A Unified Theory of Gene Expression

Allis, 1980, Proteolytic processing of histone H3 in chromatin, Cell, 20, 55, 10.1016/0092-8674(80)90234-2 Barbaric, 2001, NF-κB binds P-TEFb to stimulate transcriptional elongation by RNA polymerase II, Mol. Cell, 8, 327, 10.1016/S1097-2765(01)00314-8 Barlev, 2001, Acetylation of p53 activates transcription through recruitment of coactivators/histone acetyltransferases, Mol. Cell, 8, 1243, 10.1016/S1097-2765(01)00414-2 Beaudenon, 1999, Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae, Mol. Cell. Biol., 19, 6972, 10.1128/MCB.19.10.6972 Bhoite, 2001, The Swi5 activator recruits the Mediator complex to the HO promoter without RNA polymerase II, Genes Dev., 15, 2457, 10.1101/gad.921601 Borggrefe, 2001, Quantitation of the RNA polymerase II transcription machinery in yeast, J. Biol. Chem., 276, 47150, 10.1074/jbc.M109581200 Bregman, 1996, UV-induced ubiquitination of RNA polymerase II, Proc. Natl. Acad. Sci. USA, 93, 11586, 10.1073/pnas.93.21.11586 Briggs, 2001, Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae, Genes Dev., 15, 3286, 10.1101/gad.940201 Calvo, 2001, Evolutionarily conserved interaction between CstF-64 and PC4 links transcription, polyadenylation, and termination, Mol. Cell, 7, 1013, 10.1016/S1097-2765(01)00236-2 Carmo-Fonseca, 2002, The contribution of nuclear compartmentalization to gene regulation, Cell, 108, 513, 10.1016/S0092-8674(02)00650-5 Cheung, 2000, Synergistic coupling of histone H3 phosphorylation and acetylation in response to epidermal growth factor stimulation, Mol. Cell, 5, 905, 10.1016/S1097-2765(00)80256-7 Cho, 2001, Opposing effects of Ctk1 kinase and Fcp1 phosphatase at Ser 2 of the RNA polymerase II C-terminal domain, Genes Dev., 15, 3319, 10.1101/gad.935901 Cook, 1999, The organization of replication and transcription, Science, 284, 1790, 10.1126/science.284.5421.1790 Cosma, 2001, Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF, Mol. Cell, 7, 1213, 10.1016/S1097-2765(01)00266-0 Cramer, 2001, Structural basis of transcription, Science, 292, 1863, 10.1126/science.1059493 Dantonel, 1997, Transcription factor TFIID recruits factor CPSF for formation of 3′ end of mRNA, Nature, 389, 399, 10.1038/38763 Davies, 2001, After the genome, Cell, 104, 465, 10.1016/S0092-8674(01)00233-1 Dever, 2002, Gene-specific regulation by general translation factors, Cell, 108, 545, 10.1016/S0092-8674(02)00642-6 Di Croce, 1999, Two-step synergism between the progesterone receptor and the DNA-binding domain of nuclear factor 1 on MMTV minichromosomes, Mol. Cell, 4, 45, 10.1016/S1097-2765(00)80186-0 Dieci, 1996, Facilitated recycling pathway for RNA polymerase III, Cell, 84, 245, 10.1016/S0092-8674(00)80979-4 Doerks, 2001, DDT—a novel domain in different transcription and chromosome remodeling factors, Trends Biochem. Sci., 26, 145, 10.1016/S0968-0004(00)01769-2 Ferdous, 2001, The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II, Mol. Cell, 7, 981, 10.1016/S1097-2765(01)00250-7 Fersht, 2002, Protein folding and unfolding at atomic resolution, Cell, 108, 573, 10.1016/S0092-8674(02)00620-7 Fletcher, 2000, Structure and dynamic properties of a glucocorticoid receptor-induced chromatin transition, Mol. Cell. Biol., 20, 6466, 10.1128/MCB.20.17.6466-6475.2000 Fong, 2001, Capping, splicing, and 3′ processing are