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DE NADAI, ALESSANDRA (2010) ANALISI DELLA CONSERVAZIONE DELLE SEQUENZE INTRONICHE NEI GENI CODIFICANTI PER IL RECETTORE DEGLI ESTROGENI FORMA ALFA IN TELEOSTEI E MAMMIFERI. [Tesi di dottorato]

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Abstract (inglese)

INTRODUCTION
For many years, introns have been considered only an additional cost to replication and transcription; earliest studies described them as ‘junk DNA’ (Wong, 2000). Subsequent observations revealed that some intronic sequences show regulative control on their own genes. Nevertheless, the enormous space occupied by introns in the cell genome cannot be justified only by these data.
Some remarks about intron presence can be done considering the literature. Roy and Gilbert (2006) showed that introns density and organism complexity share a relation of proportionality. Introns can also increase transcription efficiency, as proved by some studies on transgenic mice (Le Hir et al., 2003). mRNA stability is improved by intron presence that protects the transcript from degradation. Moreover, despite introns being not as conserved as associated exons, many studies demonstrated unexpected conservation patterns between orthologue introns (Mattick, 1994). These and other data suggest that introns play a pivotal role in the regulatory network of the cell.

AIM OF THE THESIS
In the present study, intronic sequences of estrogen receptor alpha (ERalpha) gene in mammals and teleosts have been analyzed. A preliminary bioinformatic investigation has been utilized to choose a conserved intronic sequence in order test the potential binding to protein factors. The examination of these sequences concerns the structure, the location of important sites for transcription and splicing, the research of conserved regions, and the recognition of repetitive elements and potential binding sites for transcription factors. After that, by means of gelshift experiment, the binding of DNA and RNA probes to elements of nuclear protein extracts has been examined.

MATERIALS AND METHODS
Bioinformatic analysis was led on intronic and exonic sequences of ERalpha gene available at Ensembl database (Homo sapiens, Macaca mulatta, Canis familiaris, Mus musculus, Bos taurus, Monodelphis domestica, Oryctolagus cuniculus, Echinops telfairi and Ochotona princeps). Also one intron of some teleosts was sequenced and analyzed (Atherina boyeri, Barbus plebejus, Chondrostoma genei, Rutilus aula, Rutilus rutilus, Phoxinus phoxinus, Rhodeus amarus, Gasterosteus aculeatus, Psetta maxima, Scorpaena porcus, Polyprion americanus and Sparus aurata). The same intron for Danio rerio, Takifugu rubripes and Oryzia latipes was obtained from Ensembl database.
Alignment: peculiar features of intronic sequences are their considerable lengths that are hardly comparable, low conservation rates and presence of insertions, deletions and inversions. MLAGAN alignment software (Brudno et al., 2003) has been a useful tool to align sequences that show these cha-racteristics. The software also gives back fragments of sequences, defined as Conserved Non-Coding Sequences (CNS), that show more than 70% of identity.
Dotplot: The software dotplot was used to find exact conserved words between two sequences.
Transcription factors: the presence of putative binding sites for tran-scription factors was identified by means of TFSEARCH version 1.3. The potential binding sites were analyzed in and out of CNS.
Repetitions: the search of tandem repetitions inside introns was done with mreps software (Kolpakov et al., 2003). After that , the repetitions inside CNS were compared to the non-conserved repetitions.
MicroRNAs: the presence of putative precursors of microRNAs was ex-amined with the softwares RNA22, proMirII (Nam et al., 2006) and mipred (Jiang et al., 2007).
Gelshift: binding experiments were performed with DNA and RNA probes of intron I117 from D. rerio and nuclear protein extracts from tissues expressing ERalpha in female D. rerio.
RESULTS AND DISCUSSION
Splicing: the presence of consensus sequences necessary for the branch-ing of introns and the 5’ and 3’ splice sites (Zhuang et al., 1989) was investigated. The consensus sequence for the formation of the lariat isn’t present in some of the introns considered, while in others it exists in many copies. Conversely, 5’ and 3’ termini are highly conserved and always present.
Alignments: conserved regions were studied calculating the average length and percentage of average identity of the conserved regions, the number of conserved regions and the number of nucleotides in the conserved regions, the ratio between the number of nucleotides inside the conserved regions and the length of the same intron sequence. These data show a great number of regions sharing more than 70% identity. Some pairwise alignments reveal that more than half of the intron’s length may show conservation (for example the same intron in H. sapiens and C. familiaris).
Transcription factors: this analysis disclosed a great number of putative binding sites for transcription factors, mostly for CdxA (caudal type homeo-box transcription factor 1) and SRY (sex determining factor). The massive presence of binding sites for SRY is probably related to ERα function. Consi-dering the percentages of transcription factor binding sites nucleotides inside and outside CNS, a common pattern was not found.
Repetitions: nearly all the repeated words found in the intronic se-quences are microsatellites. In teleosts, repeated words are present only in some introns and always outside conserved regions. In mammalian introns, repetitions are more frequently placed in non-conserved region.
MicroRNAs: in mammalian introns, RNA22, ProMirII and mipred softwares found stem-loop structures that are potential precursor of micro-RNA. These structure have been found in introns of C. familiaris, H. sapiens, M. domestica and M. musculus. In teleosts, no precursors were identified.
Gelshift: considering the result of bioinformatic studies, a conserved re-gion of intron I117 from D. rerio was chosen for the binding experiments. This intron is placed between the DNA binding domain region and the D region of the ERalpha gene. EMSA experiments reveal binding of both DNA and RNA probes. With DNA probes, the best result was obtained with liver nuclear protein extract. For RNA probes, a binding reaction was revealed probably involving many factors. These results suggest a putative regulative role of I117 in D. rerio.

