RNA regolatori e controllo posttrascrizionale dell’espressione genica 21 Aprile 2017 Corso di Genetica Molecolare CeciliaMannironi Is.tutodiBiologiaePatologiaMolecolaridelCNR [email protected] Human Genome Project (HGP) 1990-2003 Progetto di sequenziamento delle regioni eucromatiche del genoma. Non sono state sequenziate le regioni eterocromatiche, dei centromeri e dei telomeri. In parallelo sono stati sequenziati i genomi di vari organismi modello come Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis ecc Febbraio 2011 HumanGeneCount:MoreThanaChicken,LessThanaGrape NB!inumerisonorela.viaigenicodifican.perproteine PerteaM,SalzbergSL.2010.Betweenachickenandagrape:es.ma.ngthenumberofhumangenes. GenomeBiol11:206. La stima del numero dei geni umani si è ridotta progressivamente con lo sviluppo di nuove tecnologie per il sequenziamento del DNA MOLECULAR BIOLOGY AND EVOLUTION: Can Genes Explain Biological Complexity? Szathmary et al. Science 18 May 2001: Vol. 292. no. 5520, pp. 1315 – 1316 Il n° dei geni codificanti per proteine presenti nel genoma di un organismo non è una misura della sua complessita’ biologica. Le regioni codificanti del genoma sono identiche al 99.7% nell’uomo e nello scimpanzè I COMPONENTI DEL GENOMA UMANO retrotransposons TRASCRIZIONE PERVASIVA Il 70% del genoma umano è trascritto ma solo l’1.5-2% dei trascritti codifica per proteine COMPOSIZIONE DEL TRASCRITTOMA NEI MAMMIFERI Gli RNA non codificanti (non coding RNAs, ncRNAs) sono trascritti che non contengono open reading frames (ORF) o che hanno accumulato mutazione che li rendono inattivi (pseudogeni). Caratteristiche degli RNA cellulari A.F.PalazzoandE.S.Lee,“Non-codingRNA:whatisfunc.onalandwhatisjunk?,”Front.Genet.,vol.6,no.61,p.326,Jan.2015. I microRNA (miRNA) sono piccoli RNA silenziatori I miRNA sono ncRNA, lunghi 19-24 nt, a singolo filamento. Ad oggi nell’uomo sono stati identificati 1881 miRNA diversi (www.mirbase.org/) che si pensa regolino l’espressione di 2/3 dei geni cellulari. 5’ 5’ • I miRNA interagiscono con un mRNA bersaglio (target) mediante appaiamento imperfetto. • L’espressione dell’mRNA target è inibita. BIOGENESI dei miRNA miRISC* siRNA-RISC miRISC delle piante *miRNA-Induced Silencing Complex I geni dei microRNA possono essere unita’ geniche indipendenti o far parte di geni codificanti per un mRNA Geni miRNA : • Unita’ geniche indipendenti con un proprio promotore • Mirtron: Intragenici, situati all’interno delle sequenze introniche di un altro gene, con cui condividono il promotore I geni dei microRNA possono essere mono o policistronici I pri-miRNA hanno una struttura comune Questa struttura ha permesso l’identificazione dei geni dei miRNA all’interno del genoma …..cosi’ come i pre-miRNA I miRNA sono inibitori dell’espressione genica Ipotetici meccanismi di repressione genica mediati dai miRNA Krol et al. The widespread regulation of microRNA biogenesis, function and decay. Nature Reviews Genetics (2010) vol. 11 (9) pp. 597-610 Analisi bioinformatica dei potenziali target di un miRNA Esistono algoritmi che permettono di predire, per un dato miRNA, gli mRNA potenziali target, e/o per un dato mRNA i miRNA che potenzialmente lo possono legare. La predizione si basa sulla complementarieta’ di sequenza, sulla conservazione evolutiva del complesso, sulla posizione sulla 3’UTR, ecc. Tra gli algoritmi piu’ noti: microRNA.org, targetScan, Pictar, Diana, ecc ecc Predicted miRNA target sites within the human EDN1 3′UTR (NM_001955) were determined using microRNA.org Bartel,DavidP."MicroRNAs:genomics,biogenesis,mechanism,andfunc.on.”Cell116.2(2004):281-297. Un miRNA puo’ controllare l’espressione di centinaia di mRNA target Silenziamento genico mediato dai miRNA nei mammiferi e nelle piante mammiferi piante La scoperta dei microRNA I miRNA rappresentano la punta di un