Genetics and Regulatory Impact of Alternative Polyadenylation in Human B-Lymphoblastoid Cells

English version České info

Gene expression varies widely between individuals of a population, and regulatory change can underlie phenotypes of evolutionary and biomedical relevance. A key question in the field is how DNA sequence variants impact gene expression, with most mechanistic studies to date focused on the effects of genetic change on regulatory regions upstream of protein-coding sequence. By contrast, the role of RNA 3′-end processing in regulatory variation remains largely unknown, owing in part to the challenge of identifying functional elements in 3′ untranslated regions. In this work, we conducted a genomic survey of transcript ends in lymphoblastoid cells from genetically distinct human individuals. Our analysis mapped the cis-regulatory architecture of 3′ gene ends, finding that transcript end positions did not fall randomly in untranslated regions, but rather preferentially flanked the locations of 3′ regulatory elements, including miRNA sites. The usage of these transcript length forms and motifs varied across human individuals, and polymorphisms in polyadenylation signals and other 3′ motifs were significant predictors of expression levels of the genes in which they lay. Independent single-gene experiments confirmed the effects of polyadenylation variants on steady-state expression of their respective genes, and validated the regulatory function of 3′ cis-regulatory sequence elements that mediated expression of these distinct RNA length forms. Focusing on the immune regulator IRF5, we established the effect of natural variation in RNA 3′-end processing on regulatory response to antigen stimulation. Our results underscore the importance of two mechanisms at play in the genetics of 3′-end variation: the usage of distinct 3′-end processing signals and the effects of 3′ sequence elements that determine transcript fate. Our findings suggest that the strategy of integrating observed 3′-end positions with inferred 3′ regulatory motifs will prove to be a critical tool in continued efforts to interpret human genome variation.

Vyšlo v časopise: Genetics and Regulatory Impact of Alternative Polyadenylation in Human B-Lymphoblastoid Cells. PLoS Genet 8(8): e32767. doi:10.1371/journal.pgen.1002882
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002882

Souhrn

Zdroje

1. FarberCR, LusisAJ (2008) Integrating global gene expression analysis and genetics. Adv Genet 60 : 571–601.

2. RockmanMV, KruglyakL (2006) Genetics of global gene expression. Nat Rev Genet 7 : 862–872.

3. CooksonW, LiangL, AbecasisG, MoffattM, LathropM (2009) Mapping complex disease traits with global gene expression. Nat Rev Genet 10 : 184–194.

4. SchadtEE (2009) Molecular networks as sensors and drivers of common human diseases. Nature 461 : 218–223.

5. RockmanMV (2008) Reverse engineering the genotype-phenotype map with natural genetic variation. Nature 456 : 738–744.

6. VeyrierasJB, KudaravalliS, KimSY, DermitzakisET, GiladY, et al. (2008) High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 4: e1000214 doi:10.1371/journal.pgen.1000214.

7. ZhengW, ZhaoH, ManceraE, SteinmetzLM, SnyderM (2010) Genetic analysis of variation in transcription factor binding in yeast. Nature 464 : 1187–1191.

8. RonaldJ, BremRB, WhittleJ, KruglyakL (2005) Local regulatory variation in Saccharomyces cerevisiae. PLoS Genet 1: e25 doi:10.1371/journal.pgen.0010025.

9. GuhaThakurtaD, XieT, AnandM, EdwardsSW, LiG, et al. (2006) Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations. BMC Genomics 7 : 235.

10. KasowskiM, GrubertF, HeffelfingerC, HariharanM, AsabereA, et al. (2010) Variation in transcription factor binding among humans. Science 328 : 232–235.

11. NagarajanM, VeyrierasJB, de DieuleveultM, BottinH, FehrmannS, et al. (2010) Natural single-nucleosome epi-polymorphisms in yeast. PLoS Genet 6: e1000913 doi:10.1371/journal.pgen.1000913.

12. JohannesF, ColotV, JansenRC (2008) Epigenome dynamics: a quantitative genetics perspective. Nat Rev Genet 9 : 883–890.

13. ZhangX, RichardsEJ, BorevitzJO (2007) Genetic and epigenetic dissection of cis regulatory variation. Curr Opin Plant Biol 10 : 142–148.

14. ZhangH, LeeJY, TianB (2005) Biased alternative polyadenylation in human tissues. Genome Biol 6: R100.

15. GrahamRR, KyogokuC, SigurdssonS, VlasovaIA, DaviesLR, et al. (2007) Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus. Proc Natl Acad Sci U S A 104 : 6758–6763.

