1
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Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M. The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions. J Biol Chem 2020; 295:11435-11454. [PMID: 32518159 DOI: 10.1074/jbc.ra120.013426] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/05/2020] [Indexed: 11/06/2022] Open
Abstract
mRNA levels are determined by the balance between mRNA synthesis and decay. Protein factors that mediate both processes, including the 5'-3' exonuclease Xrn1, are responsible for a cross-talk between the two processes that buffers steady-state mRNA levels. However, the roles of these proteins in transcription remain elusive and controversial. Applying native elongating transcript sequencing (NET-seq) to yeast cells, we show that Xrn1 functions mainly as a transcriptional activator and that its disruption manifests as a reduction of RNA polymerase II (Pol II) occupancy downstream of transcription start sites. By combining our sequencing data and mathematical modeling of transcription, we found that Xrn1 modulates transcription initiation and elongation of its target genes. Furthermore, Pol II occupancy markedly increased near cleavage and polyadenylation sites in xrn1Δ cells, whereas its activity decreased, a characteristic feature of backtracked Pol II. We also provide indirect evidence that Xrn1 is involved in transcription termination downstream of polyadenylation sites. We noted that two additional decay factors, Dhh1 and Lsm1, seem to function similarly to Xrn1 in transcription, perhaps as a complex, and that the decay factors Ccr4 and Rpb4 also perturb transcription in other ways. Interestingly, the decay factors could differentiate between SAGA- and TFIID-dominated promoters. These two classes of genes responded differently to XRN1 deletion in mRNA synthesis and were differentially regulated by mRNA decay pathways, raising the possibility that one distinction between these two gene classes lies in the mechanisms that balance mRNA synthesis with mRNA decay.
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Affiliation(s)
- Jonathan Fischer
- Computer Science Division, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA.,Chan Zuckerberg BioHub, San Francisco, California, USA
| | - Nir Yosef
- Chan Zuckerberg BioHub, San Francisco, California, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Julia di Iulio
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mordechai Choder
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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2
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Mischo HE, Chun Y, Harlen KM, Smalec BM, Dhir S, Churchman LS, Buratowski S. Cell-Cycle Modulation of Transcription Termination Factor Sen1. Mol Cell 2018; 70:312-326.e7. [PMID: 29656924 PMCID: PMC5919780 DOI: 10.1016/j.molcel.2018.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 06/26/2017] [Accepted: 03/08/2018] [Indexed: 01/14/2023]
Abstract
Many non-coding transcripts (ncRNA) generated by RNA polymerase II in S. cerevisiae are terminated by the Nrd1-Nab3-Sen1 complex. However, Sen1 helicase levels are surprisingly low compared with Nrd1 and Nab3, raising questions regarding how ncRNA can be terminated in an efficient and timely manner. We show that Sen1 levels increase during the S and G2 phases of the cell cycle, leading to increased termination activity of NNS. Overexpression of Sen1 or failure to modulate its abundance by ubiquitin-proteasome-mediated degradation greatly decreases cell fitness. Sen1 toxicity is suppressed by mutations in other termination factors, and NET-seq analysis shows that its overexpression leads to a decrease in ncRNA production and altered mRNA termination. We conclude that Sen1 levels are carefully regulated to prevent aberrant termination. We suggest that ncRNA levels and coding gene transcription termination are modulated by Sen1 to fulfill critical cell cycle-specific functions. Transcription termination factor Sen1 levels fluctuate throughout the cell cycle APC targets Sen1 for degradation during G1 Reduced Sen1 levels lower efficiency of Sen1-mediated termination Sen1 overexpression reduces cell viability because of excessive termination
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Affiliation(s)
- Hannah E Mischo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK; Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms EN6 3LD, UK.
| | - Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Harlen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan M Smalec
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK
| | | | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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3
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Lukačišin M, Landon M, Jajoo R. Sequence-specific thermodynamic properties of nucleic acids influence both transcriptional pausing and backtracking in yeast. PLoS One 2017; 12:e0174066. [PMID: 28301878 PMCID: PMC5354634 DOI: 10.1371/journal.pone.0174066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 03/02/2017] [Indexed: 01/22/2023] Open
Abstract
RNA Polymerase II pauses and backtracks during transcription, with many consequences for gene expression and cellular physiology. Here, we show that the energy required to melt double-stranded nucleic acids in the transcription bubble predicts pausing in Saccharomyces cerevisiae far more accurately than nucleosome roadblocks do. In addition, the same energy difference also determines when the RNA polymerase backtracks instead of continuing to move forward. This data-driven model corroborates—in a genome wide and quantitative manner—previous evidence that sequence-dependent thermodynamic features of nucleic acids influence both transcriptional pausing and backtracking.
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Affiliation(s)
- Martin Lukačišin
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- IST Austria, Klosterneuburg, Austria
| | - Matthieu Landon
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
- Ecole des Mines de Paris, Mines Paristech, Paris, France
| | - Rishi Jajoo
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America
- * E-mail:
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4
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Schaughency P, Merran J, Corden JL. Genome-wide mapping of yeast RNA polymerase II termination. PLoS Genet 2014; 10:e1004632. [PMID: 25299594 PMCID: PMC4191890 DOI: 10.1371/journal.pgen.1004632] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/21/2014] [Indexed: 12/22/2022] Open
Abstract
Yeast RNA polymerase II (Pol II) terminates transcription of coding transcripts through the polyadenylation (pA) pathway and non-coding transcripts through the non-polyadenylation (non-pA) pathway. We have used PAR-CLIP to map the position of Pol II genome-wide in living yeast cells after depletion of components of either the pA or non-pA termination complexes. We show here that Ysh1, responsible for cleavage at the pA site, is required for efficient removal of Pol II from the template. Depletion of Ysh1 from the nucleus does not, however, lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators, but in contrast to Nrd1, this readthrough is less processive, or more susceptible to pausing. The data presented here provide delineation of in vivo Pol II termination regions and highlight differences in the sequences that signal termination of different classes of non-pA transcripts. Transcription termination is an important regulatory event for both non-coding and coding transcripts. Using high-throughput sequencing, we have mapped RNA Polymerase II's position in the genome after depletion of termination factors from the nucleus. We found that depletion of Ysh1 and Sen1 cause build up of polymerase directly downstream of coding and non-coding genes, respectively. Depletion of Nrd1 causes an increase in polymerase that is distributed up to 1,000 bases downstream of non-coding genes. The depletion of Nrd1 helped us to identify more than 250 unique termination regions for non-coding RNAs. Within this set of newly identified non-coding termination regions, we are further able to classify them based on sequence motif similarities, suggesting a functional role for different terminator motifs. The role of these factors in transcriptional termination of coding and/or non-coding transcripts can be inferred from the effect of polymerase's position downstream of given termination sites. This method of depletion and sequencing can be used to further elucidate other factors whose importance to transcription has yet to be determined.
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Affiliation(s)
- Paul Schaughency
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
| | - Jonathan Merran
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
| | - Jeffry L. Corden
- Department of Molecular Biology and Genetics, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
- * E-mail:
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5
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Mischo HE, Proudfoot NJ. Disengaging polymerase: terminating RNA polymerase II transcription in budding yeast. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:174-85. [PMID: 23085255 PMCID: PMC3793857 DOI: 10.1016/j.bbagrm.2012.10.003] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 11/29/2022]
Abstract
Termination of transcription by RNA polymerase II requires two distinct processes: The formation of a defined 3′ end of the transcribed RNA, as well as the disengagement of RNA polymerase from its DNA template. Both processes are intimately connected and equally pivotal in the process of functional messenger RNA production. However, research in recent years has elaborated how both processes can additionally be employed to control gene expression in qualitative and quantitative ways. This review embraces these new findings and attempts to paint a broader picture of how this final step in the transcription cycle is of critical importance to many aspects of gene regulation. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Hannah E Mischo
- Cancer Research UK London Research Institute, Blanche Lane South Mimms, Herts, UK.
