Transcriptional interference - A crash course

Trends in Genetics

Volumn 21, Issue 6, 2005, Pages 339-345

  Shearwin, Keith E ^a   Callen, Benjamin P ^b   Egan, J Barry ^a  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTOME;

DNA FLANKING REGION; ESCHERICHIA COLI; GENE ACTIVITY; GENE CONTROL; GENE EXPRESSION REGULATION; GENE REPRESSION; GENETIC TRANSCRIPTION; HUMAN; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; REGULATORY MECHANISM; REVIEW; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ESCHERICHIA COLI; PROMOTER REGIONS (GENETICS); RNA INTERFERENCE; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

EID: 19444377759     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2005.04.009     Document Type: Review

References (74)

1. F. Rojo Mechanisms of transcriptional repression Curr. Opin. Microbiol. 4 2001 145 151
2. K. Delaval, and R. Feil Epigenetic regulation of mammalian genomic imprinting Curr. Opin. Genet. Dev. 14 2004 188 195
3. V. Epshtein Transcription through the roadblocks: the role of RNA polymerase cooperation EMBO J. 22 2003 4719 4727
4. K.M. Wassarman RNA regulators of transcription Nat. Struct. Mol. Biol. 11 2004 803 804
5. E.J. Kuhn, and P.K. Geyer Genomic insulators: connecting properties to mechanism Curr. Opin. Cell Biol. 15 2003 259 265
6. G. Meister, and T. Tuschl Mechanisms of gene silencing by double-stranded RNA Nature 431 2004 343 349
7. S. Tanaka Transcription through the yeast origin of replication ARS1 ends at the ABFI binding site and affects extrachromosomal maintenance of minichromosomes Nucleic Acids Res. 22 1994 3904 3910
8. I. Cajiao Bystander gene activation by a locus control region EMBO J. 23 2004 3854 3863
9. J. Gribnau Intergenic transcription and developmental remodeling of chromatin subdomains in the human β-globin locus Mol. Cell 5 2000 377 386
10. M.L. Opel The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons Mol. Microbiol. 39 2001 1109 1115
11. N.J. Proudfoot Transcriptional interference and termination between duplicated α-globin gene constructs suggests a novel mechanism for gene regulation Nature 322 1986 562 565
12. I.H. Greger Transcriptional interference perturbs the binding of Sp1 to the HIV-1 promoter Nucleic Acids Res. 26 1998 1294 1301
13. E.M. Prescott, and N.J. Proudfoot Transcriptional collision between convergent genes in budding yeast Proc. Natl. Acad. Sci. U. S. A. 99 2002 8796 8801
14. S.K. Eszterhas Transcriptional interference by independently regulated genes occurs in any relative arrangement of the genes and is influenced by chromosomal integration position Mol. Cell. Biol. 22 2002 469 479
15. M. Padidam, and Y. Cao Elimination of transcriptional interference between tandem genes in plant cells Biotechniques 31 2001 328 334
16. I. Ingelbrecht Transcriptional interference in transgenic plants Gene 109 1991 239 242
17. E.N. Olson Know your neighbors: three phenotypes in null mutants of the myogenic bHLH gene MRF4 Cell 85 1996 1 4
18. A.J. Thompson, and S.C. Myatt Tetracycline-dependent activation of an upstream promoter reveals transcriptional interference between tandem genes within T-DNA in tomato Plant Mol. Biol. 34 1997 687 692
19. I.B. Dodd, and J.B. Egan Action at a distance in CI repressor regulation of the bacteriophage 186 genetic switch Mol. Microbiol. 45 2002 697 710
20. B.P. Callen Transcriptional interference between convergent promoters caused by elongation over the promoter Mol. Cell 14 2004 647 656
21. J.A. Martens Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene Nature 429 2004 571 574
22. P. Wang Demonstration that the TyrR protein and RNA polymerase complex formed at the divergent P3 promoter inhibits binding of RNA polymerase to the major promoter, P1, of the aroP gene of Escherichia coli J. Bacteriol. 180 1998 5466 5472
23. O. Boussadia Transcription of unr (upstream of N-ras) down-modulates N-ras expression in vivo FEBS Lett. 420 1997 20 24
24. E. Whitelaw, and N. Proudfoot Alpha-thalassaemia caused by a poly(A) site mutation reveals that transcriptional termination is linked to 3′ end processing in the human alpha 2 globin gene EMBO J. 5 1986 2915 2922
25. G. Jagura-Burdzy, and C.M. Thomas Dissection of the switch between genes for replication and transfer of promiscuous plasmid RK2: basis of the dominance of trfAp over trbAp and specificity for KorA in controlling the switch J. Mol. Biol. 265 1997 507 518
26. S. Brantl, and E.G. Wagner Dual function of the copR gene product of plasmid pIP501 J. Bacteriol. 179 1997 7016 7024
27. G. Lavorgna In search of antisense Trends Biochem. Sci. 29 2004 88 94
28. E. Giordano RNAi triggered by symmetrically transcribed transgenes in Drosophila melanogaster Genetics 160 2002 637 648
29. C.J. Sherr The INK4a/ARF network in tumour suppression Nat. Rev. Mol. Cell Biol. 2 2001 731 737
30. J.R. Fincham, and G.R. Sastry Controlling elements in maize Annu. Rev. Genet. 8 1974 15 50
31. E. Whitelaw, and D.I. Martin Retrotransposons as epigenetic mediators of phenotypic variation in mammals Nat. Genet. 27 2001 361 365
32. R. Druker Complex patterns of transcription at the insertion site of a retrotransposon in the mouse Nucleic Acids Res. 32 2004 5800 5808
