RNA Polymerases and Transcription Basics

Abbondanzieri, E.A., W.J. Greenleaf, J.W. Shaevitz, R. Landick, and S.M. Block. 2005. Direct observation of base-pair stepping by RNA polymerase. Nature 438:460–465. A description of how individual polymerase molecules can be analyzed.

Carninci, P., T. Kasukawa, S. Katayama, J. Gough, M.C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309:1559–1563. This paper exemplifies a common research approach to analyzing when and where transcription occurs within an entire genome. The bottom line: many transcripts do not correspond to protein-coding genes, implying that these transcripts correspond to functional RNAs.

Darnell, J.E. Jr. 2002. Transcription factors as targets for cancer therapy. Nat. Rev. Cancer 2:740–749.

Gong, X.Q., C. Zhang, M. Feig, and Z.F. Burton. 2005. Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II. Mol. Cell 18:461–470.

Hurwitz, J. 2005. The discovery of RNA polymerase. J. Biol. Chem. 280:42,477–42,485. A summary of work in several different laboratories using complementary approaches.

Malik, S., and R.G. Roeder. 2006. Dynamic regulation of Pol II transcription by the mammalian Mediator complex. Trends Biochem. Sci. 30:256–263. This review is a good source for more information on the complexities of transcription in vivo.

Studitsky, V.M., W. Walter, M. Kireeva, M. Kashlev, and G. Felsenfeld. 2004. Chromatin remodeling by RNA polymerases. Trends Biochem. Sci. 29:127–135. A review of data and models for transcription in vivo.

Transcription in Bacteria

Darst, S.A. 2004. New inhibitors targeting bacterial RNA polymerase. Trends Biochem. Sci. 29:159–160.

Holmes, S.F., T.J. Santangelo, C.K. Cunningham, J.W. Roberts, and D.A. Erie. 2006. Kinetic investigation of Escherichia coli RNA polymerase mutants that influence nucleotide discrimination and transcription fidelity. J. Biol. Chem. 281:18,677–18,683.

Young, B.A., T.M. Gruber, and C.A. Gross. 2004. Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting. Science 303:1382–1384.

Transcription in Eukaryotes

Björklund, S., and C.M. Gustafsson. 2005. The yeast Mediator complex and its regulation. Trends Biochem. Sci. 30:240–244.

Deato, M.D., and R. Tjian. 2007. Switching of the core transcription machinery during myogenesis. Genes Dev. 21:2137–2149.

Halasz, G., M.F. van Batenburg, J. Perusse, S. Hua, X.J. Lu, K.P. White, and H.J. Bussemaker. 2006. Detecting transcriptionally active regions using genomic tiling arrays. Genome Biol. 7:R59. Description of a comprehensive method for detecting transcripts in cell extracts.

Jacquier, A. 2009. The complex eukaryotic transcriptome: Unexpected pervasive transcription and novel small RNAs. Nat. Rev. Genet. 10:833–844.

Vierbuchen, T., A. Ostermeier, Z.P. Pang, Y. Kokubu, T.C. Südhof, and M. Wernig. 2010. Direct conversion of fibroblasts to functional neurons by defined factors. Nature 463:1035–1041.

Voss, T.C., and G.L. Hager. 2014. Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat. Rev. Genet. 15:69–81.

Willingham, A.T., and T.R. Gingeras. 2006. TUF love for “junk” DNA. Cell 125:1215–1220. A short, informative review of noncoding transcripts and their possible biological functions.

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