Transposable elements (TEs) are genetic elements characterized by the ability to insert themselves in novel genome locations of the host creating genetic variability on which natural selection acts. Moreover, they increase in number by replication creating pronounced differences in genome size. However, their transposition activity can have negative effects as altering or disrupting genes and creating genome instability. The host genome evolved various mechanisms of control and silencing of TEs using small RNAs and Kruppel-associated zinc finger box proteins (KRAB-ZNFs) that recruit proteins of the Nucleosome Remodelling and Deacetylase (NuRD) complex, increasing the heterochromatin level. Recently, a huge number of works has been published reporting that the transposition activity seems to be influenced by abiotic factors such as temperature, pH, and salinity. This suggests that TEs may have an important role in regulating mechanisms for adaptation to specific environmental conditions. In this PhD thesis, attention was focused on ray-finned fish, adapted to different ecological niches and responsive to environmental changes. The TE content in 24 fish genomes was analysed using an in-house bioinformatics pipeline highlighting a link with environmental conditions in migratory species. Moreover, TE transcriptional activity and systems involved in their silencing were investigated in teleosts in relation to salinity and temperature changes revealing for the first time a TE tissue-specific activation that might favour species adaptation and resilience. Finally, the interaction of two proteins that might be involved in the recruitment of NuRD system in fish were tested by docking simulations and in vitro by co-immunoprecipitation (co-IP) assay. For comparison, basal sarcopterygian species, interesting for their genome size and phylogenetic position, were also investigated.
Gli elementi trasponibili (TE) sono elementi genetici capaci di inserirsi in nuove posizioni del genoma dell'ospite incrementando la variabilità genetica su cui agisce la selezione naturale. Inoltre, essi aumentano in numero creando differenze nella dimensione del genoma. Tuttavia, la loro attività di trasposizione può avere effetti negativi alterando o distruggendo i geni e creando instabilità genomica. Il genoma dell’ospite ha evoluto vari meccanismi di controllo e silenziamento dell'attività dei TE utilizzando piccoli RNA e proteine Kruppel-associated zinc finger box (KRAB-ZNFs) che reclutano il complesso Nucleosome Remodelling and Deacetylase (NuRD), aumentando il livello di eterocromatizzazione. Recentemente, numerosi lavori riportano che la trasposizione sembra essere influenzata da fattori abiotici come temperatura, pH e salinità. Ciò suggerisce che i TE possono avere un ruolo importante nella regolazione dei meccanismi di adattamento a specifiche condizioni ambientali. In questa tesi di dottorato, l'attenzione si è concentrata sugli Attinopterigi, adattati a diverse nicchie ecologiche e sensibili ai cambiamenti ambientali. Pertanto, il contenuto di TE in 24 genomi di pesci è stato analizzato utilizzando una pipeline bioinformatica che ha evidenziato un legame con le condizioni ambientali nelle specie migratorie. Inoltre, l'attività trascrizionale dei TE e dei sistemi coinvolti nel loro silenziamento sono stati studiati in relazione ai cambiamenti di salinità e temperatura, rivelando per la prima volta nei pesci un'attivazione TE tessuto-specifica che potrebbe favorire l'adattamento e la resilienza delle specie. Infine, l’interazione di due proteine che potrebbero essere coinvolte nel reclutamento del sistema NuRD nei pesci sono state validate attraverso simulazioni docking e co-immunoprecipitazione in vitro. Per confronto, sono state studiate anche specie di Sarcopterygii basali, interessanti per le dimensioni del genoma e la posizione filogenetica.
Environmental adaptation of rayfinned fish: new insights on the balance between transposable elements and their silencing mechanisms / Carotti, Elisa. - (2023 Jun 15).
Environmental adaptation of rayfinned fish: new insights on the balance between transposable elements and their silencing mechanisms
CAROTTI, ELISA
2023-06-15
Abstract
Transposable elements (TEs) are genetic elements characterized by the ability to insert themselves in novel genome locations of the host creating genetic variability on which natural selection acts. Moreover, they increase in number by replication creating pronounced differences in genome size. However, their transposition activity can have negative effects as altering or disrupting genes and creating genome instability. The host genome evolved various mechanisms of control and silencing of TEs using small RNAs and Kruppel-associated zinc finger box proteins (KRAB-ZNFs) that recruit proteins of the Nucleosome Remodelling and Deacetylase (NuRD) complex, increasing the heterochromatin level. Recently, a huge number of works has been published reporting that the transposition activity seems to be influenced by abiotic factors such as temperature, pH, and salinity. This suggests that TEs may have an important role in regulating mechanisms for adaptation to specific environmental conditions. In this PhD thesis, attention was focused on ray-finned fish, adapted to different ecological niches and responsive to environmental changes. The TE content in 24 fish genomes was analysed using an in-house bioinformatics pipeline highlighting a link with environmental conditions in migratory species. Moreover, TE transcriptional activity and systems involved in their silencing were investigated in teleosts in relation to salinity and temperature changes revealing for the first time a TE tissue-specific activation that might favour species adaptation and resilience. Finally, the interaction of two proteins that might be involved in the recruitment of NuRD system in fish were tested by docking simulations and in vitro by co-immunoprecipitation (co-IP) assay. For comparison, basal sarcopterygian species, interesting for their genome size and phylogenetic position, were also investigated.File | Dimensione | Formato | |
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