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6
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Ghazy MA, Gordon JMB, Lee SD, Singh BN, Bohm A, Hampsey M, Moore C. The interaction of Pcf11 and Clp1 is needed for mRNA 3'-end formation and is modulated by amino acids in the ATP-binding site. Nucleic Acids Res 2011; 40:1214-25. [PMID: 21993299 PMCID: PMC3273803 DOI: 10.1093/nar/gkr801] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Polyadenylation of eukaryotic mRNAs contributes to stability, transport and translation, and is catalyzed by a large complex of conserved proteins. The Pcf11 subunit of the yeast CF IA factor functions as a scaffold for the processing machinery during the termination and polyadenylation of transcripts. Its partner, Clp1, is needed for mRNA processing, but its precise molecular role has remained enigmatic. We show that Clp1 interacts with the Cleavage–Polyadenylation Factor (CPF) through its N-terminal and central domains, and thus provides cross-factor connections within the processing complex. Clp1 is known to bind ATP, consistent with the reported RNA kinase activity of human Clp1. However, substitution of conserved amino acids in the ATP-binding site did not affect cell growth, suggesting that the essential function of yeast Clp1 does not involve ATP hydrolysis. Surprisingly, non-viable mutations predicted to displace ATP did not affect ATP binding but disturbed the Clp1–Pcf11 interaction. In support of the importance of this interaction, a mutation in Pcf11 that disrupts the Clp1 contact caused defects in growth, 3′-end processing and transcription termination. These results define Clp1 as a bridge between CF IA and CPF and indicate that the Clp1–Pcf11 interaction is modulated by amino acids in the conserved ATP-binding site of Clp1.
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Affiliation(s)
- Mohamed A Ghazy
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
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7
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The essential N terminus of the Pta1 scaffold protein is required for snoRNA transcription termination and Ssu72 function but is dispensable for pre-mRNA 3'-end processing. Mol Cell Biol 2009; 29:2296-307. [PMID: 19188448 DOI: 10.1128/mcb.01514-08] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae Pta1 is a component of the cleavage/polyadenylation factor (CPF) 3'-end processing complex and functions in pre-mRNA cleavage, poly(A) addition, and transcription termination. In this study, we investigated the role of the N-terminal region of Pta1 in transcription and processing. We report that a deletion of the first 75 amino acids (pta1-Delta75) causes thermosensitive growth, while the deletion of an additional 25 amino acids is lethal. The pta1-Delta75 mutant is defective for snoRNA termination, RNA polymerase II C-terminal domain Ser5-P dephosphorylation, and gene looping but is fully functional for mRNA 3'-end processing. Furthermore, different regions of Pta1 interact with the CPF subunits Ssu72, Pti1, and Ysh1, supporting the idea that Pta1 acts as a scaffold to organize CPF. The first 300 amino acids of Pta1 are sufficient for interactions with Ssu72, which is needed for pre-mRNA cleavage. By the degron-mediated depletion of Pta1, we show that the removal of this essential region leads to a loss of Ssu72, yet surprisingly, in vitro cleavage and polyadenylation remain efficient. In addition, a fragment containing amino acids 1 to 300 suppresses 3'-end processing in wild-type extracts. These findings suggest that the amino terminus of Pta1 has an inhibitory effect and that this effect can be neutralized through the interaction with Ssu72.
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8
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Ansari A, Hampsey M. A role for the CPF 3'-end processing machinery in RNAP II-dependent gene looping. Genes Dev 2005; 19:2969-78. [PMID: 16319194 PMCID: PMC1315401 DOI: 10.1101/gad.1362305] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The prevailing view of the RNA polymerase II (RNAP II) transcription cycle is that RNAP II is recruited to the promoter, transcribes a linear DNA template, then terminates transcription and dissociates from the template. Subsequent rounds of transcription are thought to require de novo recruitment of RNAP II to the promoter. Several recent findings, including physical interaction of 3'-end processing factors with both promoter and terminator regions, challenge this concept. Here we report a physical association of promoter and terminator regions of the yeast BUD3 and SEN1 genes. These interactions are transcription-dependent, require the Ssu72 and Pta1 components of the CPF 3'-end processing complex, and require the phosphatase activity of Ssu72. We propose a model for RNAP II transcription in which promoter and terminator regions are juxtaposed, and that the resulting gene loops facilitate transcription reinitiation by the same molecule of RNAP II in a manner dependent upon Ssu72-mediated CTD dephosphorylation.
