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• W2012248317 abstract "Promoter-specific initiation of transcription by RNA polymerase II (Pol II) requires both gene-specific regulators and general transcription factors (GTFs: TFIIB, -D, -E, -F, and -H) (Woychik and Hampsey 2002Woychik N.A. Hampsey M. Cell. 2002; 108: 453-463Abstract Full Text Full Text PDF PubMed Scopus (203) Google Scholar). Biochemical and genetic studies in yeast led to the discovery of a Mediator (MED) complex of 20 protein subunits, linking transcriptional regulators to Pol II and GTFs (Flanagan et al. 1991Flanagan P.M. Kelleher 3rd, R.J. Sayre M.H. Tschochner H. Kornberg R.D. Nature. 1991; 350: 436-438Crossref PubMed Scopus (253) Google Scholar, Kelleher et al. 1990Kelleher 3rd, R.J. Flanagan P.M. Kornberg R.D. Cell. 1990; 61: 1209-1215Abstract Full Text PDF PubMed Scopus (283) Google Scholar, Kim et al. 1994Kim Y.J. Bjorklund S. Li Y. Sayre M.H. Kornberg R.D. Cell. 1994; 77: 599-608Abstract Full Text PDF PubMed Scopus (872) Google Scholar). In vitro, Mediator stimulates basal transcription, enables activated transcription, and relieves the interfering effect (Gill and Ptashne 1988Gill G. Ptashne M. Nature. 1988; 334: 721-724Crossref PubMed Scopus (489) Google Scholar) of a strong transcriptional activator (Kim et al. 1994Kim Y.J. Bjorklund S. Li Y. Sayre M.H. Kornberg R.D. Cell. 1994; 77: 599-608Abstract Full Text PDF PubMed Scopus (872) Google Scholar). The identification of Mediator subunits revealed that many were products of previous genetic screens (Carlson 1997Carlson M. Annu. Rev. Cell Dev. Biol. 1997; 13: 1-23Crossref PubMed Scopus (179) Google Scholar, Lee and Young 2000Lee T.I. Young R.A. Annu. Rev. Genet. 2000; 34: 77-137Crossref PubMed Scopus (611) Google Scholar, Myers and Kornberg 2000Myers L.C. Kornberg R.D. Annu. Rev. Biochem. 2000; 69: 729-749Crossref PubMed Scopus (316) Google Scholar, Nonet and Young 1989Nonet M.L. Young R.A. Genetics. 1989; 123: 715-724Crossref PubMed Google Scholar, Suzuki et al. 1988Suzuki Y. Nogi Y. Abe A. Fukasawa T. Mol. Cell. Biol. 1988; 8: 4991-4999Crossref PubMed Scopus (111) Google Scholar), and some were shown to interact directly with Pol II and GTFs (Koleske et al. 1992Koleske A.J. Buratowski S. Nonet M. Young R.A. Cell. 1992; 69: 883-894Abstract Full Text PDF PubMed Scopus (139) Google Scholar, Myers et al. 1998Myers L.C. Gustafsson C.M. Bushnell D.A. Lui M. Erdjument-Bromage H. Tempst P. Kornberg R.D. Genes Dev. 1998; 12: 45-54Crossref PubMed Scopus (250) Google Scholar, Sakurai and Fukasawa 2000Sakurai H. Fukasawa T. J. Biol. Chem. 2000; 275: 37251-37256Crossref PubMed Scopus (27) Google Scholar, Thompson et al. 1993Thompson C.M. Koleske A.J. Chao D.M. Young R.A. Cell. 1993; 73: 1361-1375Abstract Full Text PDF PubMed Scopus (385) Google Scholar). Further genetic studies demonstrated the role of Mediator in repression as well as activation (Li et al. 1995Li Y. Bjorklund S. Jiang Y.W. Kim Y.J. Lane W.S. Stillman D.J. Kornberg R.D. Proc. Natl. Acad. Sci. USA. 