Sci. 122: 3823-3830.
91. Page, B. D., S. Guedes, D. Waring, and J. R. Priess, 2001 The C. elegans E2F-and DP-related proteins are required for embryonic asymmetry and negatively regulate Ras/MAPK signaling. Mol. Cell 7: 451-460.
92. Paternot, S., L. Bockstaele, X. Bisteau, H. Kooken, K. Coulonval et al., 2010 Rb inactivation in cell cycle and cancer: the puzzle of highly regulated activating phosphorylation of CDK4 vs. constitutively active CDK-activating kinase. Cell Cycle 9: 689-699.
93. Pena, A. N., K. Tominaga, and O. M. Pereira-Smith, 2011 MRG15 activates the cdc2 promoter via histone acetylation in human cells. Exp. Cell Res. 317: 1534-1540.
94. Petrella, L. N., W. Wang, C. A. Spike, A. Rechtsteiner, V. Reinke et al., 2011 synMuv B proteins antagonize germline fate in the intestine and ensure C. elegans survival. Development 138: 1069-1079.
95. Pirrotta, V., 2002 Silence in the germ. Cell 110: 661-664.
96. Poznic, M., 2009 Retinoblastoma protein: a central processing unit. J. Biosci. 34: 305-312.
97. Praitis, V., and M. F. Maduro, 2011 Transgenesis in C. elegans. Methods Cell Biol. 106: 161-185.
98. Qiu, X., and D. S. Fay, 2006 ARI-1, an RBR family ubiquitin-ligase, functions with UBC-18 to regulate pharyngeal development in C. elegans. Dev. Biol. 291: 239-252.
99. Rechtsteiner, A., S. Ercan, T. Takasaki, T. M. Phippen, T. A. Egelhofer et al., 2010 The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. PLoS Genet. 6: pii: e1001091.
100. Reilly, P. T., J. Wysocka, and W. Herr, 2002 Inactivation of the retinoblastoma protein family can bypass the HCF-1 defect in tsBN67 cell proliferation and cytokinesis. Mol. Cell. Biol. 22: 6767-6778.
101. Rekhtman, N., K. S. Choe, I. Matushansky, S. Murray, T. Stopka et al., 2003 PU.1 and pRB interact and cooperate to repress GATA-1 and block erythroid differentiation. Mol. Cell. Biol. 23: 7460-7474.
102. Rodenas, E., E. P. Klerkx, C. Ayuso, A. Audhya, and P. Askjaer, 2009 Early embryonic requirement for nucleoporin Nup35/ NPP-19 in nuclear assembly. Dev. Biol. 327: 399-409.
103. Rual, J. F., J. Ceron, J. Koreth, T. Hao, A. S. Nicot et al., 2004 Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 14: 2162-2168.
104. Sabelli, P. A., and B. A. Larkins, 2006 Grasses like mammals? Redundancy and compensatory regulation within the retinoblastoma protein family. Cell Cycle 5: 352-355.
105. Schreiber, M. A., J. T. Pierce-Shimomura, S. Chan, D. Parry, and S. L. McIntire, 2010 Manipulation of behavioral decline in Caenorhabditis elegans with theRag GTPase raga-1. PLoSGenet. 6: e1000972.
106. Sherr, C. J., and F. McCormick, 2002 The RB and p53 pathways in cancer. Cancer Cell 2: 103-112.
107. Shi, X., I. Kachirskaia, K. L. Walter, J. H. Kuo, A. Lake et al., 2007 Proteome-wide analysis in Saccharomyces cerevisiae identifies several PHD fingers as novel direct and selective binding modules of histone H3 methylated at either lysine 4 or lysine 36. J. Biol. Chem. 282: 2450-2455.
108. Silverstein, R. A., and K. Ekwall, 2005 Sin3: a flexible regulator of global gene expression and genome stability. Curr. Genet. 47: 1-17.
109. Simonet, T., R. Dulermo, S. Schott, and F. Palladino, 2007 Antagonistic functions of SET-2/SET1 and HPL/HP1 proteins in C. elegans development. Dev. Biol. 312: 367-383.
110. Soukas, A. A., E. A. Kane, C. E. Carr, J. A. Melo, and G. Ruvkun, 2009 Rictor/TORC2 regulates fat metabolism, feeding, growth, and life span in Caenorhabditis elegans. Genes Dev. 23: 496-511.
111. Stec, I., T. J. Wright, G. J. vanOmmen, P. A. de Boer, A. vanHaeringen et al., 1998 WHSC1, a 90 kb SET domain-containing gene, expressed in early development and homologous to a Drosophila dysmorphy gene maps in the Wolf-Hirschhorn syndrome critical region and is fused to IgH in t(4;14) multiple myeloma. Hum. Mol. Genet. 7: 1071-1082.
112. Stiernagle, T. 2006 Maintenance of C. elegans (February 11, 2006), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.101.1, http://www. wormbook.org.
113. Strahl, B. D., P. A. Grant, S. D. Briggs, Z. W. Sun, J. R. Bone et al., 2002 Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol. Cell. Biol. 22: 1298-1306.
114. Sulston, J. E., and H. R. Horvitz, 1977 Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56: 110-156.
115. Takahashi, C., B. Contreras, R. T. Bronson, M. Loda, and M. E. Ewen, 2004 Genetic interaction between Rb and K-ras in the control of differentiation and tumor suppression. Mol. Cell. Biol. 24: 10406-10415.
116. Takasaki, T., Z. Liu, Y. Habara, K. Nishiwaki, J. Nakayama et al., 2007 MRG-1, an autosome-associated protein, silences Xlinked genes and protects germline immortality in Caenorhabditis elegans. Development 134: 757-767.