Abstract (italiano)

INTRODUZIONE
Per molti anni gli introni sono stati considerati un semplice costo aggiuntivo alla replicazione e alla trascrizione; nei primi studi compiuti sugli introni, questi ultimi sono stati descritti essenzialmente come “Junk DNA” (Wong, 2000). Successive osservazioni hanno rivelato che alcune delle sequenze introniche mostrano un controllo di tipo regolativo nei confronti dei geni in cui sono collocati. Nonostante ciò, l’enorme spazio occupato dagli introni nella cellula non può essere giustificato solo da questi dati.
In base alla letteratura, sono state tratte alcune considerazioni riguardo alla presenza degli introni. Roy e Gilbert (2006) mostrano che densità intronica e complessità condividono una relazione di proporzionalità diretta. Gli introni possono inoltre aumentare l’efficienza di trascrizione, come dimostrato da alcuni studi compiuti su topi transgenici (Le Hir et al., 2003). La stabilità degli mRNA è migliorata dalla presenza degli introni che agiscono proteggendo il trascritto dalla degradazione. Inoltre, nonostante gli introni non siano conservati quanto gli esoni a loro associati, molti studi dimostrano un inatteso pattern di conservazione tra introni ortologhi (Mattick, 1994). Questi e altri dati suggeriscono che gli introni abbiano un ruolo cruciale nel network regolatorio della cellula.
SCOPO DELLA TESI
Nel presente studio, sono state analizzate le sequenze introniche del gene del recettore degli estrogeni forma alfa (ERalfa) in mammiferi e teleostei. Un’indagine preliminare di tipo bioinformatico è stata utile per scegliere una sequenza intronica conservata al fine di testare il possibile binding a fattori proteici. L’esame di queste sequenze ha riguardato la struttura, la posizione di siti importanti per la trascrizione e lo splicing, la ricerca di regioni conservate, l’individuazione di elementi ripetitivi e di siti di binding potenziali per fattori di trascrizione. In seguito a questo, per mezzo di esperimenti di gelshift, è stato testato il legame di sonde a RNA e DNA a elementi di estratto nucleare proteico.
MATERIALI E METODI
Indagini bioinformatiche sono state condotte sulle sequenze introniche ed esoniche del gene ERalfa disponibili nella banca dati Ensembl (Homo sapiens, Macaca mulatta, Canis familiaris, Mus musculus, Bos taurus, Monodelphis domestica, Oryctolagus cuniculus, Echinops telfairi e Ochotona princeps). Anche un introne del medesimo gene è stato sequenziato ed analizzato (Atherina boyeri, Barbus plebejus, Chondrostoma genei, Rutilus aula, Rutilus rutilus, Phoxinus phoxinus, Rhodeus amarus, Gasterosteus aculeatus, Psetta maxima, Scorpaena porcus, Polyprion americanus and Sparus aurata). Lo stesso introne è stato ricavato dal database Ensembl per le specie Danio rerio, Takifugu rubripes e Oryzia latipes.
Allineamento: caratteristiche tipiche delle sequenze introniche sono una lunghezza considerevole e difficilmente comparabile con altre sequenze, basso tasso di conservazione e presenza di inserzioni, delezioni e inversioni. Il software MLAGAN (Brudno et al., 2003) è stato un valido strumento per allineare sequenze che condividono queste caratteristiche. Il programma restituisce anche porzioni di sequenza, definite Conserved Non-Coding Sequences o CSN, che mostrano più del 70% di identità.
Dotplot: il software Dotplot è stato sfruttato per ritrovare parole esatte conservate tra due sequenze.
Fattori di trascrizione: la presenza di potenziali siti di binding per fattori di trascrizione all’interno e all’esterno delle zone di conservazione è stata individuata tramite in programma TFSEARCH versione 1.3.
Ripetizioni: l’analisi sulle ripetizioni tandem all’interno degli introni è stata effettuata col programma mreps (Kolpakov et al., 2003). Dopo ciò, è stato eseguito un confronto tra le ripetizioni conservate e non.
