1. Elementi ARE (AU rich element)

2. ARE-binding proteins ProteinkDa MotifExpression siteAREFunction AUF1 37,40,42,45RRMUbiquitousc-myc, c-fos, GM-CSFmRNA destab. AUBF ND T cellsc-fos, INF, IL-3 v-myc, GM- CSF, (AUUUA)n ARE-binding corr. with mRNA stab. AU-A 34NDT cellsTNF, GM-CSF, c-mycND AU-B 30 AU-C 43 hnRNPA1 36RRMHuman PBMCsGM-CSF, IL-2, c-mycND hnRNPC 43 Elav-like 36–40RRMUbiquitous, nervous systemc-myc, c-fos,TNF-a,GM-CSFmRNA stab. HuR HuD HuC Hel-N1 TIAR 40, 42RRMBrain, spleen, lung, liver,testisTNF, GM-CSFTransl. inhib. TIA-1 Brain, spleen, testis TTP 44Cys3HisFibroblasts, macrophagesTNF, IL-3 GM-CSFmRNA destab. KSRP 78KHNeural cells and other typesc-fosmRNA destab. AUBF, AU binding factor ; AU-A, AU binding factor-A ; AU-B, AU binding factor-B ; AU-C, AU binding factor-C ; hnRNP, heterogeneous nuclear ribonucleoprotein ; KH, hnRNP-K homology domain; KSRP, KH-type splicing regulatory protein 1; ND, not determined; PBMC, peripheral blood mononuclear cell.

3. ARE-binding proteins

4. Modello sul ruolo delle ARE e ARE-BP

5. Degradazione dipendente dalle ARE e ARE-BP

6. Degradazione mediata da endoribonucleasi

7. AUG UAG mGppp AAAAAAAAAAAAAAAA PTC NMD (Nonsense Mediated Decay)

9. PTC nei mammiferi

10. Formazione EJC

11. Non-sense Mediated Decay (NMD): complesso EJC

12. Non-sense Mediated Decay (NMD)

14. "Pioneer round" of translation

16. 3 2 Meccanismo dell’NMD UAG (PTC)AUGSTOP mGppp AAAAAAAAAAAAAAAA 33 2 mGpp p AAAAAAAAAAAAAAAA 3 UAG AAAAAAAAAAAAAAAA mGppp UAG 33 22 1 RF

17. Degradazione normale

18. Degradazione NMD

19. Non-Stop Mediated Decay (NSMD)

20. Processing Bodies e Stress Granules

21. Cytoplasmic bodies

22. mRNP cycle

23. RNA interference Meccanismo Significato biologico Strumento di analisi della funzione dei geni

24. Co-soppressione Introduzione di copie transgeniche di un gene risulta nella ridotta espressione del transgene e del gene endogeno RNA interference Introduzione di RNA a doppio filamento (dsRNA) induce silenziamento genico

25. Componenti dell’RNAi siRNA (small interfering RNA) = frammenti di RNA 21-25 nt Dicer = endoribonucleasi specifica per dsRNA (tipo RNasi III) RISC (RNA-induced silencing complex) = complesso ribonucleoproteico RdRP (RNA-dependent RNA polymerase)

27. Inizio dell’RNAi dsRNA (80-100 nt) in piante, C. elegans, Drosophila siRNA in mammiferi

28. Effetto del dsRNA

29. Figure 2 Dicer and RISC (RNA-induced silencing complex). a, RNAi is initiated by the Dicer enzyme (two Dicer molecules with five domains each are shown), which processes double-stranded RNA into ~22-nucleotide small interfering RNAs. Based upon the known mechanisms for the RNase III family of enzymes, Dicer is thought to work as a dimeric enzyme. Cleavage into precisely sized fragments is determined by the fact that one of the active sites in each Dicer protein is defective (indicated by an asterisk), shifting the periodicity of cleavage from ~9–11 nucleotides for bacterial RNase III to ~22 nucleotides for Dicer family members. The siRNAs are incorporated into a multicomponent nuclease, RISC (green). Recent reports suggest that RISC must be activated from a latent form, containing a double-stranded siRNA to an active form, RISC*, by unwinding of siRNAs. RISC* then uses the unwound siRNA as a guide to substrate selection31. b, Diagrammatic representation of Dicer binding and cleaving dsRNA (for clarity, not all the Dicer domains are shown, and the two separate Dicer molecules are coloured differently). Deviations from the consensus RNase III active site in the second RNase III domain inactivate the central catalytic sites, resulting in cleavage at 22-nucleotide intervals.

30. Meccanismo 1.Produzione siRNA 2.Formazione complesso RISC 3.Attivazione complesso RISC 4.Taglio dell’RNA bersaglio

31. Propagazione dell’RNAi

32. Figure 3 Transitive RNAi. In transitive RNAi in C. elegans, silencing can travel in a 3’ to 5’ direction on a specific mRNA target. The simplest demonstration comes from the creation of fusion transcripts. Consider a fragment of green fluorescent protein (GFP) fused to a segment of UNC-22 (left). Targeting GFP abolishes fluorescence but also creates an unexpected, uncoordinated phenotype. This occurs because of the production of double-stranded RNA and consequently small interfering RNAs homologous to the endogenous UNC-22 gene. In a case in which GFP is fused 5’ to the UNC-22 fragment (right), GFP dsRNA still ablates fluorescence but does not produce an uncoordinated phenotype.

