References
- Haimovich G, Medina D, Causse S, et al. Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell. 2013;153:1000–1011.
- Braun KA, Young ET. Coupling mRNA synthesis and decay. Mol Cell Biol. 2014;34:4078–4087.
- Bellofatto V, Wilusz J. Transcription and mRNA stability: parental guidance suggested. Cell. 2011;147:1438–1439.
- Trcek T, Larson DR, Moldón A, et al. Single-molecule mRNA decay measurements reveal promoter regulated mRNA stability in yeast. Cell. 2011;23:1484–1497.
- Goler-Baron V, Selitrennik, M., Barkai, O, et al. Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes. Genes Dev. 2008;22:2022–2027.
- Bregman A, Avraham-Kelbert M, Barkai O, et al. Promoter elements regulate cytoplasmic mRNA decay. Cell. 2011;147:1473–1483.
- Farago M, Nahari T, Hammel C, et al. Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress. Mol Biol Cell. 2003;14:2744–2755.
- Harel-Sharvit L, Eldad N, Haimovich G, et al. RNA polymerase II subunits link transcription and mRNA decay to translation. Cell. 2010;143:552–563.
- Lotan R, Bar-On, V. G., Harel-Sharvit, L, et al. The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Gen & Dev. 2005;19:3004–3016.
- Lotan R, Goler-Baron V, Duek L, et al. The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol. 2007;178:1133–1143.
- Villanyi Z, Ribaud V, Kassem S, et al. The Not5 subunit of the Ccr4-not complex connects transcription and translation. PLOS Genet. 2014;10:1–15.
- Anderson JS, Parker R. The 30 to 50 degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 30 to 50 exonucleases of the exosome complex. Embo J. 1998;17:1497–1506.
- Parker R. RNA degradation in saccharomyces cerevisiae. Genet. 2012;191:671–702.
- Lee JE, Lee JY, Trembly J, et al. The PARN deadenylase targets a discrete set of mRNAs for decay and regulates cell motility in mouse myoblasts. PLoS Genet. 2012;8:1–13.
- Sun M, Schwalb B, Schulz D, et al. Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Res. 2012;22:1350–1359.
- Sun M, Schwalb B, Pirkl N, et al. Global analysis of eukaryotic mRNA degradation reveals Xrn1-dependent buffering of transcript levels. Mol Cell. 2013;52:52–62.
- Decker CJ, Parker R. P-bodies and stress granules: possible roles in the control of translation and mRNA degradation. Cold Spring Harb Perspect Biol. 2012;4:1–16.
- Houseley J, Tollervey D. The many pathways of RNA degradation. Cell. 2009;136:763–776.
- Collart MA, Panasenko OO. The Ccr4 – not complex. Gene. 2012;492:42–53.
- Webster MW, Chen Y-H, Stowell JAW, et al. mRNA deadenylation is coupled to translation rates by the differential activities of Ccr4-Not nucleases. Mol Cell. 2018;70:1089–1100.
- Yi H, Park J, Ha M, et al. PABP cooperates with the CCR4-NOT complex to promote mRNA deadenylation and block precocious decay. Mol Cell. 2018;70:1081–1088.
- Van-Hoof A, Lennertz P, Parker R. Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast. Embo J. 2000;19:1357–1365.
- Inada T, Makino S. Novel Roles of the multi-functional CCR4-NOT complex in post-transcriptional regulation. Front Genet. 2014;5:1–7.
- Doma MK, Parker R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature. 2006;440:61–564.
- Celik A, He F, Jacobsen A. NMD monitors Translational Fidelity 24/7. Current Genet. 2017;63:1007–1010.
- Carnes J, Jacobsen M, Leinwand L, et al. Stop codon suppression via inhibition of eRF1 expression. Rna. 2003;9:648–653.
- Deanna M, Janzen DM, Geballe AP. The effect of eukaryotic release factor depletion on translation termination in human cell lines. Nucleic Acids Res. 2004;32:4491–4502.
- Pilkington GR, Parker R. Pat1 contains distinct functional domains that promote P-body assembly and activation of decapping. Mol Cell Biol. 2007;28:1298–1312.
- Sement F, Ferrier E, Zuber H, et al. Uridylation Prevents 3ʹ Trimming of Oligoadenylated mRNAs. Nucleic Acids Res. 2013;41:7115–7127.
- Sherr CJ. G1 phase progression: cycling on cue. Cell. 1994;79:551–555.
- Morgan DO. Principles of CDK regulation. Nature. 1995;374:131–134.
- Tyakht AV, Song Q, Jia G, et al. RNA-Seq gene expression profiling of HepG2 cells: the influence of experimental factors and comparison with liver tissue. BMC Genomics. 2014;15:1–9.
- Schiavi SC, Belasco JG, Greenberg ME. Regulation of proto-oncogene mRNA stability. Biochbnica et Biophysica Acta. 1992;1114:95–106.
- Dani C, Blanchard JM, Piechaczyk M, et al. Extreme instability of myc mRNA in normal and transformed human cells. Proc Natl Acad Sci USA. 1984;81:7046–7050.
- The Computational Biology and Functional Genomics Laboratory (2012) shRNA Lentivirus Production using HEK293T cells and FuGENE. [cited 2018 Jan 20].
- Livak KJ, Schmittgen TD. Analysis of relative gene expression data using realtime quantitative PCR and the 2DDCT method. Methods. 2001;25:402–408.
- Wang Y, Liu CL, Storey JD, et al. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA. 2002;99:5860–5865.
- Zaykin DV, Zhivotovsky LA, Westfall PH, et al. Truncated product method for combining P-values. Genet Epidem. 2002;22:170–185.
- Blasco-Moreno B, de Campos-Mata L, Böttcher R, et al. The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins. Nat Comm. 2019;10:1298–1313.