Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration

References

• Haimovich G, Medina DA, Causse SZ, et al. Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell. 2013;153:1000–1011.
   PubMed Web of Science ®Google Scholar
• Choder M. mRNA imprinting: additional level in the regulation of gene expression. Cell Logist. 2011;1:37–40.
   PubMedGoogle Scholar
• Miller JE, Reese JC. Ccr4-Not complex: the control freak of eukaryotic cells. Crit Rev Biochem Mol Biol. 2012;47 VN-r:315–333.
   Web of Science ®Google Scholar
• Schmid M, Jensen TH. Controlling nuclear RNA levels. Nat Rev Genet. 2018;19:518–529.
   PubMed Web of Science ®Google Scholar
• Rambout X, Detiffe C, Bruyr J, et al. The transcription factor ERG recruits CCR4-NOT to control mRNA decay and mitotic progression. Nat Struct Mol Biol. 2016;23:663–672.
   PubMed Web of Science ®Google Scholar
• Singh P, James RS, Mee CJ, et al. mRNA levels are buffered upon knockdown of RNA decay and translation factors via adjustment of transcription rates in human HepG2 cells. RNA Biol. 2019;16:1147–1155.
   PubMed Web of Science ®Google Scholar
• Slobodin B, Bahat A, Sehrawat U, et al. Transcription dynamics regulate poly(A) tails and expression of the RNA degradation machinery to balance mRNA levels. Molecular Cell. 2020;78(3):434–444.
   PubMed Web of Science ®Google Scholar
• Abernathy E, Gilbertson S, Alla R, et al. Viral Nucleases Induce an mRNA Degradation-Transcription Feedback Loop in Mammalian Cells. Cell Host Microbe. 2015;18:243–253.
   PubMed Web of Science ®Google Scholar
• Gupta I, Villanyi Z, Kassem S, et al. Translational capacity of a cell is determined during transcription elongation via the Ccr4-not complex. Cell Rep. 2016;15:1782–1794.
   PubMed Web of Science ®Google Scholar
• Blasco-Moreno B, de Campos-mata L, Böttcher R, et al. The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins. Nat Commun. 2019;10:1298.
   PubMed Web of Science ®Google Scholar
• Shandilya J, Roberts SGE. The transcription cycle in eukaryotes: from productive initiation to RNA polymerase II recycling. Biochim Biophys Acta - Genet Regul Mech. 2012;1819:391–400.
   PubMed Web of Science ®Google Scholar
• Bentley DL. Coupling mRNA processing with transcription in time and space. Nat Rev Genet. 2014;15:163–175.
   PubMed Web of Science ®Google Scholar
• Porrua O, Boudvillain M, Libri D. Transcription termination: variations on common themes. Trends Genet. 2016;32:508–522.
   PubMed Web of Science ®Google Scholar
• Mayer A, Lidschreiber M, Siebert M, et al. Uniform transitions of the general RNA polymerase II transcription complex. Nat Struct Mol Biol. 2010;17:1272–1278.
   PubMed Web of Science ®Google Scholar
• García-Molinero V, García-Martínez J, Reja R, et al. The SAGA/TREX-2 subunit Sus1 binds widely to transcribed genes and affects mRNA turnover globally. Epigene Chromat. 2018;11:1–12.
   PubMed Web of Science ®Google Scholar
• Rodríguez-Navarro S. Insights into SAGA function during gene expression. EMBO Rep. 2009;10:843–850.
   PubMed Web of Science ®Google Scholar
• Mason PB, Struhl K. Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol Cell. 2005;17:831–840.
   PubMed Web of Science ®Google Scholar
• Gómez-Herreros F, de Miguel-jiménez L, Morillo-Huesca M, et al. TFIIS is required for the balanced expression of the genes encoding ribosomal components under transcriptional stress. Nucleic Acids Res. 2012;40:6508–6519.
   PubMed Web of Science ®Google Scholar
• Petty E, Pillus L. Balancing chromatin remodeling and histone modifications in transcription. Trends Genet. 2013;29:621–629.
   PubMed Web of Science ®Google Scholar
• Buratowski S. Progression through the RNA Polymerase II CTD Cycle. Mol Cell. 2009;36:541–546.
   PubMed Web of Science ®Google Scholar
• Millevoi S, Vagner S. Molecular mechanisms of eukaryotic pre-mRNA 3ʹ end processing regulation. Nucleic Acids Res. 2009;38:2757–2774.
   PubMed Web of Science ®Google Scholar
• van Helden J, Del Olmo M, Pérez-Ortín JE. Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res. 2000;28:1000–1010.
   PubMed Web of Science ®Google Scholar
• Jordán-Pla A, Gupta I, De Miguel-Jimnez L, et al. Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle. Nucleic Acids Res. 2015;43:787–802.
   PubMed Web of Science ®Google Scholar
• Kim J, Ljungdahl PO, Fink GR. kem mutations affect nuclear fusion in saccharomyces cerevisiae. Genetics. 1990;126:799–812.
   PubMed Web of Science ®Google Scholar
• Dykstra CC, Kitada K, Clark AB, et al. Cloning and characterization of DST2, the gene for DNA strand transfer protein beta from Saccharomyces cerevisiae. Mol Cell Biol. 1991;11:2583–2592.
   PubMedGoogle Scholar
• Clark AB, Dykstra CC, Sugino A. Isolation, DNA sequence, and regulation of a saccharomyces cerevisiae gene that encodes DNA strand transfer protein alpha. Mol Cell Biol. 1991;11:2576–2582.