1995; 92: 10864-10868Crossref PubMed Scopus (216) Google Scholar, Song et al. 1996Song W. Treich I. Qian N. Kuchin S. Carlson M. Mol. Cell. Biol. 1996; 16: 115-120Crossref PubMed Scopus (110) Google Scholar), and established the relevance of Mediator to transcription control in vivo (Barberis et al. 1995Barberis A. Pearlberg J. Simkovich N. Farrell S. Reinagel P. Bamdad C. Sigal G. Ptashne M. Cell. 1995; 81: 359-368Abstract Full Text PDF PubMed Scopus (234) Google Scholar, Holstege et al. 1998Holstege F.C. Jennings E.G. Wyrick J.J. Lee T.I. Hengartner C.J. Green M.R. Golub T.R. Lander E.S. Young R.A. Cell. 1998; 95: 717-728Abstract Full Text Full Text PDF PubMed Scopus (1575) Google Scholar, Thompson and Young 1995Thompson C.M. Young R.A. Natl. Acad. Sci. USA. 1995; 92: 4587-4590Crossref PubMed Scopus (206) Google Scholar). For some time there was no evidence for conservation of yeast Mediator through evolution. However, independent biochemical and structural studies of coactivators that, in most cases, were initially identified in functional assays have revealed true counterparts in other fungi and in higher organisms (Asturias et al. 1999Asturias F.J. Jiang Y.W. Myers L.C. Gustafsson C.M. Kornberg R.D. Science. 1999; 283: 985-987Crossref PubMed Scopus (197) Google Scholar, Boyer et al. 1999Boyer T.G. Martin M.E. Lees E. Ricciardi R.P. Berk A.J. Nature. 1999; 399: 276-279Crossref PubMed Scopus (250) Google Scholar, Chao et al. 1996Chao D.M. Gadbois E.L. Murray P.J. Anderson S.F. Sonu M.S. Parvin J.D. Young R.A. Nature. 1996; 380: 82-85Crossref PubMed Scopus (126) Google Scholar, Fondell et al. 1996Fondell J.D. Ge H. Roeder R.G. Proc. Natl. Acad. Sci. USA. 1996; 93: 8329-8333Crossref PubMed Scopus (454) Google Scholar, Gu et al. 1999Gu W. Malik S. Ito M. Yuan C.X. Fondell J.D. Zhang X. Martinez E. Qin J. Roeder R.G. Mol. Cell. 1999; 3: 97-108Abstract Full Text Full Text PDF PubMed Scopus (239) Google Scholar, Gu et al. 2002Gu J.Y. Park J.M. Song E.J. Mizuguchi G. Yoon J.H. Kim-Ha J. Lee K.J. Kim Y.J. J. Biol. Chem. 2002; 277: 27154-27161Crossref PubMed Scopus (18) Google Scholar, Ito et al. 1999Ito M. Yuan C.X. Malik S. Gu W. Fondell J.D. Yamamura S. Fu Z.Y. Zhang X. Qin J. Roeder R.G. Mol. Cell. 1999; 3: 361-370Abstract Full Text Full Text PDF PubMed Scopus (353) Google Scholar, Jiang et al. 1998Jiang Y.W. Veschambre P. Erdjument-Bromage H. Tempst P. Conaway J.W. Conaway R.C. Kornberg R.D. Proc. Natl. Acad. Sci. USA. 1998; 95: 8538-8543Crossref PubMed Scopus (255) Google Scholar, Kretzschmar et al. 1994Kretzschmar M. Stelzer G. Roeder R.G. Meisterernst M. Mol. Cell. Biol. 1994; 14: 3927-3937Crossref PubMed Scopus (55) Google Scholar, Kwon et al. 1999Kwon J.Y. Park J.M. Gim B.S. Han S.J. Lee J. Kim Y.J. Proc. Natl. Acad. Sci. USA. 1999; 96: 14990-14995Crossref PubMed Scopus (52) Google Scholar, Malik et al. 2000Malik S. Gu W. Wu W. Qin J. Roeder R.G. Mol. Cell. 2000; 5: 753-760Abstract Full Text Full Text PDF PubMed Scopus (114) Google Scholar, Meisterernst et al. 1991Meisterernst M. Roy A.L. Lieu H.M. Roeder R.G. Cell. 1991; 66: 981-993Abstract Full Text PDF PubMed Scopus (225) Google Scholar, Naar et al. 1999Naar A.M. Beaurang P.A. Zhou S. Abraham S. Solomon W. Tjian R. Nature. 