Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

English version České info

We present a large-scale experimental investigation into sequence determinants of 3’ end mediated gene expression regulation, by measuring 13,000 designed 3’ end sequences. While 3’ end sequences contribute to expression differences through a variety of mechanisms including mRNA stability and regulation of translation, we find a predominant effect of mRNA 3’ end processing efficiency. Using extensive designed mutagenesis analysis we find that out of three functional elements described in the literature as comprising the polyadenylation signal, a single element (known as the efficiency element) is responsible for most of the effect on protein expression levels. Our work highlights the importance of 3’ end processing in expression regulation and facilitates the incorporation of the effect of this region into more complete models of DNA encoded gene expression regulation.

Vyšlo v časopise: Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control. PLoS Genet 11(4): e32767. doi:10.1371/journal.pgen.1005147
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005147

Souhrn

Zdroje

1. Jackson JS, Houshmandi SS, Lopez Leban F, Olivas WM. Recruitment of the Puf3 protein to its mRNA target for regulation of mRNA decay in yeast. RNA. 2004;10 : 1625–36. doi: 10.1261/rna.7270204 15337848

2. Shalgi R, Lapidot M, Shamir R, Pilpel Y. A catalog of stability-associated sequence elements in 3’ UTRs of yeast mRNAs. Genome Biol. 2005;6: R86. doi: 10.1186/gb-2005-6-10-r86 16207357

3. Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci U S A. 2005;102 : 17675–80. doi: 10.1073/pnas.0503803102 16317069

4. Hammell CM, Gross S, Zenklusen D, Heath C V, Stutz F, Moore C, et al. Coupling of termination, 3’ processing, and mRNA export. Mol Cell Biol. 2002;22 : 6441–57. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=135649&tool=pmcentrez&rendertype=abstract 12192043

5. Birse CE, Minvielle-Sebastia L, Lee BA, Keller W, Proudfoot NJ. Coupling termination of transcription to messenger RNA maturation in yeast. Science. 1998;280 : 298–301. Available: http://www.ncbi.nlm.nih.gov/pubmed/9535662 9535662

6. Mapendano CK, Lykke-Andersen S, Kjems J, Bertrand E, Jensen TH. Crosstalk between mRNA 3’ end processing and transcription initiation. Mol Cell. 2010;40 : 410–22. doi: 10.1016/j.molcel.2010.10.012 21070967

7. West S, Proudfoot NJ. Transcriptional termination enhances protein expression in human cells. Mol Cell. 2009;33 : 354–64. doi: 10.1016/j.molcel.2009.01.008 19217409

8. Kuehner JN, Pearson EL, Moore C. Unravelling the means to an end: RNA polymerase II transcription termination. Nat Rev Mol Cell Biol. 2011;12 : 283–94. doi: 10.1038/nrm3098 21487437

9. Beer MA, Tavazoie S. Predicting gene expression from sequence. Cell. 2004;117 : 185–98. Available: http://www.ncbi.nlm.nih.gov/pubmed/15084257 15084257

10. Segal E, Raveh-Sadka T, Schroeder M, Unnerstall U, Gaul U. Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature. 2008;451 : 535–40. doi: 10.1038/nature06496 18172436

11. Pilpel Y, Sudarsanam P, Church GM. Identifying regulatory networks by combinatorial analysis of promoter elements. Nat Genet. 2001;29 : 153–9. doi: 10.1038/ng724 11547334

12. Sudarsanam P, Pilpel Y, Church GM. Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res. 2002;12 : 1723–31. doi: 10.1101/gr.301202 12421759

13. Guo Z, Sherman F. 3’-end-forming signals of yeast mRNA. Trends Biochem Sci. 1996;21 : 477–81. Available: http://www.ncbi.nlm.nih.gov/pubmed/9009831 9009831

14. Graber JH, Cantor CR, Mohr SC, Smith TF. In silico detection of control signals: mRNA 3’-end-processing sequences in diverse species. Proc Natl Acad Sci U S A. 1999;96 : 14055–60. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=24189&tool=pmcentrez&rendertype=abstract 10570197

