Zinc-dependent regulation of the adh1 antisense transcript in fission yeast

Journal of Biological Chemistry

Volumn 288, Issue 2, 2013, Pages 759-769

  Ehrensberger, Kate M ^a   Mason, Carter ^a   Corkins, Mark E ^a   Anderson, Cole ^a   Dutrow, Natalie ^b   Cairns, Bradley R ^c   Dalley, Brian ^c   Milash, Brett ^c   Bird, Amanda J ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE; ANTISENSE; CONSTITUTIVE PROMOTERS; EXPRESSION PATTERNS; FISSION YEAST; SCHIZOSACCHAROMYCES POMBE; SECONDARY MECHANISMS; TRANSCRIPTIONAL CONTROL; TRANSCRIPTIONAL LEVELS; TRANSCRIPTOME PROFILING;

ALDEHYDES; CELLS; CYTOLOGY; ETHANOL; PLANTS (BOTANY); TRANSCRIPTION; YEAST;

ZINC;

ALCOHOL DEHYDROGENASE 1; OXIDOREDUCTASE; UNCLASSIFIED DRUG; ZINC;

ADH1 GENE; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE REPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; SCHIZOSACCHAROMYCES POMBE; TRANSCRIPTION REGULATION;

ALCOHOL DEHYDROGENASE; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; POLYMERASE CHAIN REACTION; RNA, ANTISENSE; RNA, MESSENGER; SCHIZOSACCHAROMYCES; TRANSCRIPTOME; ZINC;

SCHIZOSACCHAROMYCES POMBE; SCHIZOSACCHAROMYCETACEAE;

EID: 84872285505     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M112.406165     Document Type: Article

References (48)