1999; 398: 828-832Crossref PubMed Scopus (367) Google Scholar, Park et al. 2001Park J.M. Gim B.S. Kim J.M. Yoon J.H. Kim H.S. Kang J.G. Kim Y.J. Mol. Cell. Biol. 2001; 21: 2312-2323Crossref PubMed Scopus (53) Google Scholar, Rachez et al. 1999Rachez C. Lemon B.D. Suldan Z. Bromleigh V. Gamble M. Naar A.M. Erdjument-Bromage H. Tempst P. Freedman L.P. Nature. 1999; 398: 824-828Crossref PubMed Scopus (619) Google Scholar, Ryu et al. 1999Ryu S. Zhou S. Ladurner A.G. Tjian R. Nature. 1999; 397: 446-450Crossref PubMed Scopus (296) Google Scholar, Spahr et al. 2001Spahr H. Samuelsen C.O. Baraznenok V. Ernest I. Huylebroeck D. Remacle J.E. Samuelsson T. Kieselbach T. Holmberg S. Gustafsson C.M. Proc. Natl. Acad. Sci. USA. 2001; 98: 11985-11990Crossref PubMed Scopus (33) Google Scholar, Sun et al. 1998Sun X. Zhang Y. Cho H. Rickert P. Lees E. Lane W. Reinberg D. Mol. Cell. 1998; 2: 213-222Abstract Full Text Full Text PDF PubMed Scopus (197) Google Scholar). In mammals, the positive cofactor (PC2) component of the USA coactivator activity (Kretzschmar et al. 1994Kretzschmar M. Stelzer G. Roeder R.G. Meisterernst M. Mol. Cell. Biol. 1994; 14: 3927-3937Crossref PubMed Scopus (55) Google Scholar, Meisterernst et al. 1991Meisterernst M. Roy A.L. Lieu H.M. Roeder R.G. Cell. 1991; 66: 981-993Abstract Full Text PDF PubMed Scopus (225) Google Scholar) proved to be a Mediator-related complex (Malik et al. 2000Malik S. Gu W. Wu W. Qin J. Roeder R.G. Mol. Cell. 2000; 5: 753-760Abstract Full Text Full Text PDF PubMed Scopus (114) Google Scholar). Similarly, the human TRAP complex, first identified as a discrete group of thyroid hormone receptor-associated polypeptides with a potent coactivator activity (Fondell et al. 1996Fondell J.D. Ge H. Roeder R.G. Proc. Natl. Acad. Sci. USA. 1996; 93: 8329-8333Crossref PubMed Scopus (454) Google Scholar), also was found to represent a Mediator equivalent (Ito et al. 1999Ito M. Yuan C.X. Malik S. Gu W. Fondell J.D. Yamamura S. Fu Z.Y. Zhang X. Qin J. Roeder R.G. Mol. Cell. 1999; 3: 361-370Abstract Full Text Full Text PDF PubMed Scopus (353) Google Scholar). Other metazoan Mediator-related complexes have been denoted ARC, CRSP, or DRIP owing to interactions with other nuclear receptors as well as diverse transcriptional activators (Mittler et al. 2003Mittler G. Stuhler T. Santolin L. Uhlmann T. Kremmer E. Lottspeich F. Berti L. Meisterernst M. EMBO J. 2003; 22: 6494-6504Crossref PubMed Scopus (110) Google Scholar, Naar et al. 1999Naar A.M. Beaurang P.A. Zhou S. Abraham S. Solomon W. Tjian R. Nature. 1999; 398: 828-832Crossref PubMed Scopus (367) Google Scholar, Rachez et al. 1999Rachez C. Lemon B.D. Suldan Z. Bromleigh V. Gamble M. Naar A.M. Erdjument-Bromage H. Tempst P. Freedman L.P. Nature. 1999; 398: 824-828Crossref PubMed Scopus (619) Google Scholar, Ryu et al. 1999Ryu S. Zhou S. Ladurner A.G. Tjian R. Nature. 