Drosha Promotes Splicing of a Pre-microRNA-like Alternative Exon
MicroRNAs (miRNAs) are short non-coding RNAs that function in gene silencing and are produced by cleavage from a larger primary RNA transcript through a reaction that is carried out by the Microprocessor. Primary miRNA transcripts are often located within the introns of genes. Thus, both the Microprocessor and the spliceosome, which is responsible for pre-mRNA splicing, interact with the same sequences, though little is known about how these two processes influence each other. In this study, we discovered that the alternatively spliced eIF4H exon 5 is predicted to form an RNA hairpin that resembles a Microprocessor substrate. We found that the Microprocessor can bind and cleave exon 5, which precludes inclusion of the exon in the mRNA. However, we find that Drosha, a component of the Microprocessor, primarily functions to enhance exon 5 splicing both in vitro and in cells, rather than to cleave the RNA. Our results suggest that the Microprocessor has a role in splicing that is distinct from its role in miRNA biogenesis. This Microprocessor activity represents a new function for the complex that may be an important mechanism for regulating alternative splicing.
Vyšlo v časopise:
Drosha Promotes Splicing of a Pre-microRNA-like Alternative Exon. PLoS Genet 10(5): e32767. doi:10.1371/journal.pgen.1004312
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1004312
Souhrn
MicroRNAs (miRNAs) are short non-coding RNAs that function in gene silencing and are produced by cleavage from a larger primary RNA transcript through a reaction that is carried out by the Microprocessor. Primary miRNA transcripts are often located within the introns of genes. Thus, both the Microprocessor and the spliceosome, which is responsible for pre-mRNA splicing, interact with the same sequences, though little is known about how these two processes influence each other. In this study, we discovered that the alternatively spliced eIF4H exon 5 is predicted to form an RNA hairpin that resembles a Microprocessor substrate. We found that the Microprocessor can bind and cleave exon 5, which precludes inclusion of the exon in the mRNA. However, we find that Drosha, a component of the Microprocessor, primarily functions to enhance exon 5 splicing both in vitro and in cells, rather than to cleave the RNA. Our results suggest that the Microprocessor has a role in splicing that is distinct from its role in miRNA biogenesis. This Microprocessor activity represents a new function for the complex that may be an important mechanism for regulating alternative splicing.
Zdroje
1. DenliAM, TopsBB, PlasterkRH, KettingRF, HannonGJ (2004) Processing of primary microRNAs by the Microprocessor complex. Nature 432: 231–235.
2. GregoryRI, YanKP, AmuthanG, ChendrimadaT, DoratotajB, et al. (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235–240.
3. HanJ, LeeY, YeomKH, KimYK, JinH, et al. (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18: 3016–3027.
4. LandthalerM, YalcinA, TuschlT (2004) The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis. Curr Biol 14: 2162–2167.
5. LeeY, AhnC, HanJ, ChoiH, KimJ, et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415–419.
6. ZengY, YiR, CullenBR (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. Embo J 24: 138–148.
7. BernsteinE, CaudyAA, HammondSM, HannonGJ (2001) Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363–366.
8. GrishokA, PasquinelliAE, ConteD, LiN, ParrishS, et al. (2001) Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106: 23–34.
9. HutvagnerG, McLachlanJ, PasquinelliAE, BalintE, TuschlT, et al. (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293: 834–838.
10. KettingRF, FischerSE, BernsteinE, SijenT, HannonGJ, et al. (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15: 2654–2659.
11. KnightSW, BassBL (2001) A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293: 2269–2271.
12. GolanD, LevyC, FriedmanB, ShomronN (2010) Biased hosting of intronic microRNA genes. Bioinformatics 26: 992–995.
13. KimYK, KimVN (2007) Processing of intronic microRNAs. Embo J 26: 775–783.
14. GuilS, CaceresJF (2007) The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a. Nat Struct Mol Biol 14: 591–596.
15. MichlewskiG, GuilS, SempleCA, CaceresJF (2008) Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol Cell 32: 383–393.
16. MichlewskiG, CaceresJF (2010) Antagonistic role of hnRNP A1 and KSRP in the regulation of let-7a biogenesis. Nat Struct Mol Biol 17: 1011–1018.
17. TrabucchiM, BriataP, Garcia-MayoralM, HaaseAD, FilipowiczW, et al. (2009) The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature 459: 1010–1014.
18. WuH, SunS, TuK, GaoY, XieB, et al. (2010) A splicing-independent function of SF2/ASF in microRNA processing. Mol Cell 38: 67–77.
19. KataokaN, FujitaM, OhnoM (2009) Functional association of the Microprocessor complex with the spliceosome. Mol Cell Biol 29: 3243–3254.
20. SiomiH, SiomiMC (2010) Posttranscriptional regulation of microRNA biogenesis in animals. Mol Cell 38: 323–332.
21. Agranat-TamirL, ShomronN, SperlingJ, SperlingR (2014) Interplay between pre-mRNA splicing and microRNA biogenesis within the supraspliceosome. Nucleic Acids Res [epub ahead of print].
22. MorlandoM, BallarinoM, GromakN, PaganoF, BozzoniI, et al. (2008) Primary microRNA transcripts are processed co-transcriptionally. Nat Struct Mol Biol 15: 902–909.
23. PawlickiJM, SteitzJA (2008) Primary microRNA transcript retention at sites of transcription leads to enhanced microRNA production. J Cell Biol 182: 61–76.
24. JanasMM, KhaledM, SchubertS, BernsteinJG, GolanD, et al. (2011) Feed-forward microprocessing and splicing activities at a microRNA-containing intron. PLoS Genet 7: e1002330.
