Adam AC, Gonzáles-Blasco G, Rubio-Texeira M and Polaina J. Transformation of Escherichia coli with DNA from Saccharomyces cerevisiae Cell Lysates. Appl Environ Micriobol 65(12) 5303-306 1999. doi: 10.1128/AEM.65.12.5303-5306.1999
Amberg DC, Burke D, Strathern JN, Burke D, Cold Spring Harbor Laboratory. Methods in yeast genetics : a Cold Spring Harbor Laboratory course manual [Internet]. Cold Spring Harbor Laboratory Press; 2005. Available: https://books.google.co.jp/books/about/Methods_in_Yeast_Genetics.html?id=47zspjkK kCwC&redir_esc=y
Amon A. Regulation of B-type cyclin proteolysis by Cdc28-associated kinases in budding yeast. EMBO J 10:2693-702 1997. Doi: 10.1093/emboj/16.10.269.
Arraiano CM, Andrade JM, Domingues S, Guinote IB, Malecki M, Matos RG, Moreira RN, Pobre V, Reis FP, Saramago M, Silva IJ, Viegas SC. The critical role of RNA processing and degradation in the control of gene expression. FEMS Microbiology Reviews V 34 (5) 2010. Doi:10.1111/j.157406976.2010.00242.x
Blanchard JM. Cyclin A2 transcriptional regulation: modulation of cell cycle control at the G1/S transition by peripheral cues. Biochem Pharmacol 2000 60(8):1179-84. Doi: 10.1016/s0006-2952(00)00384-1.
Booher, R and Beach D. Interaction between cdc13 and cdc2 in the control of mitosis in fission yeast, dissociation of the G1 and G2 roles of the cdc2 protein kinase. 1987. EMBO J 6: 3441-47.
Booher RN, Deshaies RJ, Kirschner MW. Properties of Saccharomyces cerevisiae wee1 and its differential regulation of p34CDC28 in response to G1 and G2 cyclins EMBO J. 1993 Sep;12(9):3417-26.
Bueno A, Richardson H. Reed SI and Russell P. A fission yeast B-type cyclin functioning early in the cell cycle. 1991. Cell 66: 149-59.
Collart MA. The Ccr4-Not complex is a key regulator of eukaryotic gene expression. WIREs RNA (7) 438-454. 2016. Doi:10.1002/wrna.1332
Collart MA. Global control of gene expression in yeast by Ccr4-Not complex. Gene 313 1-16 2003. Doi:10.1016/s0378-1119(03)00672-3.
Collart MA, Struhl K. NOT1(CDC39), NOT2(CDC36), NOT3, and NOT4 encode a global- negative regulator of transcription that differentially affects TATA-element utilization. Genes Dev. 1994 Mar 1;8(5):525-37. doi: 10.1101/gad.8.5.525.
Cosentino GP, Schmelzle T, Haghighat A, Helliwell S , Hall MN, Sonenberg N. Eap1p, a novel eukaryotic translation initiation factor 4E-associated protein in Saccharomyces cerevisiae. Mol Cell Biol. 2000 Jul;20(13):4604-13. doi: 10.1128/MCB.20.13.4604- 4613.2000.
Duy DL, Suda Y, Irie K. Cytoplasmic deadenylase Ccr4 is required for translational repression of LRG1 mRNA in the stationary phase. PLoS one 12 (2) 2017. doi:10.1371/journal.pone.0172476.
Edfors F, Danielsson F, Hallstro BM, Ka ̈ll L, Lundberg E, Ponte ́n F, Forsstro ̈m B and Uhle ́n M. Gene-specific correlation of RNA and protein levels in human cells and tissues. 2016. Mol. Syst. Biol., 12, 883. doi: 10.15252/msb.20167144.
Forrest ME, Pinkard O, Martin S, Sweet TJ, Hanson G and Coller J. Codon and amino acid content are associated with mRNA stability in mammalian cells. 2020. PLoS One 15(2):e0228730. doi: 10.1371/journal.pone.0228730.
Futcher B. Cell cycle synchronization. Methods Cell Sci. 1999;21(2-3):79-86. doi:10.1023/a:1009872403440
Garí E, Volpe T, Wang H, Gallego C, Futcher B and Aldea M. Whi3 binds the mRNA of the G1 cyclin CLN3 to modulate cell fate in budding yeast. Genes Dev 15(21):2803-8 2001. doi: 10.1101/gad.203501.