16. SinghP, AlleyTL, WrightSM, KamdarS, SchottW, et al. (2009) Global changes in processing of mRNA 3′ untranslated regions characterize clinically distinct cancer subtypes. Cancer Res 69 : 9422–9430.

17. FlomenR, MakoffA (2011) Increased RNA editing in EAAT2 pre-mRNA from amyotrophic lateral sclerosis patients: involvement of a cryptic polyadenylation site. Neurosci Lett 497 : 139–143.

18. ChenJM, FerecC, CooperDN (2006) A systematic analysis of disease-associated variants in the 3′ regulatory regions of human protein-coding genes I: general principles and overview. Hum Genet 120 : 1–21.

19. DanckwardtS, HentzeMW, KulozikAE (2008) 3′ end mRNA processing: molecular mechanisms and implications for health and disease. EMBO J 27 : 482–498.

20. WiestnerA, TehraniM, ChiorazziM, WrightG, GibelliniF, et al. (2007) Point mutations and genomic deletions in CCND1 create stable truncated cyclin D1 mRNAs that are associated with increased proliferation rate and shorter survival. Blood 109 : 4599–4606.

21. FraserHB, XieX (2009) Common polymorphic transcript variation in human disease. Genome Res 19 : 567–575.

22. KwanT, BenovoyD, DiasC, GurdS, ProvencherC, et al. (2008) Genome-wide analysis of transcript isoform variation in humans. Nat Genet 40 : 225–231.

23. MillevoiS, VagnerS (2010) Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation. Nucleic Acids Res 38 : 2757–2774.

24. MooreMJ, ProudfootNJ (2009) Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136 : 688–700.

25. TranterM, HelsleyRN, PauldingWR, McGuinnessM, BrokampC, et al. (2011) Coordinated post-transcriptional regulation of HSP70.3 gene expression by micro-RNA and alternative polyadenylation. J Biol Chem

26. LauAG, IrierHA, GuJ, TianD, KuL, et al. (2010) Distinct 3′UTRs differentially regulate activity-dependent translation of brain-derived neurotrophic factor (BDNF). Proc Natl Acad Sci U S A 107 : 15945–15950.

27. AnJJ, GharamiK, LiaoGY, WooNH, LauAG, et al. (2008) Distinct role of long 3′ UTR BDNF mRNA in spine morphology and synaptic plasticity in hippocampal neurons. Cell 134 : 175–187.

28. Al-AhmadiW, Al-GhamdiM, Al-HajL, Al-SaifM, KhabarKS (2009) Alternative polyadenylation variants of the RNA binding protein, HuR: abundance, role of AU-rich elements and auto-Regulation. Nucleic Acids Res 37 : 3612–3624.

29. SandbergR, NeilsonJR, SarmaA, SharpPA, BurgeCB (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320 : 1643–1647.

30. TianB, HuJ, ZhangH, LutzCS (2005) A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res 33 : 201–212.

31. GhoshT, SoniK, ScariaV, HalimaniM, BhattacharjeeC, et al. (2008) MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene. Nucleic Acids Res 36 : 6318–6332.

32. NatalizioBJ, MunizLC, ArhinGK, WiluszJ, LutzCS (2002) Upstream elements present in the 3′-untranslated region of collagen genes influence the processing efficiency of overlapping polyadenylation signals. J Biol Chem 277 : 42733–42740.

33. Hall-PogarT, ZhangH, TianB, LutzCS (2005) Alternative polyadenylation of cyclooxygenase-2. Nucleic Acids Res 33 : 2565–2579.

34. LiuD, FritzDT, RogersMB, ShatkinAJ (2008) Species-specific cis-regulatory elements in the 3′-untranslated region direct alternative polyadenylation of bone morphogenetic protein 2 mRNA. J Biol Chem 283 : 28010–28019.

35. MayrC, BartelDP (2009) Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138 : 673–684.

36. JiZ, LeeJY, PanZ, JiangB, TianB (2009) Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci U S A 106 : 7028–7033.

37. JiZ, TianB (2009) Reprogramming of 3′ untranslated regions of mRNAs by alternative polyadenylation in generation of pluripotent stem cells from different cell types. PLoS ONE 4: e8419 doi:10.1371/journal.pone.0008419.

38. LiuD, BrockmanJM, DassB, HutchinsLN, SinghP, et al. (2007) Systematic variation in mRNA 3′-processing signals during mouse spermatogenesis. Nucleic Acids Res 35 : 234–246.

39. FlavellSW, KimTK, GrayJM, HarminDA, HembergM, et al. (2008) Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection. Neuron 60 : 1022–1038.

40. FuY, SunY, LiY, LiJ, RaoX, et al. (2011) Differential genome-wide profiling of tandem 3′ UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Research 21 : 741–747.

