Regulation of gene expression by reiterative transcription.

Gene regulation involves many different types of transcription control mechanisms, including mechanisms based on reiterative transcription in which nucleotides are repetitively added to the 3' end of a nascent transcript due to upstream transcript slippage. In these mechanisms, reiterative transcription is typically modulated by interactions between RNA polymerase and its nucleoside triphosphate substrates without the involvement of regulatory proteins. This review describes the current state of knowledge of gene regulation involving reiterative transcription. It focuses on the methods by which reiterative transcription is controlled and emphasizes the different fates of transcripts produced by this reaction. The review also includes a discussion of possible new and fundamentally different mechanisms of gene regulation that rely on conditional reiterative transcription.

[1]  R. Switzer,et al.  Regulation of Transcription of the Bacillus subtilis pyrG Gene, Encoding Cytidine Triphosphate Synthetase , 2001, Journal of bacteriology.

[2]  J. Barr,et al.  Polymerase Slippage at Vesicular Stomatitis Virus Gene Junctions To Generate Poly(A) Is Regulated by the Upstream 3′-AUAC-5′ Tetranucleotide: Implications for the Mechanism of Transcription Termination , 2001, Journal of Virology.

[3]  E. Amiott,et al.  Sensitivity of the Yeast Mitochondrial RNA Polymerase to +1 and +2 Initiating Nucleotides* , 2006, Journal of Biological Chemistry.

[4]  C. Turnbough,et al.  Regulation of pyrBI operon expression in Escherichia coli by UTP-sensitive reiterative RNA synthesis during transcriptional initiation. , 1994, Genes & development.

[5]  D. Kolakofsky,et al.  Pseudo-templated transcription in prokaryotic and eukaryotic organisms. , 1991, Genes & development.

[6]  J. Roberts,et al.  Heterogeneous initiation due to slippage at the bacteriophage 82 late gene promoter in vitro. , 1990, Biochemistry.

[7]  M. Chamberlin,et al.  DEOXYRIBONUCLEIC ACID-DIRECTED SYNTHESIS OF RIBONUCLEIC ACID BY AN ENZYME FROM ESCHERICHIA COLI , 1962 .

[8]  D. Garcin,et al.  The Versatility of Paramyxovirus RNA Polymerase Stuttering , 1999, Journal of Virology.

[9]  Ivica Tamas,et al.  Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts , 2008, Proceedings of the National Academy of Sciences.

[10]  D. Brow,et al.  Regulation of a eukaryotic gene by GTP-dependent start site selection and transcription attenuation. , 2008, Molecular cell.

[11]  Philippe Sansonetti,et al.  Transcriptional slippage controls production of type III secretion apparatus components in Shigella flexneri , 2006, Molecular microbiology.

[12]  C. Combet,et al.  Transcriptional slippage prompts recoding in alternate reading frames in the hepatitis C virus (HCV) core sequence from strain HCV-1. , 2008, The Journal of general virology.

[13]  R. Switzer,et al.  Regulation of pyrG expression in Bacillus subtilis: CTP‐regulated antitermination and reiterative transcription with pyrG templates in vitro , 2007, Molecular microbiology.

[14]  G. Varani,et al.  The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. , 2000, EMBO reports.

[15]  J. F. Atkins,et al.  Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[16]  A. Elsholz,et al.  The Number of G Residues in the Bacillus subtilis pyrG Initially Transcribed Region Governs Reiterative Transcription-Mediated Regulation , 2006, Journal of bacteriology.

[17]  D. Luse,et al.  Strong Natural Pausing by RNA Polymerase II within 10 Bases of Transcription Start May Result in Repeated Slippage and Reextension of the Nascent RNA , 2002, Molecular and Cellular Biology.

[18]  J. Goodrich,et al.  TATA-binding Protein and Transcription Factor IIB Induce Transcript Slipping during Early Transcription by RNA Polymerase II* , 2009, Journal of Biological Chemistry.

[19]  C. Turnbough,et al.  Regulation of Pyrimidine Biosynthetic Gene Expression in Bacteria: Repression without Repressors , 2008, Microbiology and Molecular Biology Reviews.

[20]  M. Kashlev,et al.  The 8-Nucleotide-long RNA:DNA Hybrid Is a Primary Stability Determinant of the RNA Polymerase II Elongation Complex* , 2000, The Journal of Biological Chemistry.

[21]  B. Moss,et al.  Characterization and temporal regulation of mRNAs encoded by vaccinia virus intermediate-stage genes , 1993, Journal of virology.

[22]  C. Martin,et al.  Processivity in early stages of transcription by T7 RNA polymerase. , 1988, Biochemistry.

[23]  K. I. Sørensen,et al.  Nucleotide pool-sensitive selection of the transcriptional start site in vivo at the Salmonella typhimurium pyrC and pyrD promoters , 1993, Journal of bacteriology.

[24]  Hanah Margalit,et al.  PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites , 2001, Nucleic Acids Res..

[25]  C. Turnbough,et al.  Multiple control mechanisms for pyrimidine-mediated regulation of pyrBI operon expression in Escherichia coli K-12 , 1989, Journal of bacteriology.

[26]  C. Turnbough,et al.  Attenuation control of pyrG expression in Bacillus subtilis is mediated by CTP-sensitive reiterative transcription. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  S. Young,et al.  Reading-frame Restoration by Transcriptional Slippage at Long Stretches of Adenine Residues in Mammalian Cells* , 1997, The Journal of Biological Chemistry.

[28]  C. Turnbough,et al.  A Long T · A Tract in the uppInitially Transcribed Region Is Required for Regulation ofupp Expression by UTP-Dependent Reiterative Transcription inEscherichia coli , 2001, Journal of bacteriology.

[29]  W. Mcallister,et al.  Termination and slippage by bacteriophage T7 RNA polymerase. , 1993, Journal of Molecular Biology.

[30]  B. Dujon,et al.  Transcription and nuclear transport of CAG/CTG trinucleotide repeats in yeast. , 2002, Nucleic acids research.

[31]  J. F. Atkins,et al.  Recoding : expansion of decoding rules enriches gene expression , 2010 .

[32]  W. Lane,et al.  Molecular evolution of multisubunit RNA polymerases: sequence analysis. , 2010, Journal of molecular biology.

[33]  C. Turnbough,et al.  Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli , 1994, Journal of bacteriology.

[34]  S. Young,et al.  Long runs of adenines and human mutations. , 1998, American journal of medical genetics.

[35]  W. Reznikoff,et al.  Transcriptional slippage during the transcription initiation process at a mutant lac promoter in vivo. , 1993, Journal of molecular biology.

[36]  D. Temiakov,et al.  Maintenance of RNA-DNA Hybrid Length in Bacterial RNA Polymerases* , 2009, Journal of Biological Chemistry.

[37]  B. Séraphin,et al.  Futile cycle of transcription initiation and termination modulates the response to nucleotide shortage in S. cerevisiae. , 2008, Molecular cell.

[38]  Andrew W. Hammer,et al.  Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression , 2005, Genome Biology.

[39]  C. Turnbough,et al.  Regulation of codBA operon expression in Escherichia coli by UTP-dependent reiterative transcription and UTP-sensitive transcriptional start site switching. , 1995, Journal of molecular biology.