iceberg del mondo dei ncRNA e ad oggi sono i ncRNA meglio caratterizzati V.Ambros T.Tuschl probe compared with the Ddel probe, indicating that lin-4S starts 5 nt upstream of the end of the Ddel probe. (B) S1 analysis of total RNA from wild-type N2 using 3! end–labeled rfMGH8 as a probe. The temperature at which the S1 digestion was performed is indicated above each lane. S1 digestion was for 1 hr. The size of 5! end-labeled oligonucleotide markers is indicated to the right. Lin-4 è il primo miRNA identificato (Victor Ambros 1993) Cell, Vol. 75, 843–854, December 3, 1993, Copyright ©1993 by Cell Press The C. elegans Heterochronic Gene lin-4 Encodes Small RNAs The C. elegans Heterochronic Gene lin-4 Encodes Small RNAs Complementarity to lin-14 with Antisense Cell, Vol. 75, 843–854, December 3, 1993, Copyright ©1993 by Cell Press with Antisense Complementarity to lin-14 Caenorhabditis elegans Rosalind C. Lee,*† Rhonda L. Feinbaum,* ‡ Ambros and Horvitz, 1987). Animals carrying a lin-4 lossRosalind C. Lee,*† Rhonda L. Feinbaum,* ‡ Ambros and Horvitz, 1987). Animals carrying a lin-4 loss† † and Victor Ambros and Victor Ambros tion or rearrangement that removes at least 5 kb in(lf)the lin-4 lin-4(e912), of-function (lf) mutation, lin-4(e912), display reiterations o of-function mutation, display reiterations of Harvard University early fates at inappropriately late developmental stages; Harvard University region, including the entire lin-4S- and lin-4L-transcribed early fates at inappropriately late developmental stages Department of Cellular and Developmental Biology, cell lineage patterns normally specific for the L1 are reiterLavoro citato 8774 volte! sequences. To 02138 test further the functional significance of Department of Cellular and Developmental Biology, Cambridge, Massachusetts cell execute lineage patterns normally specific for the L1 are reiterated at later stages, and the animals extra larval transcribed sequences, a noncomplem the lin-4 Massachusetts Cambridge, 02138we usedmolts (Chalfie et al., 1981). Theated consequences of these at later stages, and the animals execute extra larva heterochronic developmental patterns include the abentation screen (see Experimental Procedures) to isolate a et al., 1981). The consequences of these sence of adult structures (suchmolts as adult (Chalfie cuticle and the novel lin-4 mutation and then identified the corresponding vulva) and the prevention of eggheterochronic laying. developmental patterns include the abSummary molecular lesion. Over 20,000 mutagenized lin-14 nullchromo(0) mutations cause a phenotype opposite to oflin-4(lf), adult structures (such as adult cuticle and the that of lin-4(lf) are completelysence epistatic to which somes for were screened, and a single novel lin-4and allele, lin-4 is essential the normal temporal control of isanimals consistentwas with amlin-4 acting as a negative regulator of diverse ma161, postembryonic developmental events in ma161 C. vulva) and the prevention of egg laying. was identified. DNA from Summary lin-14 (Ambros and Horvitz, 1987; Ambros, 1989). lin-14(0) elegans. lin-4 acts by negatively regulating the level of plified by PCR and sequenced. The onlymutants sequence lin-14 nulland (0)premutations cause a phenotype opposite to skip the alterexpression of L1-specific events LIN-14 protein, creating a temporal decrease in LIN-14 ation inin the 693larval bp lin-4 ma161cociously DNA was a Cprograms to execute normally specific for the L2, protein starting the first stage region (L1). We of have that of lin-4(lf) and are completely epistatic to lin-4(lf), which lin-4 is C.essential for theby normal temporal control of L3, L4, adult point stages. lin-14 gain-of-function (gf) mutacloned the elegans lin-4 locus pair chromosomal T transition at base 517 (see Figure 