microRNA: è stata infine ricercata la presenza di precursori di microRNA con i software RNA22, proMirII (Nam et al., 2006) e mipred (Jiang et al., 2007).
Gelshift: esperimenti di binding sono stati effettuati con sonde a DNA e RNA dell’introne I117 di D. rerio ed estratti nucleari proteici da tessuti e-sprimenti ERalfa nelle femmine di D. rerio.
RISULTATI E DISCUSSIONE
Splicing: è stata ricercata la presenza di sequenze consenso necessarie per il branching degli introni e di splice sites conservati. La sequenza consenso necessaria per la formazione del laccio non è stata riscontrata in tutti gli introni, in altri invece era presente in copie multiple. Gli splice sites al terminale 5’ e 3’ sono risultati altamente conservati.
Allineamento: le regioni conservate sono state studiate considerando la lunghezza media e la percentuale di identità media delle regioni conservate, il numero di regioni conservate, il numero di nucleotidi conservati nella sequenza, il rapporto tra il numero di nucleotidi all’interno delle CNS e la lunghezza totale della sequenza. Questi dati mostrano una grande quantità di regioni che condividono più del 70% di identità. Alcuni allineamenti pairwise rivelano che più di metà della lunghezza dell’introne può essere conservata (questo avviene ad esempio tra alcuni introni di C. familiaris e H. sapiens).
Fattori di trascrizione: questa analisi ha rivelato un gran numero di potenziali siti di binding per fattori di trascrizione. Si può inoltre precisare che i fattori di trascrizione più rappresentati sono CdxA (caudal type homeobox transcription factor 1) e SRY (sex determining factor). La considerevole presenza di copie del sito di binding per SRY è probabilmente correlabile alla funzione di ERalfa. Tuttavia considerando la percentuale di siti di binding all’interno e all’esterno delle CNS, non si riscontra un pattern comune per tutte le sequenze.
Ripetizioni: quasi tutte le sequenze ripetute trovate nelle sequenze introniche sono microsatelliti. Nei teleostei le ripetizioni sono presenti solo in alcuni introni e comunque sempre al di fuori delle zone conservate. Anche nei mammiferi, le ripetizioni sono state riscontrate più frequentemente nelle regioni non conservate.
MicroRNA: negli introni dei mammiferi sono state trovate strutture a stem-loop potenziali precursori di microRNA. Sono stati riscontrati negli introni C. familiaris, H. sapiens, M. domestica e M. musculus. Nei teleostei non sono stati ritrovati precursori.
Gelshift: considerando i risultati degli studi bioinformatici, per gli esperimenti di binding è stato scelto l’introne I117 di D. rerio. Questo introne è collocato tra il DNA binding domain e la regione cerniera del gene dell’ERalfa. Gli esperimenti di gel retardation hanno rivelato la presenza di binding sia per la sonda a RNA che per la sonda a DNA. Per le sonde a DNA sono stati ottenuti i risultati migliori con l’estratto nucleare proteico di fegato. Per le sonde a RNA è stato individuato il binding ma, probabilmente a causa del legame con più fattori, i risultati sono al momento di complessa interpretazione. Ad ogni modo, questi risultati suggeriscono un potenziale ruolo regolativo per l’introne I117 di D. rerio.

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Tipo di EPrint:Tesi di dottorato
Relatore:COLOMBO, LORENZO
Dottorato (corsi e scuole):Ciclo 22 > Scuole per il 22simo ciclo > BIOLOGIA E MEDICINA DELLA RIGENERAZIONE > ENDOCRINOLOGIA COMPARATA
Data di deposito della tesi:NON SPECIFICATO
Anno di Pubblicazione:31 Gennaio 2010
Parole chiave (italiano / inglese):INTRONE, RECETTORE DEGLI ESTROGENI, CONSERVAZIONE, DANIO RERIO, GELSHIFT
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Struttura di riferimento:Dipartimenti > Dipartimento di Biologia
Codice ID:2920
Depositato il:20 Set 2010 10:47
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