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Affiliation(s)
- Athar Ansari
- Division of Nucleic Acids Research, Department of Biochemistry, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, 08854, USA
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9
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Gillette TG, Gonzalez F, Delahodde A, Johnston SA, Kodadek T. Physical and functional association of RNA polymerase II and the proteasome. Proc Natl Acad Sci U S A 2004; 101:5904-9. [PMID: 15069196 PMCID: PMC395896 DOI: 10.1073/pnas.0305411101] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2003] [Indexed: 12/17/2022] Open
Abstract
Recent studies from a number of laboratories have revealed a surprising number of connections between RNA polymerase II transcription and the ubiquitin/proteasome pathway. We now find yet another intersection of these pathways by showing that the 26S proteasome associates with regions of the GAL1, GAL10, and HSP82 genes, including the 3' ends, in a transcription-dependent fashion. The appearance of the proteasome on these inducible genes correlates with both the accumulation of transcripts and the buildup of RNA polymerase II complexes in the same region. Furthermore, the 26S proteasome and RNA polymerase II coimmunoprecipitate, and inhibition of 26S proteolytic activity leads to increased read through of a transcription termination site. We suggest that the proteasome is generally recruited to the DNA at sites of stalled RNA polymerase and may act to resolve these complexes.
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Affiliation(s)
- Thomas G Gillette
- Center for Biomedical Inventions and Departments of Internal Medicine, Molecular Biology, and Microbiology, 5323 Harry Hines Boulevard, University of Texas Southwestern Medical Center, Dallas, TX 75390-8573, USA
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10
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Graber JH, McAllister GD, Smith TF. Probabilistic prediction of Saccharomyces cerevisiae mRNA 3'-processing sites. Nucleic Acids Res 2002; 30:1851-8. [PMID: 11937640 PMCID: PMC113205 DOI: 10.1093/nar/30.8.1851] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a tool for the prediction of mRNA 3'-processing (cleavage and polyadenylation) sites in the yeast Saccharomyces cerevisiae, based on a discrete state-space model or hidden Markov model. Comparison of predicted sites with experimentally verified 3'-processing sites indicates good agreement. All predicted or known yeast genes were analyzed to find probable 3'-processing sites. Known alternative 3'-processing sites, both within the 3'-untranslated region and within the protein coding sequence were successfully identified, leading to the possibility of prediction of previously unknown alternative sites. The lack of an apparent 3'-processing site calls into question the validity of some predicted genes. This is specifically investigated for predicted genes with overlapping coding sequences.
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Affiliation(s)
- Joel H Graber
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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11
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Gross S, Moore CL. Rna15 interaction with the A-rich yeast polyadenylation signal is an essential step in mRNA 3'-end formation. Mol Cell Biol 2001; 21:8045-55. [PMID: 11689695 PMCID: PMC99971 DOI: 10.1128/mcb.21.23.8045-8055.2001] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2001] [Accepted: 08/28/2001] [Indexed: 11/20/2022] Open
Abstract
In Saccharomyces cerevisiae, four factors [cleavage factor I (CF I), CF II, polyadenylation factor I (PF I), and poly(A) polymerase (PAP)] are required for maturation of the 3' end of the mRNA. CF I and CF II are required for cleavage; a complex of PAP and PF I, which includes CF II subunits, participates in polyadenylation, along with CF I. These factors are directed to the appropriate site on the mRNA by two sequences: one A-rich and one UA-rich. CF I contains five proteins, two of which, Rna15 and Hrp1, interact with the mRNA through RNA recognition motif-type RNA binding motifs. Previous work demonstrated that the UV cross-linking of purified Hrp1 to RNA required the UA-rich element, but the contact point of Rna15 was not known. We show here that Rna15 does not recognize a particular sequence in the absence of other proteins. However, in complex with Hrp1 and Rna14, Rna15 specifically interacts with the A-rich element. The Pcf11 and Clp1 subunits of CF I are not needed to position Rna15 at this site. This interaction is essential to the function of CF I. A mutant Rna15 with decreased affinity for RNA is defective for in vitro RNA processing and lethal in vivo, while an RNA with a mutation in the A-rich element is not processed in vitro and can no longer be UV cross-linked to the Rna15 subunit assembled into CF I. Thus, the recognition of the A-rich element depends on the tethering of Rna15 through an Rna14 bridge to Hrp1 bound to the UA-rich motif. These results illustrate that the yeast 3' end is defined and processed by a mechanism surprisingly different from that used by the mammalian system.