1999; 397: 446-450Crossref PubMed Scopus (296) Google Scholar, Yang et al. 2004Yang F. DeBeaumont R. Zhou S. Naar A.M. Proc. Natl. Acad. Sci. USA. 2004; 101: 2339-2344Crossref PubMed Scopus (99) Google Scholar). A systematic analysis of proteins present in the most highly purified mammalian complexes by tandem mass spectrometry led to the identification of up to 30 distinct MED subunits (MEDs) (Sato et al. 2003aSato S. Tomomori-Sato C. Banks C.A. Parmely T.J. Sorokina I. Brower C.S. Conaway R.C. Conaway J.W. J. Biol. Chem. 2003; 278 (a): 49671-49674Crossref PubMed Scopus (43) Google Scholar, Tomomori-Sato et al. 2004Tomomori-Sato C. Sato S. Parmely T.J. Banks C.A. Sorokina I. Florens L. Zybailov B. Washburn M.P. Brower C.S. Conaway R.C. et al.J. Biol. Chem. 2004; 279: 5846-5851Crossref PubMed Scopus (22) Google Scholar). Initial studies identified 8 MEDs conserved from fungi to humans: Med6/Pmc5/ARC/DRIP33/TRAP32, Med7/ARC/DRIP/TRAP34/CRSP33, Nut2/Med10/TRAP15, Srb7/SURB7/TRAP19, Rgr1/Pmc1/ARC/CRSP/DRIP150/TRAP170, Soh1/TRAP18 (note that Soh1 has not been yet identified in purified yeast Mediator), Srb10/Ssn3/Ume5/Gig2/Nut7/Rye5/CDK8, and Srb11/Ssn8/Ume3/Gig3/Nut9/Rye2/Cyclin C) (for reviews see Malik and Roeder 2000Malik S. Roeder R.G. Trends Biochem. Sci. 2000; 25: 277-283Abstract Full Text Full Text PDF PubMed Scopus (302) Google Scholar, Rachez and Freedman 2001Rachez C. Freedman L.P. Curr. Opin. Cell Biol. 2001; 13: 274-280Crossref PubMed Scopus (225) Google Scholar). However, extensive cross-species comparisons in several labs have more recently detected metazoan counterparts for nearly all yeast MEDs (see Table 1) (Borggrefe et al. 2002Borggrefe T. Davis R. Erdjument-Bromage H. Tempst P. Kornberg R.D. J. Biol. Chem. 2002; 277: 44202-44207Crossref PubMed Scopus (127) Google Scholar, Boube et al. 2002Boube M. Joulia L. Cribbs D.L. Bourbon H.M. Cell. 2002; 110: 143-151Abstract Full Text Full Text PDF PubMed Scopus (207) Google Scholar, Gustafsson and Samuelsson 2001Gustafsson C.M. Samuelsson T. Mol. Microbiol. 2001; 41: 1-8Crossref PubMed Scopus (26) Google Scholar, Samuelsen et al. 2003Samuelsen C.O. Baraznenok V. Khorosjutina O. Spahr H. Kieselbach T. Holmberg S. Gustafsson C.M. Proc. Natl. Acad. Sci. USA. 2003; 100: 6422-6427Crossref PubMed Scopus (98) Google Scholar, Sato et al. 2003bSato S. Tomomori-Sato C. Banks C.A. Sorokina I. Parmely T.J. Kong S.E. Jin J. Cai Y. Lane W.S. Brower C.S. et al.J. Biol. Chem. 2003; 278 (b): 15123-15127Crossref PubMed Scopus (44) Google Scholar, Spahr et al. 2001Spahr H. Samuelsen C.O. Baraznenok V. Ernest I. Huylebroeck D. Remacle J.E. Samuelsson T. Kieselbach T. Holmberg S. Gustafsson C.M. Proc. Natl. Acad. Sci. USA. 2001; 98: 11985-11990Crossref PubMed Scopus (33) Google Scholar, Tomomori-Sato et al. 2004Tomomori-Sato C. Sato S. Parmely T.J. Banks C.A. Sorokina I. Florens L. Zybailov B. Washburn M.P. Brower C.S. Conaway R.C. et al.J. Biol. Chem. 2004; 279: 5846-5851Crossref PubMed Scopus (22) Google Scholar). Further