Control of Gene Expression in Bacteria

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Campbell, E. A., L. F. Westblade, and S. A. Darst. 2008. Regulation of bacterial RNA polymerase sigma factor activity: a structural perspective. Curr. Opin. Microbiol. 11:121–127.

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Fürtig, B., et al. 2015. Multiple conformational states of riboswitches fine-tune gene regulation. Curr. Opin. Struc. Biol. 30:112–124.

Halford, S. E., and J. F. Marko. 2004. How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res. 32:3040–3052.

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Lawson, C. L., et al. 2004. Catabolite activator protein: DNA binding and transcription activation. Curr. Opin. Struc. Biol. 14:10–20.

Muller-Hill, B. 1998. Some repressors of bacterial transcription. Curr. Opin. Microbiol. 1:145–151.

Murakami, K. S., and S. A. Darst. 2003. Bacterial RNA polymerases: the whole story. Curr. Opin. Struc. Biol. 13:31–39.

Sharma, U. K., and D. Chatterji. 2010. Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity. FEMS Microbiol. Rev. 34:646–657.

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Overview of Eukaryotic Gene Control

Brenner, S., et al. 2002. Conserved regulation of the lymphocyte-specific expression of lck in the Fugu and mammals. P. Natl. Acad. Sci. USA 99:2936–2941.

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RNA Polymerase II Promoters and General Transcription Factors

Baumann, M., J. Pontiller, and W. Ernst. 2010. Structure and basal transcription complex of RNA polymerase II core promoters in the mammalian genome: an overview. Mol. Biotechnol. 45:241–247.

Brueckner, F., J. Ortiz, and P. Cramer. 2009. A movie of the RNA polymerase nucleotide addition cycle. Curr. Opin. Struc. Biol. 19:294–299.

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Hahn, S. 2004. Structure and mechanism of the RNA polymerase II transcription machinery. Nat. Struct. Mol. Biol. 11:394–403.

Illingworth, R. S., and A. P. Bird. 2009. CpG islands—“a rough guide.” FEBS Lett. 583:1713–1720.

Jun, S. H., et al. 2011. Archaeal RNA polymerase and transcription regulation. Crit. Rev. Biochem. Mol. 46:27–40.

Kornberg, R. D. 2007. The molecular basis of eukaryotic transcription. P. Natl. Acad. Sci. USA 104:12955–12961.

Müller, F., A. Zaucker, and L. Tora. 2010. Developmental regulation of transcription initiation: more than just changing the actors. Curr. Opin. Genet. Devel. 20:533–540.

Papai, G., P. A. Weil, and P. Schultz. 2011. New insights into the function of transcription factor TFIID from recent structural studies. Curr. Opin. Genet. Devel. 21:219–224.

Price, D. H. 2008. Poised polymerases: on your mark … get set … go! Mol. Cell 30:7–10.

Roeder, R. G. 1996. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 21:327–335.

Sainsbury, S., C. Bernecky, and P. Cramer. 2015. Structural basis of transcription initiation by RNA polymerase II. Nat. Rev. Mol. Cell Biol. 16:129–143.

Sandelin, A., et al. 2007. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat. Rev. Genet. 8:424–436.

Seila, A. C., et al. 2009. Divergent transcription: a new feature of active promoters. Cell Cycle 8:2557–2564.

Selth, L. A., S. Sigurdsson, and J. Q. Svejstrup. 2010. Transcript elongation by RNA polymerase II. Annu. Rev. Biochem. 79:271–293.

Sikorski, T. W., and S. Buratowski. 2009. The basal initiation machinery: beyond the general transcription factors. Curr. Opin. Cell Biol. 21:344–351.

Thomas, M. C., and C. M. Chiang. 2006. The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. 41:105–178.

Wade, J. T., and K. Struhl. 2008. The transition from transcriptional initiation to elongation. Curr. Opin. Genet. Devel. 18:130–136.

Yamada, T., et al. 2006. P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation. Mol. Cell 21:227–237.