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Affiliation(s)
- S Gross
- Department of Molecular Biology and Microbiology, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts 02111, USA
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12
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van Helden J, del Olmo M, Pérez-Ortín JE. Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res 2000; 28:1000-10. [PMID: 10648794 PMCID: PMC102588 DOI: 10.1093/nar/28.4.1000] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/1999] [Revised: 12/22/1999] [Accepted: 12/22/1999] [Indexed: 11/14/2022] Open
Abstract
The study of a few genes has permitted the identification of three elements that constitute a yeast polyadenyl-ation signal: the efficiency element (EE), the positioning element and the actual site for cleavage and poly-adenyl-ation. In this paper we perform an analysis of oligonucleotide composition on the sequences located downstream of the stop codon of all yeast genes. Several oligonucleotide families appear over-represented with a high significance (referred to herein as 'words'). The family with the highest over-representation includes the oligonucleotides shown experimentally to play a role as EEs. The word with the highest score is TATATA, followed, among others, by a series of single-nucleotide variants (TATGTA, TACATA, TAAATA.) and one-letter shifts (ATATAT). A position analysis reveals that those words have a high preference to be in 3' flanks of yeast genes and there they have a very uneven distribution, with a marked peak around 35 bp after the stop codon. Of the predicted ORFs, 85% show one or more of those sequences. Similar results were obtained using a data set of EST sequences. Other clusters of over-represented words are also detected, namely T- and A-rich signals. Using these results and previously known data we propose a general model for the 3' trailers of yeast mRNAs.
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Affiliation(s)
- J van Helden
- Unité de Conformation des Macromolécules Biologiques, Université Libre de Bruxelles, CP 160/16, 50 avenue F.D. Roosevelt, B-1050 Bruxelles, Belgium.
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13
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Zhao J, Hyman L, Moore C. Formation of mRNA 3' ends in eukaryotes: mechanism, regulation, and interrelationships with other steps in mRNA synthesis. Microbiol Mol Biol Rev 1999; 63:405-45. [PMID: 10357856 PMCID: PMC98971 DOI: 10.1128/mmbr.63.2.405-445.1999] [Citation(s) in RCA: 808] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Formation of mRNA 3' ends in eukaryotes requires the interaction of transacting factors with cis-acting signal elements on the RNA precursor by two distinct mechanisms, one for the cleavage of most replication-dependent histone transcripts and the other for cleavage and polyadenylation of the majority of eukaryotic mRNAs. Most of the basic factors have now been identified, as well as some of the key protein-protein and RNA-protein interactions. This processing can be regulated by changing the levels or activity of basic factors or by using activators and repressors, many of which are components of the splicing machinery. These regulatory mechanisms act during differentiation, progression through the cell cycle, or viral infections. Recent findings suggest that the association of cleavage/polyadenylation factors with the transcriptional complex via the carboxyl-terminal domain of the RNA polymerase II (Pol II) large subunit is the means by which the cell restricts polyadenylation to Pol II transcripts. The processing of 3' ends is also important for transcription termination downstream of cleavage sites and for assembly of an export-competent mRNA. The progress of the last few years points to a remarkable coordination and cooperativity in the steps leading to the appearance of translatable mRNA in the cytoplasm.