Garneau NL, Wilusz J, Wilusz CJ. The highways and byways of mRNA decay. Nature Reviews Molecular Cell Biology 8, 113-126. 2007.
Gay S, Piccini D, Bruhn C, Ricciardi S, Soffientini P, Carotenuto W, Biffo S, Foiani M. A Mad2-Mediated Translational Regulatory Mechanism Promoting S-Phase Cyclin Synthesis Controls Origin Firing and Survival to Replication Stress. Mol Cell. 2018 May 17;70(4):628-638.e5. doi: 10.1016/j.molcel.2018.04.020.
Geissler R and Grimson A. A position-specific 3´UTR sequence that accelerates mRNA decay. 2016. RNA biol 13(11):1075-1077. doi: 10.1080/15476286.2016.1225645.
Gietz R D, Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988 Dec 30;74(2):527-34. doi: 10.1016/0378-1119(88)90185-0.
Gill T, Cai T, Aulds J, Wierzbicki S, Schmitt ME. RNAse MRP cleaves the CLB2 mRNA to promote cell cycle progression: novel method of mRNA degradation. Mol Cell Biol 24(3) 945-53 2004. Doi: 10.1128/MCB.24.3.945-953.2004.
Goldstrohm AC, Seay DJ, Hook BA, Wickens M. PUF Protein-mediated Deadenylation Is Catalyzed by Ccr4p. Journal of Biological Chemistry 282 (1) 109-114 2007. Doi:10.1074/jbc.M609413200
Glotzer M, Murray AW and Kirschner MW. Cyclin is degraded by the ubiquitin pathway. Nature. 1991 349(6305):132-8. doi: 10.1038/349132a0.
Hagan IM, Hayles J and Nurse P. Cloning ang sequencing of the cyclin related cdc13 gene and a cytological study of its role in fission yeast mitosis. 1988. J. Cell Sci. 91:587-95.
Hershko A. Mechanisms and regulation of the degradation of cyclin B. Philos Trans R Soc Lond B Biol Sci 354(138):1571-5 1999. doi: 10.1098/rstb.1999.0500.
Holder J, Mohammed S and Barr FA. Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit. Elife 9:e59885 2020. Doi: 10.7554/eLife.59885.
Holmes KJ, Klass DM, Guiney EL, Cyert MS. Whi3, an S. cerevisiae RNA-binding protein, is a component of stress granules that regulates levels of its target mRNAs. PLoS One. 2013 Dec 27;8(12):e84060. doi: 10.1371/journal.pone.0084060. eCollection 2013.
Ito W, Li X, Irie K, Mizuno T, Irie K. RNA-binding protein Khd1 and Ccr4 deadenylase play overlapping roles in the cell wall integrity pathway in Saccharomyces cerevisiae. Eukaryot Cell. 2011; 10(10): 1340-7. doi: 10.1128/EC.05181-11 PMID: 21873511.
Jackson LP, Reed SI and Haase SB. Distinct Mechanisms Control the Stability of the Related S- phase Cyclins Clb5 and Clb6. 2006. Mol Cell Biol 26(6):2456-66. doi: 10.1128/MCB.26.6.2456-2466.2006. doi: 10.1016/j.bbrc.2005.11.055.
Kimura Y, Irie K, Irie K. Pbp1 is involved in Ccr4- and Khd1-mediated regulation of cell growth through association with ribosomal proteins Rpl12a and Rpl12b. Eukaryot Cell. 2013; 12(6): 864-74. doi: 10.1128/EC.00370-12 PMID: 23563484
Koh WS, Porter JR and Batchelor E. Tuning of mRNA stability through alterign 3´-UTR sequences generates distinct output expression in a synthetic circuit driven by p53 oscillations. 2019. Sci rep 9(1)5976. doi: 10.1038/s41598-019-42509-y.
Kushnirov VV. Rapid and reliable protein extraction from yeast. Yeast. 2000;16(9):857-60. doi: 10.1002/1097-0061(20000630)16:9<857::AID-YEA561>3.0.CO;2-B. PMID:10861908
Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, Amon A, Martin KC. Molecular Cell Biology Eight Edition. W.H. Freeman and Company 2016.