15. Graber JH, McAllister GD, Smith TF. Probabilistic prediction of Saccharomyces cerevisiae mRNA 3’-processing sites. Nucleic Acids Res. 2002;30 : 1851–8. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=113205&tool=pmcentrez&rendertype=abstract 11937640

16. Graber JH, Cantor CR, Mohr SC, Smith TF. Genomic detection of new yeast pre-mRNA 3’-end-processing signals. Nucleic Acids Res. 1999;27 : 888–94. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=148262&tool=pmcentrez&rendertype=abstract 9889288

17. Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell. 2010;143 : 1018–29. doi: 10.1016/j.cell.2010.11.020 21145465

18. Moqtaderi Z, Geisberg J V, Jin Y, Fan X, Struhl K. Species-specific factors mediate extensive heterogeneity of mRNA 3’ ends in yeasts. Proc Natl Acad Sci U S A. 2013;110 : 11073–8. doi: 10.1073/pnas.1309384110 23776204

19. Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA. 3 : 385–96. doi: 10.1002/wrna.116 22012871

20. Mogno I, Kwasnieski JC, Cohen BA. Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants. Genome Res. 2013; doi: 10.1101/gr.157891.113

21. White MA, Myers CA, Corbo JC, Cohen BA. Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks. Proc Natl Acad Sci U S A. 2013;110 : 11952–7. doi: 10.1073/pnas.1307449110 23818646

22. Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, et al. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res. 2013;23 : 800–11. doi: 10.1101/gr.144899.112 23512712

23. Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, Rogov P, et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol. 2012;30 : 271–7. doi: 10.1038/nbt.2137 22371084

24. Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, Lotan-Pompan M, et al. Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet. 2012;44 : 743–50. doi: 10.1038/ng.2305 22634752

25. Zeevi D, Sharon E, Lotan-Pompan M, Lubling Y, Shipony Z, Raveh-Sadka T, et al. Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res. 2011;21 : 2114–28. doi: 10.1101/gr.119669.110 22009988

26. Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci U S A. 2013;110 : 14024–9. doi: 10.1073/pnas.1301301110 23924614

27. Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, et al. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol. 2012;30 : 521–30. doi: 10.1038/nbt.2205 22609971

28. Patwardhan RP, Lee C, Litvin O, Young DL, Pe’er D, Shendure J. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol. 2009;27 : 1173–5. doi: 10.1038/nbt.1589 19915551

29. Kinney JB, Murugan A, Callan CG, Cox EC. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci U S A. 2010;107 : 9158–63. doi: 10.1073/pnas.1004290107 20439748

30. Shalgi R, Lapidot M, Shamir R, Pilpel Y. A catalog of stability-associated sequence elements in 3’ UTRs of yeast mRNAs. Genome Biol. 2005;6: R86. doi: 10.1186/gb-2005-6-10-r86 16207357

31. Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proc Natl Acad Sci U S A. 2005;102 : 17675–80. doi: 10.1073/pnas.0503803102 16317069

32. Russo P, Li WZ, Guo Z, Sherman F. Signals that produce 3’ termini in CYC1 mRNA of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1993;13 : 7836–49. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=364855&tool=pmcentrez&rendertype=abstract 8246998

33. Sharon E, Lubliner S, Segal E. A feature-based approach to modeling protein-DNA interactions. PLoS Comput Biol. 2008;4: e1000154. doi: 10.1371/journal.pcbi.1000154 18725950

34. Zeevi D, Sharon E, Lotan-Pompan M, Lubling Y, Shipony Z, Raveh-Sadka T, et al. Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters. Genome Res. 2011; doi: 10.1101/gr.119669.110

35. 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. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=98971&tool=pmcentrez&rendertype=abstract 10357856

36. Mandel CR, Bai Y, Tong L. Protein factors in pre-mRNA 3’-end processing. Cell Mol Life Sci. 2008;65 : 1099–122. doi: 10.1007/s00018-007-7474-3 18158581

37. Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, et al. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A. 2009;106 : 3264–9. doi: 10.1073/pnas.0812841106 19208812

38. Keren L, Zackay O, Lotan-Pompan M, Barenholz U, Dekel E, Sasson V, et al. Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol. 2013;9 : 701. doi: 10.1038/msb.2013.59 24169404