   PubMed Web of Science ®Google Scholar
• Davies CJ, Trgovcich J, Hutchison CA. Homologue of TFIIS in yeast. Nature. 1990;345:298.
   PubMedGoogle Scholar
• Larimer FW, Stevens A. Disruption of the gene XRN1, coding for a 5′→3′ exoribonuclease, restricts yeast cell growth. Gene. 1990;95:85–90.
   PubMed Web of Science ®Google Scholar
• Chang JH, Xiang S, Xiang K, et al. Structural and biochemical studies of the 5′→3′ exoribonuclease Xrn1. Nat Struct Mol Biol. 2011;18:270–276.
   PubMed Web of Science ®Google Scholar
• Jinek M, Coyle SM, Doudna JA. Coupled 5′ nucleotide recognition and processivity in Xrn1-mediated mRNA decay. Mol Cell. 2011;41:600–608.
   PubMed Web of Science ®Google Scholar
• Begley V, Corzo D, Jordán-Pla A, et al. The mRNA degradation factor Xrn1 regulates transcription elongation in parallel to Ccr4. Nucleic Acids Res. 2019;47:9524–9541.
   PubMed Web of Science ®Google Scholar
• Collart MA. The Ccr4-Not complex is a key regulator of eukaryotic gene expression. Wiley Interdiscip Rev RNA. 2016;7:438–454.
   PubMed Web of Science ®Google Scholar
• Amberg DC, Burke DJ, Strathern JN. Methods in yeast genetics. Cold Spring Harb. Lab. Course Man.. 2005;2005 edn.
   Google Scholar
• Rodríguez-Gil A, García-Martínez J, Pelechano V, et al. The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors. Nucleic Acids Res. 2010;38:4651–4664.
   PubMed Web of Science ®Google Scholar
• Candelli T, Challal D, Briand J, et al. High‐resolution transcription maps reveal the widespread impact of roadblock termination in yeast. Embo J. 2018;37:1–18.
   PubMed Web of Science ®Google Scholar
• Jordán-Pla A, Miguel A, Serna E, et al. Biotin-genomic run-on (Bio-GRO): a high-resolution method for the analysis of nascent transcription in yeast. Methods Mol Biol. 2016;1361:pp. 125–139.
   PubMedGoogle Scholar
• Wilkening S, Pelechano V, Järvelin AI, et al. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res. 2013;41:e65.
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–359.
   PubMed Web of Science ®Google Scholar
• Robinson JT, Thorvaldsdóttir H, Winckler W, et al. Integrative Genome Viewer. Nat Biotechnol. 2011;29:24–26.
   PubMed Web of Science ®Google Scholar
• Chen S, Huang T, Zhou Y, et al. AfterQC: automatic filtering, trimming, error removing and quality control for fastq data. BMC Bioinformatics. 2017;18:80.
   PubMed Web of Science ®Google Scholar
• Chen K, Xi Y, Pan X, et al. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 2013;23:341–351.
   PubMed Web of Science ®Google Scholar
• Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120.
   PubMed Web of Science ®Google Scholar
• Shen L, Shao N, Liu X, et al. Ngs.plot: quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics. 2014;15:1–14.
   PubMed Web of Science ®Google Scholar
• Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27:863–864.
   PubMed Web of Science ®Google Scholar
• Ramírez F, Ryan DP, Grüning B, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44:W160–5.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Challal D, Barucco M, Kubik S, et al. General regulatory factors control the fidelity of transcription by restricting non-coding and ectopic initiation. Mol Cell. 2018;72(955–969):e7.
   PubMedGoogle Scholar
• García-Martínez J, Troulé K, Chávez S, et al. Growth rate controls mRNA turnover in steady and non-steady states. RNA Biol. 2016;13:1175–1181.
   PubMed Web of Science ®Google Scholar
• Gutiérrez G, Millán-Zambrano G, Medina DA, et al. Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning. Epigenetics Chromatin. 2017;10:58.
   PubMed Web of Science ®Google Scholar
• Sung Rhee H, Franklin Pugh B. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature. 2012;487:128.
   Web of Science ®Google Scholar
• Mayer A, Heidemann M, Lidschreiber M, et al. CTD tyrosine phosphorylation impairs termination factor recruitment to RNA polymerase II. Science. 2012;336:1723–1725.
   PubMed Web of Science ®Google Scholar
• Collin P, Jeronimo C, Poitras C, et al. RNA polymerase II CTD TYROSINE 1 IS REQUIRED FOR EFFICIENT TERMINATION BY the Nrd1-Nab3-Sen1 pathway. Mol Cell. 2019;73(655–669):e7.
   PubMedGoogle Scholar
• Braun KA, Young ET. Coupling mRNA synthesis and decay. Mol Cell Biol. 2014;34:4078–4087.
   PubMed Web of Science ®Google Scholar
• Mena A, Media DA, Garcia-Martinez J, et al. Asymmetric cell division requires specific mechanisms for adjusting global transcription. Nucleic Acids Res. 2017;in press:1–12.
   Google Scholar
• Fischer J, Song YS, Yosef N, et al. The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5ʹ and 3ʹ gene regions. J Biol Chem. 2020;295:11435–11454.
   PubMed Web of Science ®Google Scholar
• Kim M, Krogan NJ, Vasiljeva L, et al. The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II. Nature. 2004;432:517–522.
   PubMed Web of Science ®Google Scholar
• Ehara H, Kujirai T, Fujino Y, et al. Structural insight into nucleosome transcription by RNA polymerase II with elongation factors. Science. 2019;363:744–747.
   PubMed Web of Science ®Google Scholar