Longtine MS, Mckenzie III A, Demarini DJ, Shah NG, Wach A, Brachat A, et al. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998;14: 953–961. doi:10.1002/(SICI)1097- 0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U
Manukyan A, Zhang J, Thippeswamy U, Yang J, Zavala N, Mudannayake MP, Asmussen M, Schneider C and Schneider BL. Ccr4 Alters Cell Size in Yeast by Modulating the Timing of CLN1 and CLN2 Expression. 2008. Genetics 179(1):345-57. doi: 10.1534/genetics.108.086744.
Matoulkova E, Michalova E, Vojtesek B, Hrstka R. The role of the 30 untranslated region in post- transcriptional regulation of protein expression in mammalian cells. 2012. RNA Biol 9:563-76; PMID:22614827; http://dx.doi.org/10.4161/rna.20231
Messier V, Zenklusen D, Michnick SW. A nutrient-responsive pathway that determines M phase timing through control of B-cyclin mRNA stability. Cell 153(5) 1080-93 2013. Doi:10.1016/j.cell.2013.04.035.
Mignone F, Gissi C, Liuni S and Pesole G. Untranslated regions of mRNAs. 2002. Genome Biol 3(3):REVIEWS0004. doi: 10.1186/gb-2002-3-3-reviews0004
Miller MA and Olivas WM. Roles of Puf proteins in mRNA degradation and translation. 2010. Wilen Interdiscip Rev RNA 2(4):471-92. doi: 10.1002/wrna.69.
Narula A, Ellis J, Taliaferro JM, and Rissland OS. Coding regions affect mRNA stability in human cells. 2019. RNA 25(12):1751-64. doi: 10.1261/rna.073239.119.
Nie L, Wu G and Zhang W. Correlation between mRNA and protein abundance in Desulfovibrio vulgraris: a multiple regression to identify sources of variations. 2006. Biochem Biophys Res Commun. 339(2):603-10.
Parker R. RNA Degradation in Saccharomyces cerevisae. Genetics 191(3) 671-702 2012. Doi: 10.1534/genetics.111.137265
Perl K, Ushakov K, Pozniak Y, Yizhar-Barnea O, Bhonker Y, Shivatzki Y, Shivatzki S, Geiger T, Avraham KB and Shamir R. Reduced changes in protein compared to mRNA levels across non-proliferating tissues. 2017. Genomics 18:305. doi: 10.1186/s12864-017- 3683-9.
Presnyak V, Alhusaini N, Chen Y-H, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, et al. Codon optimality is a major determinant of mRNA stability. 2015. Cell 160: 1111–1124. doi:10.1016/j.cell.2015.02.029.
Radhakrishnan A, Chen Y-H, Martin S, Alhusaini N, Green R, Coller J. The DEAD-Box protein Dhh1p couples mRNA decay and translation by monitoring codon optimality. 2016. Cell 167: 122–132. e9. doi:10.1016/j.cell.2016.08.053
Richardson H, Lew J, Henze M, Sugimoto K and Reed SI. Cyclin-B homologs in Saccharomyces cerevisiae function in S phase and in G2..Genes and Development. 1992. 6(11):2021-34. Doi: 10.1101/gad.6.11.2021.
Russell P, Moreno S, Reed SI. Conservation of mitotic controls in fission and budding yeasts Cell. 1989 Apr 21;57(2):295-303. doi: 10.1016/0092-8674(89)90967-7.
Sakumoto N, Mukai Y, Uchida K, Kouchi T, Kuwajima J, Nakagawa Y, et al. A series of protein phosphatase gene disruptants inSaccharomyces cerevisiae. Yeast. 1999;15: 1669–1679. doi:10.1002/(SICI)1097-0061(199911)15:15<1669::AID-YEA480>3.0.CO;2-6
Schladebeck S and Mösch Hans-Ulrich. The RNA-binding protein Whi3 is a key regulator of developmental signaling and ploidy in Saccharomyces cerevisiae. 195(1):73-86 2013. doi: 10.1534/genetics.113.153775
Schlisell G, Krzyzanowski MK, Caudron F, Barral Yves and Rine J. Aggregation of the Whi3 protein, not loss of heterochromatin, causes sterility in old yeast cells. Science 355(6330):1184-87 2017. doi: 10.1126/science.aaj2103.