independently stimulated by RNA polymerase II, Genes Dev., 15, 1783, 10.1101/gad.889101 Fong, 2001, Stimulatory effect of splicing factors on transcriptional elongation, Nature, 414, 929, 10.1038/414929a Gavin, 2002, Functional organization of the yeast proteome by systematic analysis of protein complexes, Nature, 415, 141, 10.1038/415141a Ge, 1994, Purification, cloning, and characterization of a human coactivator, PC4, that mediates transcriptional activation of class II genes, Cell, 78, 513, 10.1016/0092-8674(94)90428-6 Gerber, 2001, RNA editing by base deamination, Trends Biochem. Sci., 26, 376, 10.1016/S0968-0004(01)01827-8 Gnatt, 2001, Structural basis of transcription, Science, 292, 1876, 10.1126/science.1059495 Gozes, 1977, Synthesis of tubulin and actin by neuronal and glial nuclear preparations from developing rat brain, J. Biol. Chem., 252, 1819, 10.1016/S0021-9258(17)40624-7 Greenleaf, 1993, Positive patches and negative noodles, Trends Biochem. Sci., 18, 117, 10.1016/0968-0004(93)90016-G Hampsey, 1999, RNA polymerase II as a control panel for multiple coactivator complexes, Curr. Opin. Genet. Dev., 9, 132, 10.1016/S0959-437X(99)80020-3 Heard, 2001, Methylation of histone H3 at Lys-9 is an early mark on the X chromosome during X inactivation, Cell, 107, 727, 10.1016/S0092-8674(01)00598-0 Hirose, 2000, RNA polymerase II and the integration of nuclear events, Genes Dev., 14, 1415, 10.1101/gad.14.12.1415 Huang, 2001, Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA, Mol. Cell, 7, 899, 10.1016/S1097-2765(01)00233-7 Huibregtse, 1997, The large subunit of RNA polymerase II is a substrate of the Rsp5 ubiquitin-protein ligase, Proc. Natl. Acad. Sci. USA, 94, 3656, 10.1073/pnas.94.8.3656 Hunter, 2000, Signaling—2000 and beyond, Cell, 100, 113, 10.1016/S0092-8674(00)81688-8 Iborra, 2001, Coupled transcription and translation within nuclei of mammalian cells, Science, 293, 1139, 10.1126/science.1061216 Ivanov, 2000, Domains in the SPT5 protein that modulate its transcriptional regulatory properties, Mol. Cell. Biol., 20, 2970, 10.1128/MCB.20.9.2970-2983.2000 Iyer, 2001, Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF, Nature, 409, 533, 10.1038/35054095 Jeanmougin, 1997, The bromodomain revisited, Trends Biochem. Sci., 22, 151, 10.1016/S0968-0004(97)01042-6 Jenuwein, 2001, Translating the histone code, Science, 293, 1074, 10.1126/science.1063127 Kanazawa, 2000, Ta+ completes with CIITA for the binding to P-TEFb and blocks the expression MHC class II genes in HIV infection, Immunity, 12, 61, 10.1016/S1074-7613(00)80159-4 Kim, 2001, Positive transcription elongation factor B phosphorylates hSPT5 and RNA polymerase II carboxyl-terminal domain independently of cyclin-dependent kinase-activating kinase, J. Biol. Chem., 276, 12317, 10.1074/jbc.M010908200 Kim, 2002, Human elongator facilitates RNA polymerase II transcription through chromatin, Proc. Natl. Acad. Sci. USA, in press Kleiman, 2001, The BARD1-CstF-50 interaction links mRNA 3′ end formation to DNA damage and tumor suppression, Cell, 104, 743, 10.1016/S0092-8674(01)00270-7 Kloc, 2002, Mechanisms of subcellular mRNA localization, Cell, 108, 533, 10.1016/S0092-8674(02)00651-7 Komarnitsky, 2000, Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription, Genes Dev., 14, 2452, 10.1101/gad.824700 Lee, 