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Affiliation(s)
- J Zhao
- Department of Molecular Biology and Microbiology, School of Medicine, Tufts University, Boston, Massachusetts 02111, USA
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14
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Abstract
Downstream elements (DSEs) with transcriptional pausing activity play an important role in transcription termination of RNA polymerase II. We have defined two such DSEs in Schizosaccharomyces pombe, one for the ura4 gene and a new one in the 3'-end region of the nmt2 gene. Although these DSEs do not have sequence homology, both are orientation specific and are composed of multiple and redundant sequence elements that work together to achieve full pausing activity. Previous studies on the nmt1 and nmt2 genes revealed that transcription extends several kilobases past the genes' poly(A) sites. We show that the insertion of either DSE immediately downstream of the nmt1 poly(A) site induces more immediate termination. nmt2 termination efficiency can be increased by moving the DSE closer to the poly(A) site. These results suggest that DSEs may be a common feature in yeast genes.
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Affiliation(s)
- A Aranda
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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15
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Hansen K, Birse CE, Proudfoot NJ. Nascent transcription from the nmt1 and nmt2 genes of Schizosaccharomyces pombe overlaps neighbouring genes. EMBO J 1998; 17:3066-77. [PMID: 9606189 PMCID: PMC1170646 DOI: 10.1093/emboj/17.11.3066] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have determined the extent of the primary transcription unit for the two highly expressed genes nmt1 and nmt2 of Schizosaccharomyces pombe. Transcription run-on analysis in permeabilized yeast cells was employed to map polymerase density across the 3'-flanking region of these two genes. Surprisingly, polymerases were detected 4.3 kb beyond the nmt1 polyadenylation [poly(A)] site and 2.4 kb beyond the nmt2 poly(A) site, which in each case have transcribed through an entire convergent downstream transcription unit. However, the steady-state levels of both downstream genes were unaffected by the high level of nmt1 or nmt2 nascent transcription. Analysis of nmt1 and nmt2 RNA 3' end formation signals indicates that efficient termination of transcription requires not only a poly(A) signal but also additional pause elements. The absence of such pause elements close to the poly(A) sites of these genes may account for their extended nascent transcripts.
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Affiliation(s)
- K Hansen
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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16
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Kessler MM, Henry MF, Shen E, Zhao J, Gross S, Silver PA, Moore CL. Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 3'-end formation in yeast. Genes Dev 1997; 11:2545-56. [PMID: 9334319 PMCID: PMC316558 DOI: 10.1101/gad.11.19.2545] [Citation(s) in RCA: 193] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/1997] [Accepted: 07/31/1997] [Indexed: 02/05/2023]
Abstract
In yeast, four factors (CF I, CF II, PF I, and PAP) are required for accurate pre-mRNA cleavage and polyadenylation in vitro. CF I can be separated further into CF IA and CF IB. Here we show that CF IB is the 73-kD Hrp1 protein. Recombinant Hrp1p made in Escherichia coli provides full CF IB function in both cleavage and poly(A) addition assays. Consistent with the presence of two RRM-type motifs, Hrp1p can be UV cross-linked to RNA, and this specific interaction requires the (UA)6 polyadenylation efficiency element. Furthermore, the CF II factor enhances the binding of Hrp1p to the RNA precursor. A temperature-sensitive mutant in HRP1 yields mRNAs with shorter poly(A) tails when grown at the nonpermissive temperature. Genetic analyses indicate that Hrp1p interacts with Rna15p and Rna14p, two components of CF 1A. The HRP1 gene was originally isolated as a suppressor of a temperature-sensitive npl3 allele, a gene encoding a protein involved in mRNA export. Like Npl3p, Hrp1p shuttles between the nucleus and cytoplasm, providing a potential link between 3'-end processing and mRNA export from the nucleus.
