Where to Start

Liu, X., Bushnell, D. A., and Kornberg, R. D. 2013. RNA polymerase II transcription: Structure and mechanism. Biochim. Biophys. Acta 1829:2–8.

Kornberg, R. D. 2007. The molecular basis of eukaryotic transcription. Proc. Natl. Acad. Sci. U.S.A. 104:12955–12961.

Pabo, C. O., and Sauer, R. T. 1984. Protein–DNA recognition. Annu. Rev. Biochem. 53:293–321.

Struhl, K. 1989. Helix-turn-helix, zinc-finger, and leucine-zipper motifs for eukaryotic transcriptional regulatory proteins. Trends Biochem. Sci. 14:137–140.

Struhl, K. 1999. Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98:1–4.

Korzus, E., Torchia, J., Rose, D. W., Xu, L., Kurokawa, R., McInerney, E. M., Mullen, T. M., Glass, C. K., and Rosenfeld, M. G. 1998. Transcription factor-specific requirements for coactivators and their acetyltransferase functions. Science 279:703–707.

Aalfs, J. D., and Kingston, R. E. 2000. What does “chromatin remodeling” mean? Trends Biochem. Sci. 25:548–555.

McKnight, S. L., and Yamamoto, K. R. (Eds.). 1992. Transcriptional Regulation (vols. 1 and 2). Cold Spring Harbor Laboratory Press.

Latchman, D. S. 2004. Eukaryotic Transcription Factors (4th ed.). Academic Press.

Wolffe, A. 1992. Chromatin Structure and Function. Academic Press.

Lodish, H., Berk, A., Kaiser, C. A., Krieger, M., Bretscher, A., Pleogh, H., Amon, A., and Scott, M. P. 2012. Molecular Cell Biology (7th ed.). W. H. Freeman and Company.

Sadeh, R. and Allis, C. D. 2011. Genome-wide “re”-modeling of nucleosome positions. Cell 147:263–266.

Lorch, Y., Maier-Davis, B., and Kornberg, R. D. 2010. Mechanism of chromatin remodeling. Proc. Natl. Acad. Sci. U.S.A. 107:3458–3462.

Tang, L., Nogales, E., and Ciferri, C. 2010. Structure and function of SWI/SNF chromatin remodeling complexes and mechanistic implications for transcription. Prog. Biophys. Mol. Biol. 102:122–128.

Jenuwein, T., and Allis, C. D. 2001. Translating the histone code. Science 293:1074–1080.

Jiang, C., and Pugh, B. F. 2009. Nucleosome positioning and gene regulation: Advances through genomics. Nat. Rev. Genet. 10:161–172.

Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129:823–837.

Weintraub, H., Larsen, A., and Groudine, M. 1981. β-Globin-gene switching during the development of chicken embryos: Expression and chromosome structure. Cell 24:333–344.

Ren, B., Robert, F., Wyrick, J. J., Aparicio, O., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., et al. 2000. Genome-wide location and function of DNA-binding proteins. Science 290:2306–2309.

Goodrich, J. A., and Tjian, R. 1994. TBP-TAF complexes: Selectivity factors for eukaryotic transcription. Curr. Opin. Cell. Biol. 6:403–409.

B38

Bird, A. P., and Wolffe, A. P. 1999. Methylation-induced repression: Belts, braces, and chromatin. Cell 99:451–454.

Cairns, B. R. 1998. Chromatin remodeling machines: Similar motors, ulterior motives. Trends Biochem. Sci. 23:20–25.

Albright, S. R., and Tjian, R. 2000. TAFs revisited: More data reveal new twists and confirm old ideas. Gene 242:1–13.

Urnov, F. D., and Wolffe, A. P. 2001. Chromatin remodeling and transcriptional activation: The cast (in order of appearance). Oncogene 20:2991–3006.

Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and Richmond, T. J. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251–260.

Arents, G., and Moudrianakis, E. N. 1995. The histone fold: A ubiquitous architectural motif utilized in DNA compaction and protein dimerization. Proc. Natl. Acad. Sci. U.S.A. 92:11170–11174.

Baxevanis, A. D., Arents, G., Moudrianakis, E. N., and Landsman, D. 1995. A variety of DNA-binding and multimeric proteins contain the histone fold motif. Nucleic Acids Res. 23:2685–2691.

Green, M. R. 2005. Eukaryotic transcription activation: Right on target. Mol. Cell 18:399–402.

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

Clements, A., Rojas, J. R., Trievel, R. C., Wang, L., Berger, S. L., and Marmorstein, R. 1999. Crystal structure of the histone acetyltransferase domain of the human PCAF transcriptional regulator bound to coenzyme A. EMBO J. 18:3521–3532.

Deckert, J., and Struhl, K. 2001. Histone acetylation at promoters is differentially affected by specific activators and repressors. Mol. Cell. Biol. 21:2726–2735.

