3′ Untranslated Regions Mediate Transcriptional Interference between Convergent Genes Both Locally and Ectopically in Saccharomyces cerevisiae

PLoS Genetics

Volumn 10, Issue 1, 2014, Pages

  Wang, Luwen ^a   Jiang, Ning ^a   Wang, Lin ^a   Fang, Ou ^a   Leach, Lindsey J ^b   Hu, Xiaohua ^a   Luo, Zewei ^a,b  

^a FUDAN UNIVERSITY   (China)

^b UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; COMPLEMENTARY RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ADE1 GENE; APT1 GENE; ARTICLE; AXL2 GENE; CELL BUDDING; CELL CYCLE; CONTROLLED STUDY; DNA MODIFICATION; FRAMESHIFT MUTATION; FUNGAL GENE; FUNGAL STRAIN; GENE EXPRESSION; HAPLOIDY; KIN3 GENE; NONHUMAN; OPEN READING FRAME; PHENOTYPE; REV7 GENE; RNA SEQUENCE; SACCHAROMYCES CEREVISIAE; SHM1 GENE; UNG1 GENE; UPREGULATION; YEAST CELL; YPT10 GENE; FUNGAL GENOME; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS;

3' UNTRANSLATED REGIONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENOME, FUNGAL; MICRORNAS; OPEN READING FRAMES; RNA, ANTISENSE; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

EID: 84896692153     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004021     Document Type: Article

References (42)

1. Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, et al. (2004) In search of antisense. Trends Biochem Sci 29: 88-94.
2. Guell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, et al. (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268-1271.
3. Zhang Y, Liu XS, Liu QR, Wei L, (2006) Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 34: 3465-3475.
4. Chen N, Stein LD, (2006) Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans. Genome Res 16: 606-617.
5. Krom N, Ramakrishna W, (2008) Comparative analysis of divergent and convergent gene pairs and their expression patterns in rice, Arabidopsis, and populus. Plant Physiol 147: 1763-1773.
6. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW, (2008) The antisense transcriptomes of human cells. Science 322: 1855-1857.
7. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, et al. (2005) Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
8. Nishizawa M, Komai T, Katou Y, Shirahige K, Ito T, et al. (2008) Nutrient-regulated antisense and intragenic RNAs modulate a signal transduction pathway in yeast. PLoS Biol 6: 2817-2830.
9. Hongay CF, Grisafi PL, Galitski T, Fink GR, (2006) Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127: 735-745.
10. Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F, (2007) Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131: 706-717.
11. Camblong J, Beyrouthy N, Guffanti E, Schlaepfer G, Steinmetz LM, et al. (2009) Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 23: 1434-1445.
12. Gullerova M, Proudfoot NJ, (2008) Cohesin complex promotes transcriptional termination between convergent genes in S. pombe. Cell 132: 983-995.
13. Prescott EM, Proudfoot NJ, (2002) Transcriptional collision between convergent genes in budding yeast. Proc Natl Acad Sci USA 99: 8796-8801.
14. Shearwin KE, Callen BP, Egan JB, (2005) Transcriptional interference-a crash course. Trends Genet 21: 339-345.
15. Faghihi MA, Wahlestedt C, (2009) Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 10: 637-643.
16. Crampton N, Bonass WA, Kirkham J, Rivetti C, Thomson NH, (2006) Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy. Nucleic Acids Res 34: 5416-5425.
17. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349.
18. Churchman LS, Weissman JS, (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 469 (20):: 368-375.
19. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, et al. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res 37: e123.
20. Hu XH, Wang MH, Tan T, Li JR, Yang H, et al. (2007) Genetic dissection of ethanol tolerance in the budding yeast Saccharomyces cerevisiae. Genetics 175: 1479-1487.
21. Wilson WA, Roach PJ, (2002) Nutrient-regulated protein kinases in budding yeast. Cell 111: 155-158.
22. Daignan-Fornier B, Fink GR, (1992) Coregulation of purine and histidine biosynthesis by the transcriptional activators BAS1 and BAS2. Proc Natl Acad Sci USA 89: 6746-6750.
23. Struhl K, (1995) Yeast transcriptional regulatory mechanisms. Annu Rev Genetics 29: 651-674.
24. Goeffeau A, Barrell BG, Bussey H, Davis RW, Dujon B, et al. (1996) Life with 6000 genes. Science 274: 546-567.
25. Gullerova M, Moazed D, Proudfoot NJ, (2011) Autoregulation of convergent RNAi genes in fission yeast. Genes Dev 25: 556-568.
26. Drinnenberg IA, Weinberg DE, Xie KT, Mower JP, Wolfe KH, et al. (2009) RNAi in budding yeast. Science 326: 544-550.
27. Grewal SI, Jia S, (2007) Heterochromatin revisited. Nat Rev Genet 8: 35-46.
28. Kitazono AA, Tobe BT, Kalton H, Diamant N, Kron SJ, (2002) Marker-fusion PCR for one-step mutagenesis of essential genes in yeast. Yeast 19: 141-149.
29. McNabb DS, Reed R, Marciniak RA, (2005) Dual luciferase assay system for rapid assessment of gene expression in Saccharomyces cerevisiae. Eukaryot Cell 4: 1539-1549.
30. Schmitt ME, Brown TA, Trumpower BL, (1990) A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res 18: 3091-3092.
31. Del Aguila EM, Dutra MB, Silva JT, Paschoalin VM, (2005) Comparing protocols for preparation of DNA-free total yeast RNA suitable for RT-PCR. BMC Mol Biol 6: 9.
32. Yazawa H, Iwahashi H, Kamisaka Y, Kimura K, Uemura H, (2009) Production of polyunsaturated fatty acids in yeast Saccharomyces cerevisiae and its relation to alkaline pH tolerance. Yeast 26: 167-184.
33. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
34. Emmerth S, Schober H, Gaidatzis D, Roloff T, Jacobeit K, et al. (2010) Nuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly. Dev Cell 18: 102-113.
35. Souto G, Giacometti R, Silberstein S, Giasson L, Cantore ML, et al. (2006) Expression of TPK1 and TPK2 genes encoding PKA catalytic subunits during growth and morphogenesis in Candida albicans. Yeast 23: 591-603.
36. Estrella LA, Wilkinson MF, Gonzalez CI, (2009) The shuttling protein Npl3 promotes translation termination accuracy in Saccharomyces cerevisiae. J Mol Biol 394: 410-422.
37. Fang F, Salmon K, Shen MW, Aeling KA, Ito E, et al. (2011) A vector set for systematic metabolic engineering in Saccharomyces cerevisiae. Yeast 28: 123-136.
38. Stowers CC, Boczko EM, (2007) Reliable cell disruption in yeast. Yeast 24: 533-541.
39. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, et al. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9: 3273-3297.
40. Fujita M, Hori Y, Shirahige K, Tsurimoto T, Yoshikawa H, et al. (1998) Cell cycle dependent topological changes of chromosomal replication origins in Saccharomyces cerevisiae. Genes Cells 3: 737-749.
41. Tang F, Barbacioru C, Nordman E, Li B, Xu N, et al. (2010) RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5: 516-535.
42. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.