117. Thomas, D. M., S. A. Carty, D. M. Piscopo, J. S. Lee, W. F. Wang et al., 2001 The retinoblastoma protein acts as a transcriptional coactivator required for osteogenic differentiation. Mol. Cell 8: 303-316.
118. Thomas, J. H., and H. R. Horvitz, 1999 The C. elegans gene lin-36 acts cell autonomously in the lin-35 Rb pathway. Development 126: 3449-3459.
119. Thomas, J. H., C. J. Ceol, H. T. Schwartz, and H. R. Horvitz, 2003 New genes that interact with lin-35 Rb to negatively regulate the let-60 ras pathway in Caenorhabditis elegans. Genetics 164: 135-151.
120. Timmons, L., 2006 Delivery methods for RNA interference in C. elegans. Methods Mol. Biol. 351: 119-125.
121. Timmons, L., D. L. Court, and A. Fire, 2001 Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263: 103-112.
122. Tyagi, S., A. L. Chabes, J. Wysocka, and W. Herr, 2007 E2F activation of S phase promoters via association with HCF-1 and the MLL family of histone H3K4 methyltransferases. Mol. Cell 27: 107-119.
123. Van Aken, O., J. Whelan, and F. Van Breusegem, 2010 Prohibitins: mitochondrial partners in development and stress response. Trends Plant Sci. 15: 275-282.
124. van den Heuvel, S., and N. J. Dyson, 2008 Conserved functions of the pRB and E2F families. Nat. Rev. Mol. Cell Biol. 9: 713-724.
125. Vanrobays, E., P. E. Gleizes, C. Bousquet-Antonelli, J. Noaillac-Depeyre, M. Caizergues-Ferrer et al., 2001 Processing of 20S pre-rRNA to 18S ribosomal RNA in yeast requires Rrp10p, an essential non-ribosomal cytoplasmic protein. EMBO J. 20: 4204-4213.
126. Viatour, P., and J. Sage, 2011 Newly identified aspects of tumor suppression by RB. Dis. Model Mech. 4: 581-585.
127. Voutev, R., D. J. Killian, J. H. Ahn, and E. J. Hubbard, 2006 Alterations in ribosome biogenesis cause specific defects in C. elegans hermaphrodite gonadogenesis. Dev. Biol. 298: 45-58.
128. Walkley, C. R., V. G. Sankaran, and S. H. Orkin, 2008 Rb and hematopoiesis: stem cells to anemia. Cell Div. 3: 13.
129. Wang, D., S. Kennedy, D. Conte Jr., J. K. Kim, H. W. Gabel et al., 2005 Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature 436: 593-597.
130. Wang, S., N. Nath, M. Adlam, and S. Chellappan, 1999a Prohibitin, a potential tumor suppressor, interacts with RB and regulates E2F function. Oncogene 18: 3501-3510.
131. Wang, S., N. Nath, G. Fusaro, and S. Chellappan, 1999b Rb and prohibitin target distinct regions of E2F1 for repression and respond to different upstream signals. Mol. Cell. Biol. 19: 7447-7460.
132. Wang, S., G. Fusaro, J. Padmanabhan, and S. P. Chellappan, 2002 Prohibitin co-localizes with Rb in the nucleus and recruits N-CoR and HDAC1 for transcriptional repression. Oncogene 21: 8388-8396.
133. Wheeler, J. M., and J. H. Thomas, 2006 Identification of a novel gene family involved in osmotic stress response in Caenorhabditis elegans. Genetics 174: 1327-1336.
134. Wikenheiser-Brokamp, K. A., 2006 Retinoblastoma family proteins: insights gained through genetic manipulation of mice. Cell. Mol. Life Sci. 63: 767-780.
135. Witkiewicz, A. K., K. E. Knudsen, A. P. Dicker, and E. S. Knudsen, 2011 The meaning of p16(ink4a) expression in tumors: functional significance, clinical associations and future developments. Cell Cycle 10: 2497-2503.
136. Wu, M., P. F. Wang, J. S. Lee, S. Martin-Brown, L. Florens et al., 2008 Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS. Mol. Cell. Biol. 28: 7337-7344.
137. Wysocka, J., M. P. Myers, C. D. Laherty, R. N. Eisenman, and W. Herr, 2003 Human Sin3 deacetylase and trithorax-related Set1/Ash2 histone H3-K4 methyltransferase are tethered together selectively by the cell-proliferation factor HCF-1. Genes Dev. 17: 896-911.
138. Xiao, Y., C. Bedet, V. J. Robert, T. Simonet, S. Dunkelbarger et al., 2011 Caenorhabditis elegans chromatin-associated proteins SET-2 and ASH-2 are differentially required for histone H3 Lys 4 methylation in embryos and adult germ cells. Proc. Natl. Acad. Sci. USA 108: 8305-8310.
139. Xie, Y., and A. Varshavsky, 2000 Physical association of ubiquitin ligases and the 26S proteasome. Proc. Natl. Acad. Sci. USA 97: 2497-2502.
140. Xu, L., and S. Strome, 2001 Depletion of a novel SET-domain protein enhances the sterility of mes-3 and mes-4 mutants of Caenorhabditis elegans. Genetics 159: 1019-1029.
141. Yokoyama, A., Z. Wang, J. Wysocka, M. Sanyal, D. J. Aufiero et al., 2004 Leukemia proto-oncoprotein MLL forms a SET1-like histone methyltransferase complex with menin to regulate Hox gene expression. Mol. Cell. Biol. 24: 5639-5649.
142. Zanelli, C. F., and S. R. Valentini, 2007 Is there a role for eIF5A in translation? Amino Acids 33: 351-358.
143. Zaros, C., and P. Thuriaux, 2005 Rpc25, a conserved RNA polymerase III subunit, is critical for transcription initiation. Mol. Microbiol. 55: 104-114.