Regulatory Sequences in Protein-Coding Genes and the Proteins Through Which They Function

de Wit, E., and W. de Laat. 2012. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26:11–24.

ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74.

Fuxreiter, M., et al. 2008. Malleable machines take shape in eukaryotic transcriptional regulation. Nat. Chem. Biol. 4:728–737.

Garvie, C. W., and C. Wolberger. 2001. Recognition of specific DNA sequences. Mol. Cell 8:937–946.

Kadonaga, J. T. 2004. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 116:247–257.

Kaufmann, K., A. Pajoro, and G. C. Angenent. 2010. Regulation of transcription in plants: mechanisms controlling developmental switches. Nat. Rev. Genet. 11:830–842.

Riechmann, J. L., et al. 2000. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science 290:2105–2110.

Tupler, R., G. Perini, and M. R. Green. 2001. Expressing the human genome. Nature 409:832–833.

Vaquerizas, J. M., et al. 2009. A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet. 10:252–263.

Molecular Mechanisms of Transcription Repression and Activation

Bannister, A. J., and T. Kouzarides. 2011. Regulation of chromatin by histone modifications. Cell Res. 21:381–395.

Berger, S. L. 2007. The complex language of chromatin regulation during transcription. Nature 447:407–412.

Bulger, M., and M. Groudine. 2011. Functional and mechanistic diversity of distal transcription enhancers. Cell 144:327–339.

Cairns, B. R. 2009. The logic of chromatin architecture and remodelling at promoters. Nature 461:193–198.

Conaway, R. C., and J. W. Conaway. 2011. Function and regulation of the Mediator complex. Curr. Opin. Genet. Devel. 21:225–230.

Courey, A. J., and S. Jia. 2001. Transcriptional repression: the long and the short of it. Genes Dev. 15:2786–2796.

Deaton, A. M., and A. Bird. 2011. CpG islands and the regulation of transcription. Genes Dev. 25:1010–1022.

Hargreaves, D. C., and G. R. Crabtree. 2011. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 21:396–420.

Kornberg, R. D. 2005. Mediator and the mechanism of transcriptional activation. Trends Biochem. Sci. 30:235–239.

Li, B., M. Carey, and J. L. Workman. 2007. The role of chromatin during transcription. Cell 128:707–719.

Malik, S., and R. G. Roeder. 2010. The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat. Rev. Genet. 11:761–772.

Malladi, V. S., et al. 2015. Ontology application and use at th ENCODE DCC. Database (Oxford). doi: 10.1093/database/bav010.

Mohrmann, L., and C. P. Verrijzer. 2005. Composition and functional specificity of SWI2/SNF2 class chromatin remodeling complexes. Biochim. Biophys. Acta 1681:59–73.

Perissi, V., et al. 2010. Deconstructing repression: evolving models of co-repressor action. Nat. Rev. Genet. 11:109–123.

Plaschka, C., et al. 2015. Architecture of the RNA polymerase II-Mediator core initiation complex. Nature 518:376–380.

Rothbart, S. B., and B. D. Strahl. 2014. Interpreting the language of histone and DNA modifications. Biochim. Biophys. Acta. 1839:627–643.

Smith, C. L., and C. L. Peterson. 2005. ATP-dependent chromatin remodeling. Curr. Top. Dev. Biol. 65:115–148.

Taatjes, D. J. 2010. The human Mediator complex: a versatile, genome-wide regulator of transcription. Trends Biochem. Sci. 35:315–322.

Venters, B. J., and B. F. Pugh. 2009. How eukaryotic genes are transcribed. Crit. Rev. Biochem. Mol. Biol. 44:117–141.

Yun, M., et al. 2011. Readers of histone modifications. Cell Res. 21:564–578.

Zaret, K. S., and J. S. Carroll. 2011. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25:2227–2241.

Regulation of Transcription-Factor Activity

Altarejos, J. Y., and M. Montminy. 2011. CREB and the CRTC co-activators: sensors for hormonal and metabolic signals. Nat. Rev. Mol. Cell Biol. 12:141–151.