1. Hahn, S., and Young, E. T. (2011) Transcriptional regulation in Saccharomyces cerevisiae: transcription factor regulation and function, mechanisms of initiation, and roles of activators and coactivators. Genetics 189, 705-736
2. Ehrensberger, K. M., and Bird, A. J. (2011) Hammering out details: regulating metal levels in eukaryotes. Trends Biochem. Sci. 36, 524-531
3. Günther, V., Lindert, U., and Schaffner, W. (2012) The taste of heavy metals: gene regulation by MTF-1. Biochim. Biophys. Acta 1823, 1416-1425
4. Hentze, M. W., Muckenthaler, M. U., Galy, B., and Camaschella, C. (2010) Two to tango: regulation of mammalian iron metabolism. Cell 142, 24-38
5. Puig, S., Askeland, E., and Thiele, D. J. (2005) Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation. Cell 120, 99-110 (Pubitemid 40094606)
6. Matsui, A., Ishida, J., Morosawa, T., Mochizuki, Y., Kaminuma, E., Endo, T. A., Okamoto, M., Nambara, E., Nakajima, M., Kawashima, M., Satou, M., Kim, J. M., Kobayashi, N., Toyoda, T., Shinozaki, K., and Seki, M. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol. 49, 1135-1149
7. Ni, T., Tu, K., Wang, Z., Song, S., Wu, H., Xie, B., Scott, K. C., Grewal, S. I., Gao, Y., and Zhu, J. (2010) The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe. PLoS ONE 5, e15271
8. Yassour, M., Pfiffner, J., Levin, J. Z., Adiconis, X., Gnirke, A., Nusbaum, C., Thompson, D. A., Friedman, N., and Regev, A. (2010) Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol. 11, R87
9. Faghihi, M. A., Kocerha, J., Modarresi, F., Engström, P. G., Chalk, A. M., Brothers, S. P., Koesema, E., St. Laurent, G., 3rd, and Wahlestedt, C. (2010) RNAi screen indicates widespread biological function for human natural antisense transcripts. PLoS ONE 5, e13177
10. Faghihi, M. A., Modarresi, F., Khalil, A. M., Wood, D. E., Sahagan, B. G., Morgan, T. E., Finch, C. E., St. Laurent, G., 3rd, Kenny, P. J., and Wahlestedt, C. (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase. Nat. Med. 14, 723-730
11. Houseley, J., Rubbi, L., Grunstein, M., Tollervey, D., and Vogelauer, M. (2008) A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol. Cell 32, 685-695
12. Camblong, J., Beyrouthy, N., Guffanti, E., Schlaepfer, G., Steinmetz, L. M., and Stutz, F. (2009) Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev. 23, 1534-1545
13. Hongay, C. F., Grisafi, P. L., Galitski, T., and Fink, G. R. (2006) Antisense transcription controls cell fate in Saccharomyces cerevisiae. Cell 127, 735-745 (Pubitemid 44716254)
14. Werner, A., and Swan, D. (2010) What are natural antisense transcripts good for? Biochem. Soc. Trans. 38, 1144-1149
15. Li, J. T., Zhang, Y., Kong, L., Liu, Q. R., and Wei, L. (2008) Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation. Nucleic Acids Res. 36, 4833-4844
16. Faghihi, M. A., and Wahlestedt, C. (2009) Regulatory roles of natural antisense transcripts. Nat. Rev. Mol. Cell Biol. 10, 637-643
17. Prescott, E. M., and Proudfoot, N. J. (2002) Transcriptional collision between convergent genes in budding yeast. Proc. Natl. Acad. Sci. U.S.A. 99, 8796-8801 (Pubitemid 34693638)
18. Beltran, M., Puig, I., Peña, C., García, J. M., Alvarez, A. B., Peña, R., Bonilla, F., and de Herreros, A. G. (2008) A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev. 22, 756-769 (Pubitemid 351439107)
19. Peters, N. T., Rohrbach, J. A., Zalewski, B. A., Byrkett, C. M., and Vaughn, J. C. (2003) RNA editing and regulation of Drosophila 4f-rnp expression by sas-10 antisense readthrough mRNA transcripts. RNA 9, 698-710 (Pubitemid 36618198)
20. Moazed, D. (2009) Small RNAs in transcriptional gene silencing and genome defence. Nature 457, 413-420
21. Carthew, R. W., and Sontheimer, E. J. (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136, 642-655
22. Bähler, J., Wu, J. Q., Longtine, M. S., Shah, N. G., McKenzie, A., 3rd, Steever, A. B., Wach, A., Philippsen, P., and Pringle, J. R. (1998) Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe. Yeast 14, 943-951 (Pubitemid 28328000)
23. Myers, A. M., Tzagoloff, A., Kinney, D. M., and Lusty, C. J. (1986) Yeast shuttle and integrative vectors with multiple cloning sites suitable for construction of lacZ fusions. Gene 45, 299-310 (Pubitemid 17202582)
24. Keeney, J. B., and Boeke, J. D. (1994) Efficient targeted integration at leu1-32 and ura4-294 in Schizosaccharomyces pombe. Genetics 136, 849-856 (Pubitemid 24085636)
