Eukaryotic Molecular Genetics at UMBC

Transcription mechanisms

Lee TT & Young RA. 2000. Transcription of eukaryotic protein-coding genes. Annu Rev Genet. 34:77-137.

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

Asturias FJ. 2004. RNA polymerase II structure, and organization of the preinitiation complex. Curr Opin Struct Biol. 14:121-9.

Woychik NA, Hampsey M. 2002. The RNA polymerase II machinery: structure illuminates function.
Cell. 108:453-63.

Orphanides G, Reinberg D. 2002. A unified theory of gene expression. Cell. 108:439-51.

Asturias FJ, Craighead JL. 2003. RNA polymerase II at initiation. Proc Natl Acad Sci U S A. 100:6893-5.

Chromatin remodelling

Felsenfeld G, Groudine M. 2003. Controlling the double helix. Nature. 421:448-53.

Khorasanizadeh S. 2004. The nucleosome: from genomic organization to genomic regulation. Cell. 116:259-72.

Cosma MP. Ordered recruitment: gene-specific mechanism of transcription activation. Mol Cell. 2002 10:227-36.

Fry CJ, Peterson CL. 2001. Chromatin remodeling enzymes: who's on first? Curr Biol. 2001 11:R185-97.

Svejstrup JQ. 2004. The RNA polymerase II transcription cycle: cycling through chromatin.
Biochim Biophys Acta. 1677:64-73.

Svejstrup JQ. 2003. Transcription: histones face the FACT. Science. 301:1053-5.

Narlikar GJ, Fan HY, Kingston RE. 2002. Cooperation between complexes that regulate chromatin structure and transcription. Cell. 108:475-87.

Histone code

Turner BM. Cellular memory and the histone code. Cell. 2002 111:285-91.

de la Cruz X, Lois S, Sanchez-Molina S, Martinez-Balbas MA. Do protein motifs read the histone code? Bioessays. 2005 27:164-75.

Cosgrove MS, Boeke JD, Wolberger C. Regulated nucleosome mobility and the histone code. Nat Struct Mol Biol. 2004 11:1037-43.

Fischle W, Wang Y, Allis CD. Binary switches and modification cassettes in histone biology and beyond. Nature. 2003 425:475-9.

Transcription elongation

Sims RJ, Belotserkovskaya R, Reinberg D. 2004. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18:2437-68.

Dvir A, Conaway JW, Conaway RC. 2001. Mechanism of transcription initiation and promoter escape by RNA polymerase II. Curr Opin Genet Dev. 11:209-14.

Co-transcriptional processing

Kornblihtt AR, de la Mata M, Fededa JP, Munoz MJ, Nogues G. Multiple links between transcription and splicing. RNA. 2004 10:1489-98.

Neugebauer KM. On the importance of being co-transcriptional. J Cell Sci. 2002 115:3865-71.

Howe KJ. RNA polymerase II conducts a symphony of pre-mRNA processing activities. Biochim Biophys Acta. 2002 1577:308-24.

Bentley D. The mRNA assembly line: transcription and processing machines in the same factory. Curr Opin Cell Biol. 2002 14:336-42.

Reed R. Coupling transcription, splicing and mRNA export. Curr Opin Cell Biol. 2003 15:326-31.

Regulatory networks

Wyrick JJ, Young RA. 2002. Deciphering gene expression regulatory networks. Curr Opin Genet Dev. 12:130-6.

Chua G, Robinson MD, Morris Q, Hughes TR. 2004. Transcriptional networks: reverse-engineering gene regulation on a global scale. Curr Opin Microbiol. 7:638-46.

MicroRNAs

Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 116:281-97.

He L, Hannon GJ. 2004. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet. 5:522-31.

Cullen BR. 2004. Transcription and processing of human microRNA precursors. Mol Cell. 16:861-5.

Xu P, Guo M, Hay BA. 2004. MicroRNAs and the regulation of cell death. Trends Genet. 20:617-24.

Ambros V. 2004. The functions of animal microRNAs. Nature. 431:350-5.

Control of translational reinitiation

Hinnebusch AG. Translational regulation of yeast GCN4. A window on factors that control initiator-trna binding to the ribosome. J Biol Chem. 1997 272:21661-4.