3).andThis is high consistent with walking and transformation rescue. We used the C. diverse postembryonic developmental events in C. tions, which cause inappropriately lin-14 activity at lin-4 acting as a negative regulator o would alterother nucleotide 5 in lin-4L and elegans mutation clone to isolate thepresumably gene from three late stages development, result in a retarded phenotype lin-14 (Ambros and Horvitz, 1987; Ambros, 1989). lin-14(0 elegans. lin-4 acts by negatively regulating the of level of Caenorhabditis species; all four Caenorhabditis clones lin-4S. virtually identical to that of lin-4(lf) (Ambros and Horvitz, mutants skip the expression of L1-specific events and pre LIN-14 protein, a temporal in LIN-14 functionally rescue the creating lin-4 null allele of C. elegans.decrease 1987). These observations indicate that in wild-type develComparison of the lin-4 genomic sequence from these high have level of lin-14 activity in the earlyexecute L1 stage programs normally specific for the L2 cociously protein starting in the first larval stage opment (L1). aWe four species and site-directed mutagenesis of potenspecifies L1-specific programs, and lower levels of lin-14 Transcripts Are that Complementary the L3, L4, and adult stages. lin-14 gain-of-function (gf) mutacloned the C. elegans lin-4 locus chromosomal tial openlin-4 reading frames indicated lin-4 does not bytoactivity in the late L1 specify later stage-specific programs. encode a protein. Two small lin-4 transcripts of approx3!UTR of lin-14 mRNA walking and transformation rescue. We used thedevelopmental C. Thus, the normal progression from thecause exetions, which inappropriately high lin-14 activity a imately 22 and 61 nt were identified in C. elegans and cution of L1 programs to later programs depends critically Figure 8. lin-4 Transcripts and Complementarity between lin-4 and The lin-4 transcribed sequence was combined in tandem elegans clone to isolate the gene from three other found to contain sequences complementary to a relate stages of development, result in a retarded phenotype on the lin-4-dependent decrease in lin-14 activity. LIN-14 è un gene eterocronico, che controlla quando ed in che successione devono avvenire eventi lin-14 to the sequence of the lin-14 3!UTR (Wightman et al., 1991), peated sequence element in the 3! untranslated region Caenorhabditis species; all four Caenorhabditis clones virtually identical The temporal decrease in lin-14 activity reflects a de- to that of lin-4(lf) (Ambros and Horvitz (UTR) ofand lin-14this mRNA, suggesting thatsearched lin-4 regulates (A) Sequences fortiming lin-4L and particolari durante ilwas differenziamento della larva (developmental ).lin-4S RNAs, and a proposed secondary sequence for the crease formation of lin-4: in the level of LIN-14 protein. LIN-14 protein is norfunctionally rescue the lin-4 null allele of C. elegans. lin-14 translation via an antisense RNA-RNA inter1987). These observations indicate that in wild-type develstructure for lin-4L,and predicted the MULFOLD program (see Experilin-14 hybrid RNA structures, using the STEMLOOP mally abundant inprothe nuclei of late-stage embryos Lin-4 è essenziale un normale controllo temporale dello sviluppo larvalebydi C.elegans. action. Comparison of the per lin-4 genomic sequence from these mental Procedures). structure forin lin-4S not shown, opment a high of lin-14 activity the isearly L1 stage younger L1 larvae and then is barely detectable by the level L2A secondary gram of the GCGèsequence analysis package (Devereux La sua espressione inversamente proporzionale all’espressione della proteina di to the of the precise 3! LIN-14 and 5! nucleotides of lin-4S, four species and site-directed mutagenesis (Ruvkunof andpotenGiusto, 1989). lin-14owing transcripts areuncertainty constant