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Affiliation(s)
- M M Kessler
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
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Birse CE, Lee BA, Hansen K, Proudfoot NJ. Transcriptional termination signals for RNA polymerase II in fission yeast. EMBO J 1997; 16:3633-43. [PMID: 9218804 PMCID: PMC1169987 DOI: 10.1093/emboj/16.12.3633] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Transcription 'run-on' (TRO) analysis using permeabilized yeast cells indicates that transcription terminates between 180 and 380 bp downstream of the poly(A) site of the Schizosaccharomyces pombe ura4 gene. Two signals direct RNA polymerase II (pol II) to stop transcription: the previously identified 3' end formation signals located close to the poly(A) site and an additional downstream element (DSE) located at the region of termination. The downstream signal (135 bp) appears to act by pausing the elongating polymerase. TRO analysis indicates that elevated levels of transcribing polymerases accumulate over the DSE and that removal of this signal leads to transcription proceeding beyond the normal termination region. Furthermore, when inserted between two competing polyadenylation signals, this DSE increases the utilization of upstream poly(A) sites in vivo. We show that polymerase pausing over an extended region of template ensures termination of pol II transcription close to the poly(A) site.
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Affiliation(s)
- C E Birse
- Sir William Dunn School of Pathology, Chemical Pathology Unit, University of Oxford, UK
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18
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Gu X, Marzluff WF. 3' Processing and termination of mouse histone transcripts synthesized in vitro by RNA polymerase II. Nucleic Acids Res 1996; 24:3797-805. [PMID: 8871561 PMCID: PMC146179 DOI: 10.1093/nar/24.19.3797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The highly expressed mouse histone H2a-614 gene is located 800 nt 5' of the histone H3-614 gene. There is a 140 nt sequence located 500 nt from the end of the H2-614 mRNA which has been defined as a transcription termination site for RNA polymerase II. We established an in vitro transcription system in which both 3' end processing and transcription termination occur. A template containing the adenovirus major late promoter, a portion of the histone H2a-614 coding region, its 3' processing signal, followed by the transcription termination site was transcribed in a nuclear extract prepared from mouse myeloma cells. Some of the transcripts synthesized in the extract were cleaved at the histone processing site in a reaction which was dependent both on the hairpin binding factor and the U7 snRNP. The efficiency of histone 3' end formation was similar both on synthetic transcripts and transcripts synthesized by RNA polymerase II. Defined transcripts, which were not processed and which mapped to the transcription termination site, were released from the template, suggesting that they were formed by transcription termination. Termination in vitro was dependent on a functional histone processing signal.
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Affiliation(s)
- X Gu
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 27599, USA
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19
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Wei YD, Collinge DB, Smedegaard-Petersen V, Thordal-Christensen H. Characterization of the transcript of a new class of retroposon-type repetitive element cloned from the powdery mildew fungus, Erysiphe graminis. MOLECULAR & GENERAL GENETICS : MGG 1996; 250:477-82. [PMID: 8602165 DOI: 10.1007/bf02174036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The putative master transcript of a novel class of repetitive element has been cloned from the fungus erysiphe graminis f.sp. hordei. Sequence analysis of the cDNA revealed that the element, designated Eg-R1, is a member of the retroposon superfamily with properties in common with SINEs and LINEs (short or long interspersed elements). SINE-like properties include the transcript size (approximately 700 bp), and the lack of major open reading frames. In contrast, the fact that the transcript is polyadenylated and is most probably transcribed by RNA polymerase II, suggests a functional relationship to LINEs. Except for a short, but striking, sequence identity to a published SINE from the same fungus, no similar sequence was found in database searches. A constitutively high transcript level is found throughout the asexual life cycle of the fungus. Small differences in band patterns of Southern blots were observed between two isolates of E. graminis f.sp. hordei, while the band patterns in an isolate of the very close relative E. graminis f.sp. tritici in general appear dissimilar. This may imply that the element is currently active. Recent dispersal is confirmed by the observation that an approximately 550 bp internal hinfI fragment is conserved in the majority of the copies in all three isolates. Approximately 50 copies are present in E. graminis f.sp. hordei.