Schoenberg DR, Maquat LE. Regulation of cytoplasmic mRNA decay. Nature Reviews Genetics 13, 246-259. 2012
Schwob E and Nasmyth E. CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces serevisiae. 1993. Genes Dev 7(7A):1160-75. doi: 10.1101/gad.7.7a.1160.
Surana U, Robitsch H, Price C, Schuster T, Fitch I, Futcher AB, Nasmyth K. The role of CDC28 and cyclins during mitosis in the budding yeast S. cerevisiae. Cell. 1991 Apr 5;65(1):145-61. doi: 10.1016/0092-8674(91)90416-v.
Tadauchi T, Matsumoto K, Herskowitz I, Irie K. Post-transcriptional regulation through the HO 3’-UTR by Mpt5, a yeast homolog of Pumilio and FBF. Embo J 20(3) 552-61 2001. doi: 10.1093/emboj/20.3.552.
Tokumoto T, Hossain F, Jyoti MS, Ali H, Hossain B, Acharjee M, Rezanujjaman and Tokumoto M. Two-Step Mechanism of Cyclin B Degradation Initiated by Proteolytic Cleavage with the 26S Proteasome in Fish. Sci Rep 10(1):8924 2020. Doi: 10.1038/s41598-020-65009- w
Traven A, Lo TL, Lithgow T and Heierhorst J. The Yeast PUF Protein Puf5 Has Pop2- Independent Roles in Response to DNA Replication Stress. 2010. PLoS One. 5(5):e10651. doi: 10.1371/journal.pone.0010651.
Trcek T, Larson DR, Moldon A, Query CC, Singer RH. Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell 147(7) 1484-97 2011. Doi:10.1016/j.cell.2011.11.051.
Tucker M, Valencia-Sanchez MA, Staples RR, Chen J, Denis CL, Parker R. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104 (3) 377-386. 2001. Doi: 10.1016/s0092-8674(01)00225-2
Tudek A, Krawczyk PS, Mroczek S, Tomecki R, Turtola M, Matylla-Kulińska K, Jensen TH, Dziembowski A. Global view on the metabolism of RNA poly(A) tails in yeast Saccharomyces cerevisiae. Nat Commun. 2021 Aug 16;12(1):4951. doi: 10.1038/s41467- 021-25251-w.
Valderrama AL, Fujii S, Duy DL, Irie K, Mizuno T, Suda Y, Irie K. Pbp1 mediates the aberrant expression of genes involved in growth defect of ccr4Δ and pop2Δ mutants in yeast Saccharomyces cerevisiae. Genes Cells 26 (6) 381-398 2021. Doi:10.111/gtc.12846.
Valencia-Sanchez MA, Liu J, Hannon GJ, Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 2006 Mar 1’20(5):515-24. Doi: 10.1101/gad.1399806
Vogel C and Marcotte EM. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. 2012. Nat. Rev. Genet., 13, 227–232. doi: 10.1038/nrg3185
Wegler C, Ölander M, Wiśniewski JR, Lundquist P, Zettl K, Åsberg A, Hjelmesæth J, Andersson TB and Artursson P. 2019. Global variability analysis of mRNA and protein concentrations across and within human tissues. 2020. NAR Genomics and Bioinformatics 2(1). doi: 10.1093/nargab/lqz010
Westmoreland TJ, Marks JR, Olson Jr. JA, Thompson EM, Resnick MA and Bennett CB. Cell Cycle Progression in G1 and S Phases Is CCR4 Dependent following Ionizing Radiation or Replication Stress in Saccharomyces cerevisiae. 2004. Eukaryot Cell 3(2):430-46. doi: 10.1128/EC.3.2.430-446.2004.
Wilinski D, Qiu C, Lapointe CP, Nevil M, Campbell ZT, Tanaka Hall TM, et al. RNA regulatory networks diversified through curvature of the PUF protein scaffold. Nat Commun. 2015; 6: 8213. doi: 10.1038/ncomms9213 PMID: 26364903
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