bioinformatics analyses and functional studies have revealed that the human MEDs ARC105 and yeast Gal11 harbor an activator-targeted domain related to the KIX domain found in the CBP/p300 co-activators, suggesting that ARC105 and Gal11 are evolutionarily related (Novatchkova and Eisenhaber 2004Novatchkova M. Eisenhaber F. Curr. Biol. 2004; 14: R54-R55Abstract Full Text Full Text PDF PubMed Scopus (31) Google Scholar; A.M.N., unpublished data). The time now seems right to establish a unified MED nomenclature in order to enhance understanding of the scientific literature by a wide audience and to aid cross-species comparisons and proper annotation of sequence databases.Table 1New Nomenclature for MED Subunits Including the Corresponding Known or Predicted Orthologs and ParalogsC. elegansH. sapiensdAcronyms given to MEDs identified from various mammalian MED-like complexes (Malik and Roeder, 2000). Many of the components listed under Others recently have been found in both the larger and smaller complexes; however, the MED12, MED13, CDK8, and CycC components clearly are not present in the smaller complexes, consistent with their absence in a subpopulation of yeast Mediator complexes.New nameS. cerevisiaeaFrom SGD.S. pombePrevious namebFrom WormBase.New nameD. melanogastercFrom FlyBase.TRAP/SMCCARC/DRIPCRSPPC2OTHERSMED1Med1Pmc2SOP-3*MDT-1.1Trap220*TRAP220ARC/DRIP205CRSP200TRAP220PBPMED1LT23C6.1*MDT-1.2MED2Med2MED3Pgd1/Hrs1/Med3MED4Med4Pmc4/SpMed4ZK546.13*MDT-4Trap36TRAP36ARC/DRIP36TRAP36p34MED5Nut1MED6Med6Pmc5/SpMed6LET-425/MED-6MDT-6Med6hMed6ARC/DRIP33hMed6p32MED7Med7SpMed7LET-49/MED-7MDT-7Med7*hMed7ARC/DRIP34CRSP33hMed7p36MED8Med8Sep15/SpMed8Y62F5A.1b*MDT-8Arc32*ARC32mMed8MED9Cse2/Med9CG5134*Med25MED10Nut2/Med10SpNut2T09A5.6MDT-10Nut2*hNut2hMed10hNut2MED11Med11R144.9*MDT-11Med21HSPC296MED12Srb8SpSrb8DPY-22/SOP-1*MDT-12Kto*TRAP230ARC/DRIP240MED12LTRALPUSH*MED13Ssn2/Srb9SpTrap240LET-19*MDT-13Skd/Pap/Bli*TRAP240ARC/DRIP250MED13LPROSIT240MED14Rgr1Pmc1/SpRgr1RGR-1*MDT-14Trap170TRAP170ARC/DRIP150CRSP150TRAP170p110MED15Gal11SpGal11*R12B2.5b*MDT-15Arc105*ARC105PCQAPTIG-1MED16Sin4Trap95*TRAP95DRIP92TRAP95p96bMED17Srb4SpSrb4Y113G7B.18*MDT-17Trap80TRAP80ARC/DRIP77CRSP77TRAP80p78MED18Srb5Pmc6/Sep11C55B7.9*MDT-18p28/CG14802p28bMED19Rox3SpRox3Y71H2B.6*MDT-19CG5546*LCMR1MED20Srb2SPAC17G8.05*Y104H12D.1*MDT-20TrfphTRFPhTRFPp28aMED21Srb7SpSrb7C24H11.9*MDT-21Trap19hSrb7hSrb7hSrb7p21MED22Srb6SpSrb6ZK970.3*MDT-22Med24Surf5MED23SUR-2*MDT-23Trap150β*TRAP150βARC/DRIP130CRSP130TRAP150βhSur2MED24Trap100*TRAP100ARC/DRIP100CRSP100TRAP100MED25Arc92*ARC92ACID1MED26Arc70*ARC70CRSP70MED27Pmc3T18H9.6*MDT-27Trap37*TRAP37CRSP34TRAP37MED28W01A8.1*MDT-28Med23Fksg20MED29K08E3.8*MDT-29Intersex*HintersexMED30Trap25TRAP25MED31Soh1*SpSoh1/Sep10*F32H2.2*MDT-31Trap18hSoh1hSoh1CDK8Srb10/Ssn3/Ume5SpSrb10CDK-8*Cdk8hSrb10CDK8CycCSrb11/Ssn8/Ume3SpSrb11H14E04.5*CIC-1CycChSrb11CycCAsterisks indicate that the corresponding proteins have not yet been identified in purified MED complexes.a From SGD.b From WormBase.c From FlyBase.d Acronyms