specifies L1-specific programs, and lower levels of lin-14 et al., 1984), as described in Experimental Procedures. which affect structural predictions (see text). Sequences development, thatsignificantly lin-14 is negaIntroduction tial open reading frames indicated that throughout lin-4 does not indicating activity in the late L1 specify later stage-specific programs Two short blocks of lin-4 sequence were identified (Figure –86 of IRK1) have ol (1:1) (American as dried under N2 orm pure 3H-PIP2 bated with 3H-PIP2 beads. After 1 wash buffer and counted . The bound 3H tal added. For coatidylcholine (PC) heim) and 90 mg ied down together usion proteins were nd PIP2 antibodies a further 30 min. ated by 10% SDS– ECL (Amersham). esults. The relative y serial dilutions of interactions with Gsa. Biochemistry 28, 611–616 (1989). Acknowledgements. We thank E. Phan for technical assistance; I. Bezprozvanny, C. Dessauer, D. Logothetis, C.-C. Lu, O. Moe, S. Muallem and H. Yin for discussions and advice; L. Jan for GIRK1 and ROMK1 antibodies; C. Dessauer and A. Gilman for Gai1; P. Casey for Gbg; and R. Alpern for support and encouragement. This work was supported by grants from the NKF of Texas (C.L.H.) and from the AHA and NIH (D.W.H.). activity of other highly related myosin heavy-chain genes . The unc54C segment has been unique in our overall experience to date: effects of 18 other dsRNA segments (Table 1; and our unpublished observations) have all been limited to those expected from previously characterized null mutants. The pronounced phenotypes seen following dsRNA injection indicate that interference effects are occurring in a high fraction of fluorescent generally exp The mosaic pattern o was nonrandom. At low ference in the embryon when the animal hatch entiated cells persisted duced little or no additi 14 postembryonically de larval stages and these cells have come throu versus 8–9 divisions fo trations of gfp dsRNA, body-wall muscles, with cells born during both em The non-striated vulval development, appeared concentrations of inject We do not yet know ference in C. elegans. Som about possible targets an First, dsRNA segmen promoter sequences d (Table 1). Although con tional level, these exper level of the gene. Second, we found th nounced decrease or eli script (Fig. 3). For this ex 3) that is abundant in straightforward in situ h genous mex-3 mRNA dsRNA segment derive which purified mex-3 a stantial endogenous mR Third, dsRNA-media to cross cellular bounda lacZ) into the body cavit robust interference wit (Table 2). Interference arms, ruling out the occ 1998: Fire and Mello identificano l’RNA interference in Caenorhabditis elegans Correspondence and requests for materials should be addressed to C.L.H. (e-mail: chuan1@mednet. swmed.edu). Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans a b c d Andrew Fire*, SiQun Xu*, Mary K. Montgomery*, Steven A. Kostas*†, Samuel E. Driver‡ & Craig C. Mello‡ * Carnegie Institution of Washington, Department of Embryology, 115 West University Parkway, Baltimore, Maryland 21210, USA † Biology Graduate Program, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, USA ‡ Program in Molecular Medicine, Department of Cell Biology, University of Massachusetts Cancer Center, Two Biotech Suite 213, 373 Plantation Street, Worcester, Massachusetts 01605, USA Figure 3 Effects of mex-3 RNA interference on levels of the endogenous mRNA. 2001: il lab di T.Tuschl identifica in diversi organismi (uomo, topo, Drosofila) diversi miRNA simili, in struttura e funzione, a lin-4 di C. elegans + n of ROMK1 K channel 077–8081 (1994). ir2.1 inward rectifier K+ s. Neuron 13, 1413–1420 tructure and functional re 364, 802–806 (1993). nd molecular properties. multimer of two inwardly + y rectifying K channels. nkage of the cardiac ATP96). TP