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Affiliation(s)
- Y D Wei
- Department of Plant Biology, Plant Pathology Section, The Royal Veterinary and Agricultural University, Frederiksberg C, Copenhagen, Denmark
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20
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Mandart E, Parker R. Effects of mutations in the Saccharomyces cerevisiae RNA14, RNA15, and PAP1 genes on polyadenylation in vivo. Mol Cell Biol 1995; 15:6979-86. [PMID: 8524265 PMCID: PMC230953 DOI: 10.1128/mcb.15.12.6979] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The RNA14 and RNA15 gene products have been implicated in a variety of cellular processes. Mutations in these genes lead to faster decay of some mRNAs and yield extracts that are deficient in cleavage and polyadenylation in vitro. These results suggest that the RNA14 and RNA15 gene products may be involved in both adenylation and deadenylation in vivo. To explore the roles of these gene products in vivo, we examined the site of adenylation and the rate of deadenylation for individual mRNAs in rna14 and rna15 mutant strains. We observed that the rates of deadenylation are not affected by lesions in either the RNA14 or the RNA15 gene. This result suggests that the proteins encoded by these genes are not involved in regulation of the deadenylation rate. In contrast, we observed that the site of adenylation for the ACT1 transcript can be altered in these mutants. Interestingly, we also observed that mutation of the poly(A) polymerase gene altered the site of ACT1 polyadenylation. These observations suggest that the RNA14, RNA15, and PAP1 proteins are involved in poly(A) site choice. This alteration in poly(A) site choice in the rna14 mutant can be corrected by the ssm4 suppressor, indicating that this suppression acts at the level of polyadenylation and not by slowing mRNA degradation.
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Affiliation(s)
- E Mandart
- Department of Molecular and Cellular Biology, University of Arizona, Tucson 85721, USA
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Abstract
It was previously shown that three distinct but interdependent elements are required for 3' end formation of mRNA in the yeast Saccharomyces cerevisiae: (i) the efficiency element TATATA and related sequences, which function by enhancing the efficiency of positioning elements; (ii) positioning elements, such as TTAAGAAC and AAGAA, which position the poly(A) site; and (iii) the actual site of polyadenylation. In this study, we have shown that several A-rich sequences, including the vertebrate poly(A) signal AATAAA, are also positioning elements. Saturated mutagenesis revealed that optimum sequences of the positioning element were AATAAA and AAAAAA and that this element can tolerate various extents of replacements. However, the GATAAA sequence was completely ineffective. The major cleavage sites determined in vitro corresponded to the major poly(A) sites observed in vivo. Our findings support the assumption that some components of the basic polyadenylation machinery could have been conserved among yeasts, plants, and mammals, although 3' end formation in yeasts is clearly distinct from that of higher eukaryotes.
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Affiliation(s)
- Z Guo
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, New York 14642, USA
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22
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Berger SL, Meselson M. Production and cleavage of Drosophila hsp70 transcripts extending beyond the polyadenylation site. Nucleic Acids Res 1994; 22:3218-25. [PMID: 8065938 PMCID: PMC310299 DOI: 10.1093/nar/22.15.3218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Transcription downstream of the polyadenylation site was studied in the Drosophila hsp70 gene, whose high level of transcription in response to temperature elevation facilitates detection of rare and possibly short-lived transcripts. Transcription downstream of the polyadenylation site was detected both in cultured cells and in intact animals. Even shortly after temperature elevation the extended nonpolyadenylated RNAs were rare relative to mature message, and their level continued to increase following temperature elevation even after the amount of mature message stopped increasing. The extended transcripts therefore are unlikely to be message precursors. Although continuous transcripts were detected extending as far as 2 kb downstream of the normal polyadenylation site, the predominant extended transcript was 0.45 kb long, apparently produced by cleavage of longer transcripts. Its amount relative to mature message increased with the duration and severity of heat-shock. As is the case in nonpolyadenylated histone mRNA, there is a potential stem-loop structure just upstream of the cleavage site. These data and other lines of evidence suggest that this extended transcript results from an alternative mode of stable 3'-end formation.
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Affiliation(s)
- S L Berger
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, MA 02138
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