Brivanlou, A. H., and J. E. Darnell, Jr. 2002. Signal transduction and the control of gene expression. Science 295:813–818.

Chen, H., M. Tini, and R. M. Evans. 2001. HATs on and beyond chromatin. Curr. Opin. Cell Biol. 13:218–224.

Echeverria, P. C., and D. Picard. 2010. Molecular chaperones, essential partners of steroid hormone receptors for activity and mobility. Biochim. Biophys. Acta 1803:641–649.

Kirschke, E., et al. 2014. Glucocorticoid receptor function regulated by coordinated action of the Hsp90 and Hsp70 chaperone cycles. Cell 157:1685–1697.

Lefstin, J. A., and K. R. Yamamoto. 1998. Allosteric effects of DNA on transcriptional regulators. Nature 392:885–888.

Perissi, V., and M. G. Rosenfeld. 2005. Controlling nuclear receptors: the circular logic of cofactor cycles. Nat. Rev. Mol. Cell Biol. 6:542–554.

Wu, S. C., and Y. Zhang. 2009. Minireview: role of protein methylation and demethylation in nuclear hormone signaling. Mol. Endocrinol. 23:1323–1334.

York, B., and B. W. O’Malley. 2010. Steroid receptor coactivator (SRC) family: masters of systems biology. J. Biol. Chem. 285:38743–3850.

Epigenetic Regulation of Transcription

Beisel, C., and R. Paro. 2011. Silencing chromatin: comparing modes and mechanisms. Nat. Rev. Genet. 12:123–135.

Black, J. C., and J. R. Whetstine. 2011. Chromatin landscape: methylation beyond transcription. Epigenetics 6:9–15.

Clouaire, T., and I. Stancheva. 2008. Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin? Cell. Mol. Life Sci. 65:1509–1522.

Derrien, T., et al. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22:1775–1789.

Gendrel, A. V., and E. Heard. 2014. Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation. Annu. Rev. Cell Dev. Biol. 30:561–580.

Grewal, S. I. 2010. RNAi-dependent formation of heterochromatin and its diverse functions. Curr. Opin. Genet. Devel. 20:134–141.

Klose, R. J., and A. P. Bird. 2006. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31:89–97.

Lee, J. T. 2010. The X as model for RNA’s niche in epigenomic regulation. Cold Spring Harb. Perspect. Biol. 2(9):a003749 (1–12).

McHugh, C. A., et al. 2015. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521:232–236.

Minks, J., and C. J. Brown. 2009. Getting to the center of X-chromosome inactivation: the role of transgenes. Biochem. Cell. Biol. 87:759–766.

Moazed, D. 2009. Small RNAs in transcriptional gene silencing and genome defence. Nature 457:413–420.

Simon, J. A., and R. E. Kingston. 2009. Mechanisms of polycomb gene silencing: knowns and unknowns. Nat. Rev. Mol. Cell Biol. 10:697–708

Vermaak, D., and H. S. Malik. 2009. Multiple roles for heterochromatin protein 1 genes in Drosophila. Ann. Rev. Genet. 43:467–492.

Wutz, A., and J. Gribnau. 2007. X inactivation Xplained. Curr. Opin. Genet. Devel. 17:387–393.

Other Eukaryotic Transcription Systems

Dumay-Odelot, H., et al. 2010. Cell growth- and differentiation-dependent regulation of RNA polymerase III transcription. Cell Cycle 9:3687–3699.

Grummt, I. 2010. Wisely chosen paths—regulation of rRNA synthesis. FEBS J. 277:4626–4639.

Moir, R. D., and I. M. Willis. 2015. Regulating maf1 expression and its expanding biological functions. PLoS Genet. 11:e1004896.

Willis, I. M., and R. D. Moir. 2007. Integration of nutritional and stress signaling pathways by Maf1. Trends Biochem. Sci. 32:51–53.