potassium channels by hibits oncogene-induced al expression of a mouse ated potassium channel. channel by a G-protein- coupled to GTP-binding ficient in Lowe syndrome Sci. USA 92, 4853–4856 Interference contrast micrographs show in situ hybridization in embryos. The 1,262-nt mex-3 cDNA clone20 was divided into two segments, mex-3A and mex- 3B, with a short (325-nt) overlap (similar results were obtained in experiments with no overlap between interfering and probe segments). mex-3B antisense or ......................................................................................................................... dsRNA was injected into the gonads of adult animals, which were fed for 24 h Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an endogenous gene1,2. Such effects have been proposed to result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts. RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression3,4. Here we investigate the requirements for structure and delivery of the interfering RNA. To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. The effects of this interference were evident in both the injected animals and their progeny. Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous before fixation and in situ hybridization (ref. 5; B. Harfe and A.F., unpublished Nature © Macmillan Publishers Ltd 1998 NATURE | VOL 391 | 19 FEBRUARY 1998 observations). The mex-3B dsRNA produced 100% embryonic arrest, whereas .90% of embryos produced after the antisense injections hatched. Antisense probes for the mex-3A portion of mex-3 were used to assay distribution of the endogenous mex-3 mRNA (dark stain). four-cell-stage embryos are shown; similar results were observed from the one to eight cell stage and in the germ line of injected adults. a, Negative control showing lack of staining in the absence of the hybridization probe. b, Embryo from uninjected parent (showing normal pattern of endogenous mex-3 RNA20). c, Embryo from a parent injected with purified mex-3B antisense RNA. These embryos (and the parent animals) retain the mex-3 mRNA, although levels may be somewhat less than wild type. d, Embryo from a parent injected with dsRNA corresponding to mex-3B; no mex-3 RNA is detected. Each embryo is approximately 50 mm in length. Table 2 Effect of site of injection on interference in injected animals and their progeny dsRNA Site of injection Injected-animal phenotype Gonad or body cavity Gonad or body cavity No twitching Strong nuclear and mitochondrial GFP expression Gonad Body-cavity head Body-cavity tail Weak twitchers Weak twitchers Weak twitchers gfpG gfpG Gonad Body-cavity tail Lower nuclear and mitochondiral GFP expression Lower nuclear and mitochondrial GFP expression lacZL lacZL Gonad Body-cavity tail Lower nuclear GFP expression Lower nuclear GFP expresison ................................................................................................................................................................................................................................................... None None unc22B unc22B unc22B Rare Rare ................................................................................................................................................................................................................................................... Esiste una correlazione diretta tra il numero dei miRNA espressi da una data specie e la sua complessita’ morfologica Kosik.MicroRNAstellanevo–devostory.NatureRevNeurosc(2009)10:pp.1-6 miRNA e Tumori Alterazioni nell’espressione di specifici miRNA sono responsabili dell’inizio e della progressione di numerosi tumori umani. miR-15 e miR-16 sono sono soppressori tumorali; miR-17-92 sono onco-miRNA REVIEWS Epigenetic regulation of miR hypomethylation, CpG