41. JanCH, FriedmanRC, RubyJG, BartelDP (2011) Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs. Nature 469 : 97–101.

42. YoonOK, BremRB (2011) Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA 16 : 1256–1267.

43. MangoneM, ManoharanAP, Thierry-MiegD, Thierry-MiegJ, HanT, et al. (2010) The landscape of C. elegans 3′UTRs. Science 329 : 432–435.

44. ShepardPJ, ChoiEA, LuJ, FlanaganLA, HertelKJ, et al. (2011) Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA 17 : 761–772.

45. OzsolakF, KapranovP, FoissacS, KimSW, FishilevichE, et al. (2010) Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143 : 1018–1029.

46. PickrellJK, MarioniJC, PaiAA, DegnerJF, EngelhardtBE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464 : 768–772.

47. NamDK, LeeS, ZhouG, CaoX, WangC, et al. (2002) Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc Natl Acad Sci U S A 99 : 6152–6156.

48. NunesNM, LiW, TianB, FurgerA (2010) A functional human Poly(A) site requires only a potent DSE and an A-rich upstream sequence. EMBO J 29 : 1523–1536.

49. ZarudnayaMI, KolomietsIM, PotyahayloAL, HovorunDM (2003) Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res 31 : 1375–1386.

50. VenkataramanK, BrownKM, GilmartinGM (2005) Analysis of a noncanonical poly(A) site reveals a tripartite mechanism for vertebrate poly(A) site recognition. Genes Dev 19 : 1315–1327.

51. LegendreM, GautheretD (2003) Sequence determinants in human polyadenylation site selection. BMC Genomics 4 : 7.

52. ChenK, RajewskyN (2006) Natural selection on human microRNA binding sites inferred from SNP data. Nat Genet 38 : 1452–1456.

53. GruberAR, FallmannJ, KratochvillF, KovarikP, HofackerIL (2011) AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res 39: D66–69.

54. AraT, LopezF, RitchieW, BenechP, GautheretD (2006) Conservation of alternative polyadenylation patterns in mammalian genes. BMC Genomics 7 : 189.

55. HoulstonRS, CheadleJ, DobbinsSE, TenesaA, JonesAM, et al. (2010) Meta-analysis of three genome-wide association studies identifies susceptibility loci for colorectal cancer at 1q41, 3q26.2, 12q13.13 and 20q13.33. Nat Genet 42 : 973–977.

56. KratochvillF, MachacekC, VoglC, EbnerF, SedlyarovV, et al. (2011) Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation. Mol Syst Biol 7 : 560.

57. GerondakisS, GrumontRJ, BanerjeeA (2007) Regulating B-cell activation and survival in response to TLR signals. Immunol Cell Biol 85 : 471–475.

58. KhabarKS (2007) Rapid transit in the immune cells: the role of mRNA turnover regulation. J Leukoc Biol 81 : 1335–1344.

59. KoscielnyG, Le TexierV, GopalakrishnanC, KumanduriV, RiethovenJJ, et al. (2009) ASTD: The Alternative Splicing and Transcript Diversity database. Genomics 93 : 213–220.

60. de la GrangeP, DutertreM, CorreaM, AuboeufD (2007) A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. BMC Bioinformatics 8 : 180.

61. LegendreM, RitchieW, LopezF, GautheretD (2006) Differential repression of alternative transcripts: a screen for miRNA targets. PLoS Comput Biol 2: e43 doi:10.1371/journal.pcbi.0020043.

62. LanderES, LintonLM, BirrenB, NusbaumC, ZodyMC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409 : 860–921.

63. FujitaPA, RheadB, ZweigAS, HinrichsAS, KarolchikD, et al. (2011) The UCSC Genome Browser database: update 2011. Nucleic Acids Res 39: D876–882.

64. LeeJY, YehI, ParkJY, TianB (2007) PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res 35: D165–168.

65. KentWJ, SugnetCW, FureyTS, RoskinKM, PringleTH, et al. (2002) The human genome browser at UCSC. Genome Res 12 : 996–1006.

66. Lynch M, Walsh B (1998) Genetics and Analysis of Quantitative Traits. Sunderland, MA: Sinauer Associates, Inc.

67. GrimsonA, FarhKK, JohnstonWK, Garrett-EngeleP, LimLP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27 : 91–105.

68. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467 : 1061–1073.

69. NagalakshmiU, WangZ, WaernK, ShouC, RahaD, et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320 : 1344–1349.

70. AslanidisC, de JongPJ (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18 : 6069–6074.

71. UntergasserA, NijveenH, RaoX, BisselingT, GeurtsR, et al. (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35: W71–74.