2002, Transcription-coupled and DNA damage-dependent ubiquitination or RNA polymerase II in vitro, Mol. Cell. Biol., in press Lefstin, 1998, Allosteric effects of DNA on transcriptional regulators, Nature, 392, 885, 10.1038/31860 Lemaire, 2002, Stability of a PKCI-1-related mRNA is controlled by the splicing factor ASF/SF2, Genes Dev., in press Lin, 1991, Proteolytic removal of core histone amino termini and dephosphorylation of histone H1 correlate with the formation of condensed chromatin and transcriptional silencing during Tetrahymena macronuclear development, Genes Dev., 5, 1601, 10.1101/gad.5.9.1601 Litt, 2001, Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus, Science, 293, 2453, 10.1126/science.1064413 Lo, 2000, Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14, Mol. Cell, 5, 917, 10.1016/S1097-2765(00)80257-9 Lonard, 2000, The 26S proteasome is required for estrogen receptor-alpha and coactivator turnover and for efficient estrogen receptor-alpha transactivation, Mol. Cell, 5, 939, 10.1016/S1097-2765(00)80259-2 Luger, 1997, Crystal structure of the nucleosome core particle at 2.8 Å resolution, Nature, 389, 251, 10.1038/38444 Luo, 1999, Splicing is required for rapid and efficient mRNA export in metazoans, Proc. Natl. Acad. Sci. USA, 96, 14937, 10.1073/pnas.96.26.14937 Madison-Antenucci, 2002, Editing machines, Cell, 108, 435, 10.1016/S0092-8674(02)00653-0 McKenna, 2002, Combinatorial control of gene expression by nuclear receptors and coregulators, Cell, 108, 465, 10.1016/S0092-8674(02)00641-4 McNally, 2000, The glucocorticoid receptor, Science, 287, 1262, 10.1126/science.287.5456.1262 Mitsui, 1999, Ubiquitination of RNA polymerase II large subunit signaled by phosphorylation of carboxyl-terminal domain, Proc. Natl. Acad. Sci. USA, 96, 6054, 10.1073/pnas.96.11.6054 Naar, 2001, Transcriptional coactivator complexes, Annu. Rev. Biochem., 70, 475, 10.1146/annurev.biochem.70.1.475 Narlikar, 2002, Cooperation between complexes that regulate chromatin structure and transcription, Cell, 108, 475, 10.1016/S0092-8674(02)00654-2 Nishioka, 2001, Transcription. Switching partners in a regulatory tango, Science, 294, 2497, 10.1126/science.1067622 Nishioka, 2002, Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation, Genes Dev., in press Orphanides, 2000, RNA polymerase II elongation through chromatin, Nature, 407, 471, 10.1038/35035000 Orphanides, 1996, The general transcription factors of RNA polymerase II, Genes Dev., 10, 2657, 10.1101/gad.10.21.2657 Orphanides, 1998, FACT, a factor that facilitates transcript elongation through nucleosomes, Cell, 92, 105, 10.1016/S0092-8674(00)80903-4 Orphanides, 1999, The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins, Nature, 400, 284, 10.1038/22350 Otero, 1999, Elongator, a multisubunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation, Mol. Cell, 3, 109, 10.1016/S1097-2765(00)80179-3 Prives, 2001, Why is p53 acetylated?, Cell, 107, 815, 10.1016/S0092-8674(01)00619-5 Proudfoot, 2002, Integrating mRNA processing with transcription, Cell, 108, 501, 10.1016/S0092-8674(02)00617-7 Ramakrishnan, 2002, Ribosome structure and the mechanism of translation, Cell, 108, 557, 10.1016/S0092-8674(02)00619-0 Reed, 2002, A conserved mRNA export machinery coupled to pre-mRNA splicing, Cell, 108, 523, 10.1016/S0092-8674(02)00627-X