25. BielewiczD, KalakM, KalynaM, WindelsD, BartaA, et al. (2013) Introns of plant pri-miRNAs enhance miRNA biogenesis. EMBO Rep 14: 622–628.
26. SchwabR, SpethC, LaubingerS, VoinnetO (2013) Enhanced microRNA accumulation through stemloop-adjacent introns. EMBO Rep 14: 615–621.
27. SundaramGM, CommonJE, GopalFE, SrikantaS, LakshmanK, et al. (2013) ‘See-saw’ expression of microRNA-198 and FSTL1 from a single transcript in wound healing. Nature 495: 103–106.
28. MattioliC, PianigianiG, PaganiF (2013) A competitive regulatory mechanism discriminates between juxtaposed splice sites and pri-miRNA structures. Nucleic Acids Res 41(18): 8680–91.
29. MelamedZ, LevyA, Ashwal-FlussR, Lev-MaorG, MekahelK, et al. (2013) Splicing regulates biogenesis alternative of miRNAs located across exon-intron junctions. Mol Cell 50: 869–881.
30. KnucklesP, VogtMA, LugertS, MiloM, ChongMM, et al. (2012) Drosha regulates neurogenesis by controlling neurogenin 2 expression independent of microRNAs. Nat Neurosci 15: 962–969.
31. MaciasS, PlassM, StajudaA, MichlewskiG, EyrasE, et al. (2012) DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nat Struct Mol Biol 19: 760–766.
32. GromakN, DienstbierM, MaciasS, PlassM, EyrasE, et al. (2013) Drosha regulates gene expression independently of RNA cleavage function. Cell reports 5: 1499–1510.
33. HanJ, LeeY, YeomKH, NamJW, HeoI, et al. (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125: 887–901.
34. AuyeungVC, UlitskyI, McGearySE, BartelDP (2013) Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 152: 844–858.
35. HeoI, JooC, ChoJ, HaM, HanJ, et al. (2008) Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol Cell 32: 276–284.
36. BerezikovE, ChungWJ, WillisJ, CuppenE, LaiEC (2007) Mammalian mirtron genes. Mol Cell 28: 328–336.
37. HavensMA, ReichAA, DuelliDM, HastingsML (2012) Biogenesis of mammalian microRNAs by a non-canonical processing pathway. Nucleic Acids Res 40: 4626–4640.
38. SibleyCR, SeowY, SaaymanS, DijkstraKK, El AndaloussiS, et al. (2012) The biogenesis and characterization of mammalian microRNAs of mirtron origin. Nucleic Acids Res 40: 438–448.
39. AhmedF, AnsariHR, RaghavaGP (2009) Prediction of guide strand of microRNAs from its sequence and secondary structure. BMC Bioinformatics 10: 105.
40. HanJ, PedersenJS, KwonSC, BelairCD, KimYK, et al. (2009) Posttranscriptional crossregulation between Drosha and DGCR8. Cell 136: 75–84.
41. KadenerS, RodriguezJ, AbruzziKC, KhodorYL, SuginoK, et al. (2009) Genome-wide identification of targets of the drosha-pasha/DGCR8 complex. Rna 15: 537–545.
42. ShenoyA, BlellochR (2009) Genomic analysis suggests that mRNA destabilization by the microprocessor is specialized for the auto-regulation of Dgcr8. PLoS One 4: e6971.
43. VaraniG (1995) Exceptionally stable nucleic acid hairpins. Annu Rev Biophys Biomol Struct 24: 379–404.
44. BaradO, MannM, ChapnikE, ShenoyA, BlellochR, et al. (2012) Efficiency and specificity in microRNA biogenesis. Nat Struct Mol Biol 19: 650–652.
45. SunY, AtasE, LindqvistL, SonenbergN, PelletierJ, et al. (2012) The eukaryotic initiation factor eIF4H facilitates loop-binding, repetitive RNA unwinding by the eIF4A DEAD-box helicase. Nucleic Acids Res 40: 6199–6207.
46. TomonagaT, MatsushitaK, YamaguchiS, Oh-IshiM, KoderaY, et al. (2004) Identification of altered protein expression and post-translational modifications in primary colorectal cancer by using agarose two-dimensional gel electrophoresis. Clin Cancer Res 10: 2007–2014.
47. WuD, MatsushitaK, MatsubaraH, NomuraF, TomonagaT (2011) An alternative splicing isoform of eukaryotic initiation factor 4H promotes tumorigenesis in vivo and is a potential therapeutic target for human cancer. Int J Cancer 128: 1018–1030.
48. JafariN, DogahehHP, BohlooliS, OyongGG, ShirzadZ, et al. (2013) Expression levels of microRNA machinery components Drosha, Dicer and DGCR8 in human (AGS, HepG2, and KEYSE-30) cancer cell lines. Int J Clin Exp Med 6: 269–274.
49. MerrittWM, LinYG, HanLY, KamatAA, SpannuthWA, et al. (2008) Dicer, Drosha, and outcomes in patients with ovarian cancer. The New England journal of medicine 359: 2641–2650.
50. CorpetF (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16: 10881–10890.
51. ZukerM (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415.
52. LivakKJ, SchmittgenTD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402–408.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2014 Číslo 5
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
Najčítanejšie v tomto čísle
- PINK1-Parkin Pathway Activity Is Regulated by Degradation of PINK1 in the Mitochondrial Matrix
- Phosphorylation of a WRKY Transcription Factor by MAPKs Is Required for Pollen Development and Function in
- Null Mutation in PGAP1 Impairing Gpi-Anchor Maturation in Patients with Intellectual Disability and Encephalopathy
- p53 Requires the Stress Sensor USF1 to Direct Appropriate Cell Fate Decision