25. Forsburg, S. L. (1993) Comparison of Schizosaccharomyces pombe expression systems. Nucleic Acids Res. 21, 2955-2956
26. Zhao, H., and Eide, D. J. (1997) Zap1p, a metalloregulatory protein involved in zinc-responsive transcriptional regulation in Saccharomyces cerevisiae. Mol. Cell. Biol. 17, 5044-5052 (Pubitemid 27357603)
27. Dutrow, N., Nix, D. A., Holt, D., Milash, B., Dalley, B., Westbroek, E., Parnell, T. J., and Cairns, B. R. (2008) Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat. Genet. 40, 977-986
28. Peter, M., Gartner, A., Horecka, J., Ammerer, G., and Herskowitz, I. (1993) FAR1 links the signal transduction pathway to the cell cycle machinery in yeast. Cell 73, 747-760
29. Roberts, D. N., Stewart, A. J., Huff, J. T., and Cairns, B. R. (2003) The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc. Natl. Acad. Sci. U.S.A. 100, 14695-14700 (Pubitemid 37517953)
30. Guarente, L. (1983) Yeast promoters and lacZ fusions designed to study expression of cloned genes in yeast. Methods Enzymol. 101, 181-191
31. Auld, D. S., and Bergman, T. (2008) Medium- and short-chain dehydrogenase/reductase gene and protein families: the role of zinc for alcohol dehydrogenase structure and function. Cell. Mol. Life Sci. 65, 3961-3970
32. de Smidt, O., du Preez, J. C., and Albertyn, J. (2008) The alcohol dehydrogenases of Saccharomyces cerevisiae: a comprehensive review. FEMS Yeast Res. 8, 967-978
33. Dainty, S. J., Kennedy, C. A., Watt, S., Bähler, J., and Whitehall, S. K. (2008) Response of Schizosaccharomyces pombe to zinc deficiency. Eukaryot. Cell 7, 454-464 (Pubitemid 351959673)
34. Komarnitsky, P., Cho, E. J., and Buratowski, S. (2000) Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription. Genes Dev. 14, 2452-2460
35. Maundrell, K. (1990) nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. J. Biol. Chem. 265, 10857-10864
36. Camblong, J., Iglesias, N., Fickentscher, C., Dieppois, G., and Stutz, F. (2007) Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131, 706-717 (Pubitemid 350087198)
37. Iida, T., Nakayama, J., and Moazed, D. (2008) siRNA-mediated heterochromatin establishment requires HP1 and is associated with antisense transcription. Mol. Cell 31, 178-189 (Pubitemid 352001402)
38. Wu, C. Y., Bird, A. J., Chung, L. M., Newton, M. A., Winge, D. R., and Eide, D. J. (2008) Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae. BMC Genomics 9, 370
39. Eide, D. J. (2009) Homeostatic and adaptive responses to zinc deficiency in Saccharomyces cerevisiae. J. Biol. Chem. 284, 18565-18569
40. Bühler, M., Spies, N., Bartel, D. P., and Moazed, D. (2008) TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway. Nat. Struct. Mol. Biol. 15, 1015-1023
41. Neil, H., Malabat, C., d'Aubenton-Carafa, Y., Xu, Z., Steinmetz, L. M., and Jacquier, A. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457, 1038-1042
42. Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder-Münster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W., and Steinmetz, L. M. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature 457, 1033-1037
43. Zhang, X., Xia, J., Lii, Y. E., Barrera-Figueroa, B. E., Zhou, X., Gao, S., Lu, L., Niu, D., Chen, Z., Leung, C., Wong, T., Zhang, H., Guo, J., Li, Y., Liu, R., Liang, W., Zhu, J. K., Zhang, W., and Jin, H. (2012) Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function. Genome Biol. 13, R20
44. Xu, Z., Wei, W., Gagneur, J., Clauder-Münster, S., Smolik, M., Huber, W., and Steinmetz, L. M. (2011) Antisense expression increases gene expression variability and locus interdependency. Mol. Syst. Biol. 7, 468
45. Yu, W., Gius, D., Onyango, P., Muldoon-Jacobs, K., Karp, J., Feinberg, A. P., and Cui, H. (2008) Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 451, 202-206
46. Maruyama, R., Shipitsin, M., Choudhury, S., Wu, Z., Protopopov, A., Yao, J., Lo, P. K., Bessarabova, M., Ishkin, A., Nikolsky, Y., Liu, X. S., Sukumar, S., and Polyak, K. (2012) Altered antisense-to-sense transcript ratios in breast cancer. Proc. Natl. Acad. Sci. U.S.A. 109, 2820-2824
47. Taft, R. J., Pang, K. C., Mercer, T. R., Dinger, M., and Mattick, J. S. (2010) Non-coding RNAs: regulators of disease. J. Pathol. 220, 126-139
48. Tufarelli, C., Stanley, J. A., Garrick, D., Sharpe, J. A., Ayyub, H., Wood, W. G., and Higgs, D. R. (2003) Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat. Genet. 34, 157-165 (Pubitemid 36666926)