39. De Godoy LMF, Olsen J V, Cox J, Nielsen ML, Hubner NC, Fröhlich F, et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature. 2008;455 : 1251–4. doi: 10.1038/nature07341 18820680

40. Miller C, Schwalb B, Maier K, Schulz D, Dümcke S, Zacher B, et al. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol. 2011;7 : 458. doi: 10.1038/msb.2010.112 21206491

41. Russo P, Li WZ, Guo Z, Sherman F. Signals that produce 3’ termini in CYC1 mRNA of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1993;13 : 7836–49. doi: 10.1128/MCB.13.12.7836 Updated 8246998

42. Guo Z, Sherman F. Signals sufficient for 3’-end formation of yeast mRNA. Mol Cell Biol. 1996;16 : 2772–6. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=231268&tool=pmcentrez&rendertype=abstract 8649385

43. Shalem O, Carey L, Zeevi D, Sharon E, Keren L, Weinberger A, et al. Measurements of the impact of 3’ end sequences on gene expression reveal wide range and sequence dependent effects. PLoS Comput Biol. 2013;9: e1002934. doi: 10.1371/journal.pcbi.1002934 23505350

44. Tian B, Graber JH. Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA. 3 : 385–96. doi: 10.1002/wrna.116 22012871

45. Rondón AG, Mischo HE, Kawauchi J, Proudfoot NJ. Fail-safe transcriptional termination for protein-coding genes in S. cerevisiae. Mol Cell. 2009;36 : 88–98. doi: 10.1016/j.molcel.2009.07.028 19818712

46. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol. 2008;6: e255. doi: 10.1371/journal.pbio.0060255 18959479

47. Haimovich G, Medina DA, Causse SZ, Garber M, Millán-Zambrano G, Barkai O, et al. Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell. 2013;153 : 1000–11. doi: 10.1016/j.cell.2013.05.012 23706738

48. Bregman A, Avraham-Kelbert M, Barkai O, Duek L, Guterman A, Choder M. Promoter elements regulate cytoplasmic mRNA decay. Cell. 2011;147 : 1473–83. doi: 10.1016/j.cell.2011.12.005 22196725

49. Harel-Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M. RNA polymerase II subunits link transcription and mRNA decay to translation. Cell. 2010;143 : 552–63. doi: 10.1016/j.cell.2010.10.033 21074047

50. Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, et al. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol. 2008;4 : 223. doi: 10.1038/msb.2008.59 18854817

51. Shalem O, Groisman B, Choder M, Dahan O, Pilpel Y. Transcriptome kinetics is governed by a genome-wide coupling of mRNA production and degradation: a role for RNA Pol II. PLoS Genet. 2011;7: e1002273. doi: 10.1371/journal.pgen.1002273 21931566

52. Trcek T, Larson DR, Moldón A, Query CC, Singer RH. Single-molecule mRNA decay measurements reveal promoter -⁠ regulated mRNA stability in yeast. Cell. 2011;147 : 1484–97. doi: 10.1016/j.cell.2011.11.051 22196726

53. LeProust EM, Peck BJ, Spirin K, McCuen HB, Moore B, Namsaraev E, et al. Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process. Nucleic Acids Res. 2010;38 : 2522–40. doi: 10.1093/nar/gkq163 20308161

54. Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, et al. Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A. 2009;106 : 3264–9. doi: 10.1073/pnas.0812841106 19208812

55. Friedman J, Hastie T, Tibshirani R. Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw. 2010;33 : 1–22. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2929880&tool=pmcentrez&rendertype=abstract 20808728

56. Zacharioudakis I, Gligoris T, Tzamarias D. A yeast catabolic enzyme controls transcriptional memory. Curr Biol. 2007;17 : 2041–6. doi: 10.1016/j.cub.2007.10.044 17997309

57. Yeku O, Frohman MA. Rapid amplification of cDNA ends (RACE). Methods Mol Biol. 2011;703 : 107–22. doi: 10.1007/978-1-59745-248-9_8 21125486

58. Guo Z, Sherman F. Signals sufficient for 3’-end formation of yeast mRNA. Mol Cell Biol. 1996;16 : 2772–6. 8649385

59. Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981;9 : 133–48. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=326673&tool=pmcentrez&rendertype=abstract. 6163133