33. A.F. Smit Interspersed repeats and other mementos of transposable elements in mammalian genomes Curr. Opin. Genet. Dev. 9 1999 657 663
34. P. Nigumann Many human genes are transcribed from the antisense promoter of L1 retrotransposon Genomics 79 2002 628 634
35. W. Nasser Transcriptional regulation of fis operon involves a module of multiple coupled promoters EMBO J. 21 2002 715 724
36. S. Saha The cox protein of bacteriophage P2 inhibits the formation of the repressor protein and autoregulates the early operon EMBO J. 6 1987 3191 3199
37. P.A. van Rijn Regulation of phage Mu repressor transcription by IHF depends on the level of the early transcription Nucleic Acids Res. 17 1989 10203 10212
38. J. Xu, and G.B. Koudelka Mutually exclusive utilization of P(R) and P(RM) promoters in bacteriophage 434 O(R) J. Bacteriol. 182 2000 3165 3174
39. M. Kimura, and I. Yamaguchi Convergent transcription units and their promoters at both ends of pot2, an inverted repeat transposon from the rice blast fungus J. Biochem. (Tokyo) 124 1998 268 273
40. R.W. Simons Three promoters near the termini of IS10: pIN, pOUT, and pIII Cell 34 1983 673 682
41. S. Adhya, and M. Gottesman Promoter occlusion: transcription through a promoter may inhibit its activity Cell 29 1982 939 944
42. R. Gafny Isolated P2 rRNA promoters of Escherichia coli are strong promoters that are subject to stringent control J. Mol. Biol. 243 1994 152 156
43. J.E. Hirschman Genetic evidence for promoter competition in Saccharomyces cerevisiae Mol. Cell. Biol. 8 1988 4608 4615
44. S. Irniger The yeast actin intron contains a cryptic promoter that can be switched on by preventing transcriptional interference Nucleic Acids Res. 20 1992 4733 4739
45. V. Corbin, and T. Maniatis Role of transcriptional interference in the Drosophila melanogaster Adh promoter switch Nature 337 1989 279 282
46. Salgado, H. et al. (2004) RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res. 32 (Database issue), 303-306
47. K. Sneppen A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coli J. Mol. Biol. 346 2005 399 409
48. B. Tjaden Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays Nucleic Acids Res. 30 2002 3732 3738
49. A. Marin Short-range compositional correlation in the yeast genome depends on transcriptional orientation Gene 333 2004 151 155
50. V.B. Bajic Promoter prediction analysis on the whole human genome Nat. Biotechnol. 22 2004 1467 1473
51. F. Chiaromonte Gene length and proximity to neighbors affect genome-wide expression levels Genome Res. 13 2003 2602 2608
52. B.A. Cohen A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression Nat. Genet. 26 2000 183 186
53. P. Portin Historical development of the concept of the gene J. Med. Philos. 27 2002 257 286
54. D. Takai, and P.A. Jones Origins of bidirectional promoters: computational analyses of intergenic distance in the human genome Mol. Biol. Evol. 21 2004 463 467
55. K. Yamada Empirical analysis of transcriptional activity in the Arabidopsis genome Science 302 2003 842 846
56. V. Stolc A gene expression map for the euchromatic genome of Drosophila melanogaster Science 306 2004 655 660
57. Y. Okazaki Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs Nature 420 2002 563 573
58. R. Yelin Widespread occurrence of antisense transcription in the human genome Nat. Biotechnol. 21 2003 379 386
59. S. Cawley Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs Cell 116 2004 499 509
60. P. Bertone Global identification of human transcribed sequences with genome tiling arrays Science 306 2004 2242 2246
61. D.F. Ward, and N.E. Murray Convergent transcription in bacteriophage lambda: interference with gene expression J. Mol. Biol. 133 1979 249 266
62. H. Horowitz, and T. Platt Regulation of transcription from tandem and convergent promoters Nucleic Acids Res. 10 1982 5447 5465
63. S.J. Elledge, and R.W. Davis Position and density effects on repression by stationary and mobile DNA-binding proteins Genes Dev. 3 1989 185 197
64. C. Conte Promoter competition as a mechanism of transcriptional interference mediated by retrotransposons EMBO J. 21 2002 3908 3916
65. O.R. Choi, and J.D. Engel Developmental regulation of β-globin gene switching Cell 55 1988 17 26
66. S. Liang Activities of constitutive promoters in Escherichia coli J. Mol. Biol. 292 1999 19 37
67. I.H. Greger Balancing transcriptional interference and initiation on the GAL7 promoter of Saccharomyces cerevisiae Proc. Natl. Acad. Sci. U. S. A. 97 2000 8415 8420
68. E. Bateman, and M.R. Paule Promoter occlusion during ribosomal RNA transcription Cell 54 1988 985 992
69. J. Roberts, and J.S. Park Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination Curr. Opin. Microbiol. 7 2004 120 125
70. V. Epshtein, and E. Nudler Cooperation between RNA polymerase molecules in transcription elongation Science 300 2003 801 805
71. S. West Human 5′→3′ exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites Nature 432 2004 522 525
72. A. Teixeira Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination Nature 432 2004 526 530
73. A.K. Nagaich Rapid periodic binding and displacement of the glucocorticoid receptor during chromatin remodeling Mol. Cell 14 2004 163 174
74. A. Remenyi Combinatorial control of gene expression Nat. Struct. Mol. Biol. 11 2004 812 815