33. An integrated model for RNAi and PTGS. In this model, the sequential action of Dicer (to generate siRNAs) and ‘Slicer’ (to cleave the target RNA) are considered the primary route for target destruction. Amplification of the siRNAs is postulated to occur by either (or both) ‘random degradative PCR’ or production of siRNAs from aberrant RNA — that is, the copying of the target RNA or a cleavage product of the target RNA by an RNA- dependent RNA polymerase to generate a dsRNA substrate for Dicer, thereby creating new siRNAs. In the random degradative PCR scheme, the polymerase is envisioned to be primed by an siRNA guide strand. Conversion of aberrant RNA to dsRNA is drawn here unprimed.

34. Fig. 1. Models of molecular pathways involved in double-stranded RNA (dsRNA)-mediated silencing. The basic mechanism, which is probably present in most eukaryotes undergoing dsRNA-mediated silencing, is indicated by the gray and blue boxes. The remaining steps seem to occur in at least some organisms, but their generality is currently unknown and their subcellular location is mainly hypothetical. The ‘triggers’ of silencing, either direct sources of dsRNA or transcription units producing singlestranded RNAs that can be presumably converted to dsRNA, are colored red. Green RNA, endogenously transcribed single-stranded RNA; purple RNA, RNA synthesized by a putative RNA- directed RNA polymerase; blue and red RNA, double- stranded RNA introduced exogenously or resulting from viral replication, annealing of complementary ssRNAs and/or hairpin RNA. Proteins or protein complexes are indicated by yellow boxes: CAF, an Arabidopsis homolog of Dicer; Dicer, an RNase-III- like dsRNA-specific ribonuclease; RdRP, an RNA- directed RNA polymerase; and RISC, RNA-induced silencing complex. Although dsRNA is depicted in single nuclear and cytoplasmic pools, depending on the source these molecules might be delivered differently to the processing Dicer enzymes. Similarly, the RISC and RISC-like complexes might have different components and associated effector proteins depending on their functions. Although a role for dsRNA in directing methylation of homologous DNA sequences has been demonstrated in plants, the molecular machinery involved in this process and the actual nature of the ‘guide’ RNA have not been resolved. Recent evidence suggests that the RISC complex is equivalent to the miRNP complex (Fig. 2) in human cells [17].

35. Caratteristiche dell’RNAi Può agire a diversi livelli: trascrizionale, post- trascrizionale, traduzionale Può amplificarsi e diffondersi nell’organismo Può coinvolgere sequenze adiacenti

36. Viral Suppressors of RNAi The genomes of three positive-strand RNA viruses that encode suppressors of RNAi (black boxes) are shown. The polymerase genes (white boxes), other viral proteins (gray boxes), viral protease cleavage sites (diamonds), and sgRNA promoters (bent arrows) are indicated for comparison.

38. Controllo di acidi nucleici “parassiti” C. elegans senza RNAi hanno una aumentata mobilità di trasposoni endogeni In alcuni sistemi i trasposoni “silenziati” si trovano organizzati in eterocromatina Regolazione dell’espressione genica Mutazioni in componenti dell’RNAi causano alterazioni dello sviluppo (Arabidopsis, C. elegans, Drosophila) Regolazione del gene Stellate in Drosophila

39. Ruolo biologico dell’RNAi Difesa dai virus (nelle piante VISG) Controllo dei trasposoni Regolazione dell’espressione genica

40. Uso dell’RNAi Studio sistematico della funzione dei geni Terapia genica

41. Fig. 1. The DNA vector-based RNA interference (RNAi) technology. (a) Generation of a hairpin siRNA directed by a Pol III promoter. An inverted repeat is inserted at the ©≠1 position of the U6 promoter (2351 to ©≠1). The individual motif is 19–29 nt, corresponding to the coding region of the gene of interest. The two motifs that form the inverted repeat are separated by a spacer of three to nine nt. The transcriptional termination signal of five Ts are added at the 30 end of the inverted repeat. The resulting RNA is predicted to fold back to form a hairpin dsRNA as shown. The resulting siRNA starts with either a G or an A at the 50 end, dependent on the promoter used (U6 or H1) and ends with one to four uridines, forming a 30 overhang that is not complementary to the target sequences. (b) Generation of two complementary siRNA strands synthesized by two U6 promoters. Two U6 promoters either placed in tandem or on two separate plasmids (not shown) direct transcription of a sense and an antisense strand of 19-nt RNAs. The two RNA strands are predicted to form a duplex siRNA in the transfected cells, with 30 overhangs of one to four uridines.

43. Processing bodies