island histone-modification losses repr of malignant transformation76. T Delezione osservata nella have investigated whether such e leucemia linfociti cronica expression. Scott et al. showed t umana (CLL) histone deacetylase inhibition i sive and rapid alteration of miRN Saito et al. found that the combi bladder cancer cells with 5-aza-2 CdR) and the histone deacety 4-phenylbutyric acid (PBA) has Amplificazione osservata expression of miRNAs78. Sevent nei linfomi umani, ad es screened by a microarray assay) B-cell diffuse large cell than threefold, and miR-127 wa lymphomas (DLBLs) expressed. This miRNA is loc chromosome 14q32, a region th types of translocations identified cers and deleted by LOH in solid the combined treatment was acc Figure 3 | Chromosomal alterations at microRNA loci. The main chromosomal in DNA methylation and an in alterations microRNA loci, loss of heterozygosity and (November amplification,2006) are | doi:10.1038/nrc1997 Calinatand Croce (miRNA) Nature Reviews Cancer 6, 857–866 markers around the transcripti identified at two separate regions of chromosome 13. a | Shows the 13q14.3 deletion miRNA nel sistema nervoso • • • • • • circa il 70% dei miRNA è espresso nel cervello e molti miRNA sono neuro-specifici nel sistema nervoso i livelli di espressione dei miRNA è maggiore che in altri tessuti i miRNA sono coinvolti nello sviluppo del sistema nervoso e nella morfogenesi dei neuroni (nella crescita dei neuriti e nella formazione delle spine dendritiche) contribuisono al controllo delle funzioni sinaptiche e della plasticita’ nell’adulto la loro de-regolazione è stata osservata in quasi tutte le malattie neurologiche studiate sono considerati potenziali biomarker e target terapeutici nei disturbi neurologici miRNA alle sinapsi Schrad,Gerhard."microRNAsatthesynapse."NatureReviewsNeuroscience10.12(2009):842-849. ….caratteristiche degli RNA cellulari A.F.PalazzoandE.S.Lee,“Non-codingRNA:whatisfunc.onalandwhatisjunk?,”Front.Genet.,vol.6,no.61,p.326,Jan.2015. I LONG NON CODING RNA (lncRNA) Caratteristiche Funzioni biologiche dei lncRNA (ipotetiche) A. B. C. D. E. F. G. sequestrare fattori di trascrizione sequestrare i microRNA (miRNA sponges) possono essere componenti di complessi RNA-Proteine (RNP) reclutare rimodellatori e modificatori della cromatina, come nel caso di Xist modulare lo splicing inibire la traduzione bloccando l’mRNA indurre la degradazione dell’ mRNA Funzioni biologiche dei lncRNA (dimostrate) ncRNA ed evoluzione del SNC ScienCstsIdenCfyGeneDifferenceBetween HumansandChimps Si ipotizza che i ncRNA abbiamo un ruolo chiave nella rapida evoluzione del SNC umano. In uno studio del 2006 sono state identificate e analizzate le human accelerated regions (HARs), regioni del genoma che mostrano un accumulo di mutazioni significativamente accellerato nel periodo evolutivo che corrisponde all’evoluzione del nostro antenato dallo scimpanze’. Molte di queste HAR trovate sono associate con geni coinvolti nella regolazione della trascrizione e dello sviluppo del sistema nervoso. HAR1, l’elemento variato piu’ significativamente, è parte di un gene codificante per ncRNA, localizzato sul cromosoma 21 ed espresso durante lo sviluppo corticale dell’uomo. PollardKS,SalamaSR,LambertN,LambotM-A,CoppensS,PedersenJS,etal.AnRNAgeneexpressedduringcor.caldevelopmentevolved rapidlyinhumans.Nature.2006Aug16;443(7108):167–72. Pon.ngCP,LunterG.Evolu.onarybiology:humanbraingenewinsgenomerace.Nature.2006Sep14;443(7108):149–50. Tes. BiologiaMolecolare,Amaldietal BiologiaMolecolaredelgene,Watsonetal Reviews Bartel,DavidP."MicroRNAs:genomics,biogenesis,mechanism,andfunc.on.” Cell116.2(2004):281-297. CalinandCroceNatureReviewsCancer6,857–866(November2006)|doi:10.1038/ nrc1997 Schrad,Gerhard."microRNAsatthesynapse."NatureReviewsNeuroscience10.12 (2009):842-849.