Dutnall, R. N., Tafrov, S. T., Sternglanz, R., and Ramakrishnan, V. 1998. Structure of the histone acetyltransferase Hat1: A paradigm for the GCN5-related N-acetyltransferase superfamily. Cell 94:427–438.

Finnin, M. S., Donigian, J. R., Cohen, A., Richon, V. M., Rifkind, R. A., Marks, P. A., Breslow, R., and Pavletich, N. P. 1999. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 401:188–193.

Finnin, M. S., Donigian, J. R., and Pavletich, N. P. 2001. Structure of the histone deacetylase SIR2. Nat. Struct. Biol. 8:621–625.

Jacobson, R. H., Ladurner, A. G., King, D. S., and Tjian, R. 2000. Structure and function of a human TAFII250 double bromodomain module. Science 288:1422–1425.

Rojas, J. R., Trievel, R. C., Zhou, J., Mo, Y., Li, X., Berger, S. L., Allis, C. D., and Marmorstein, R. 1999. Structure of Tetrahymena GCN5 bound to coenzyme A and a histone H3 peptide. Nature 401:93–98.

Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., and Yamanaka, S. 2007. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 131:861–872.

Takahashi, K., and Yamanaka, S. 2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663–676.

Park, I. H., Arora, N., Huo, H., Maherali, N., Ahfeldt, T., Shimamura, A., Lensch, M. W., Cowan, C., Hochedlinger, K., and Daley, G. Q. 2008. Disease-specific induced pluripotent stem cells. Cell 134:877–886.

Yamanaka, S. 2009. A fresh look at iPS cells. Cell 137:13–17.

Yu, J., Hu, K., Smuga-Otto, K., Tian, S., Stewart, R., Slukvin, I. I., and Thomson, J. A. 2009. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324:797–801.

Downes, M., Verdecia, M. A., Roecker, A. J., Hughes, R., Hogenesch, J. B., Kast-Woelbern, H. R., Bowman, M. E., Ferrer, J. L., Anisfeld, A. M., Edwards, et al. 2003. A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR. Mol. Cell 11:1079–1092.

Evans, R. M. 2005. The nuclear receptor superfamily: A Rosetta stone for physiology. Mol. Endocrinol. 19:1429–1438.

Xu, W., Cho, H., Kadam, S., Banayo, E. M., Anderson, S., Yates, J. R., III, Emerson, B. M., and Evans, R. M. 2004. A methylation-mediator complex in hormone signaling. Genes Dev. 18:144–156.

Evans, R. M. 1988. The steroid and thyroid hormone receptor superfamily. Science 240:889–895.

Yamamoto, K. R. 1985. Steroid receptor regulated transcription of specific genes and gene networks. Annu. Rev. Genet. 19:209–252.

Tanenbaum, D. M., Wang, Y., Williams, S. P., and Sigler, P. B. 1998. Crystallographic comparison of the estrogen and progesterone receptor’s ligand binding domains. Proc. Natl. Acad. Sci. U.S.A. 95:5998–6003.

Schwabe, J. W., Chapman, L., Finch, J. T., and Rhodes, D. 1993. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements. Cell 75:567–578.

Shiau, A. K., Barstad, D., Loria, P. M., Cheng, L., Kushner, P. J., Agard, D. A., and Greene, G. L. 1998. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95:927–937.

Collingwood, T. N., Urnov, F. D., and Wolffe, A. P. 1999. Nuclear receptors: Coactivators, corepressors and chromatin remodeling in the control of transcription. J. Mol. Endocrinol. 23:255–275.

Rouault, T. A., Stout, C. D., Kaptain, S., Harford, J. B., and Klausner, R. D. 1991. Structural relationship between an iron-regulated RNA-binding protein (IRE-BP) and aconitase: Functional implications. Cell 64:881–883.

Klausner, R. D., Rouault, T. A., and Harford, J. B. 1993. Regulating the fate of mRNA: The control of cellular iron metabolism. Cell 72:19–28.

Gruer, M. J., Artymiuk, P. J., and Guest, J. R. 1997. The aconitase family: Three structural variations on a common theme. Trends Biochem. Sci. 22:3–6.

Theil, E. C. 1994. Iron regulatory elements (IREs): A family of mRNA noncoding sequences. Biochem. J. 304:1–11.

Ruvkun, G. 2008. The perfect storm of tiny RNAs. Nat. Med. 14:1041–1045.

Sethupathy, P., and Collins, F. S. 2008. MicroRNA target site polymorphisms and human disease. Trends Genet. 24:489–497.

Adams, B. D., Cowee, D. M., and White, B. A. 2009. The role of miR-206 in the epidermal growth factor (EGF) induced repression of estrogen receptor-α (ERα) signaling and a luminal phenotype in MCF-7 breast cancer cells. Mol. Endocrinol. 23:1215–1230.

Jegga, A. G., Chen, J., Gowrisankar, S., Deshmukh, M. A., Gudivada, R., Kong, S., Kaimal, V., and Aronow, B. J. 2007. GenomeTrafac: A whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs. Nucleic Acids Res. 35:D116–D121.