Ren, 2000, Genome-wide location and function of DNA binding proteins, Science, 290, 2306, 10.1126/science.290.5500.2306 Richards, 2002, Epigenetic codes for heterochromatin formation and silencing, Cell, 108, 489, 10.1016/S0092-8674(02)00644-X Roeder, 1996, The role of general initiation factors in transcription by RNA polymerase II, Trends Biochem. Sci., 21, 327, 10.1016/S0968-0004(96)10050-5 Roguev, 2001, The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4, EMBO J., 20, 7137, 10.1093/emboj/20.24.7137 Roth, 2001, Histone acetyltransferases, Annu. Rev. Biochem., 70, 81, 10.1146/annurev.biochem.70.1.81 Ryan, 2002, Requirements of the RNA polymerase II C-terminal domain for reconstituting pre-mRNA 3′ cleavage, Mol. Cell. Biol., 22, 10.1128/MCB.22.6.1684-1692.2002 Salghetti, 2001, Regulation of transcriptional activation domain function by ubiquitin, Science, 293, 1651, 10.1126/science.1062079 Shatkin, 2000, The ends of the affair, Nat. Struct. Biol., 7, 838, 10.1038/79583 Shuman, 1987, Purification and characterization of a transcription termination factor from vaccinia virus, J. Biol. Chem., 262, 12372, 10.1016/S0021-9258(18)45363-X Simon, 2001, Serial regulation of transcriptional regulators in the yeast cell cycle, Cell, 106, 697, 10.1016/S0092-8674(01)00494-9 Strahl, 2000, The language of covalent histone modifications, Nature, 403, 41, 10.1038/47412 Struhl, 1998, Histone acetylation and transcriptional regulatory mechanisms, Genes Dev., 12, 599, 10.1101/gad.12.5.599 Sun, 1996, Synthetic enhancement of a TFIIB defect by a mutation in SSU72, an essential yeast gene encoding a novel protein that affects transcription start site selection in vivo, Mol. Cell. Biol., 16, 1557, 10.1128/MCB.16.4.1557 Thomson, 2001, Independent dynamic regulation of histone phosphorylation and acetylation during immediate-early gene induction, Mol. Cell, 8, 1231, 10.1016/S1097-2765(01)00404-X Tupler, 2001, Expressing the human genome, Nature, 409, 832, 10.1038/35057011 Turner, 2000, Histone acetylation and an epigenetic code, Bioessays, 22, 836, 10.1002/1521-1878(200009)22:9<836::AID-BIES9>3.0.CO;2-X Uptain, 1997, Basic mechanisms of transcript elongation and its regulation, Annu. Rev. Biochem., 66, 117, 10.1146/annurev.biochem.66.1.117 Urnov, 2001, A necessary good, Mol. Endocrinol., 15, 1, 10.1210/mend.15.1.0589 Wada, 1998, DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs, Genes Dev., 12, 343, 10.1101/gad.12.3.343 Wada, 1998, Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro, EMBO J., 17, 7395, 10.1093/emboj/17.24.7395 Wen, 1999, Transcription elongation factor hSPT5 stimulates mRNA capping, Genes Dev., 13, 1774, 10.1101/gad.13.14.1774 Woychik, 2002, Simplifying the RNA polymerase II transcription complex, Cell, 108, 453, 10.1016/S0092-8674(02)00646-3 Wu, 1999, Mutational analysis of yeast TFIIB, A functional relationship between Ssu, 72, 643 Xu, 2001, A transcriptional switch mediated by cofactor methylation, Science, 294, 2507, 10.1126/science.1065961 Yamaguchi, 1999, NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation, Cell, 97, 41, 10.1016/S0092-8674(00)80713-8 Yanofsky, 1988, Transcription attenuation, J. Biol. Chem., 263, 609, 10.1016/S0021-9258(19)35394-3 Zhang, 2001, Transcription regulation by histone methylation, Genes Dev., 15, 2343, 10.1101/gad.927301