given to MEDs identified from various mammalian MED-like complexes Malik and Roeder 2000Malik S. Roeder R.G. Trends Biochem. Sci. 2000; 25: 277-283Abstract Full Text Full Text PDF PubMed Scopus (302) Google Scholar. Many of the components listed under Others recently have been found in both the larger and smaller complexes; however, the MED12, MED13, CDK8, and CycC components clearly are not present in the smaller complexes, consistent with their absence in a subpopulation of yeast Mediator complexes. Open table in a new tab Asterisks indicate that the corresponding proteins have not yet been identified in purified MED complexes. The unified nomenclature, shown in Table 1, is based on the following considerations:1.The new nomenclature complies with guidelines endorsed by the Saccharomyces Genome Database (SGD), the FlyBase and WormBase resources, and the human HUGO Gene Nomenclature Committees.2.MED is the most explicit acronym.3.This nomenclature acknowledges the discovery of MED complexes in yeast.4.In light of point 3, the original yeast MEDs will retain their names (MED1-11; note that the MED5 acronym will replace Nut1).5.The remaining yeast MEDs will be given names starting from MED12, in order of decreasing conceptual molecular weights deduced from primary sequences.6.MEDs found outside budding yeast will be given names starting from MED23 in order of decreasing calculated molecular weights (based on the human protein). At present, this list extends to MED31.7.Future bona fide new MED components will be assigned numbers starting from MED32.8.The general nomenclature will employ CDK8 and CycC, as the CDK-cyclin couple is readily identifiable for a wide scientific audience.9.Except for the specific case of C. elegans (see point 10), paralogs in the same organism will be termed MED-like, e.g., MED12L in humans.10.C. elegans MEDs will retain the specific nomenclature already adopted by WormBase, the MED acronym being used for another gene category. Thus MDT-6 (for eiaor-6) replaces MED6, but the proposed numbering from 1 to 31 would be retained. In addition, following usual recommendations in this organism, the two MED1 paralogs would be called MDT-1.1 and MDT-1.2. We believe the relative simplicity of the new, common nomenclature will expedite functional comparisons in different species, while remaining flexible enough to accommodate additional species-specific MEDs as they arise. Some uncertainties persist concerning the assignments of orthologous subunits, and the nomenclature can be updated if new data so require. To facilitate communication between researchers working inside and outside of the transcription field, we recommend that this numbering system be used in all future publications concerning Mediator complexes." @default.
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• W2012248317 title "A Unified Nomenclature for Protein Subunits of Mediator Complexes Linking Transcriptional Regulators to RNA Polymerase II" @default.
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