Ploidy Mosaicism and Allele-Specific Gene Expression Differences in the Allopolyploid Squalius Alburnoides

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Ploidy Mosaicism and Allele-Specific Gene Expression Differences in the Allopolyploid Squalius Alburnoides UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS Gene expression regulation in allopolyploid fish “Documento Definitivo” DOUTORAMENTO EM BIOLOGIA ESPECIALIDADE EM BIOLOGIA MOLECULAR Isa Maria Nunes de Matos Tese orientada por: Professora Doutora Maria Manuela Coelho Professor Doutor Manfred Schartl Documento especialmente elaborado para a obtenção do grau de doutor 2018 UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS Gene expression regulation in allopolyploid fish DOUTORAMENTO EM BIOLOGIA ESPECIALIDADE EM BIOLOGIA MOLECULAR Isa Maria Nunes de Matos Tese orientada por: Professora Doutora Maria Manuela Coelho Professor Doutor Manfred Schartl Júri: Presidente: ● Doutor Rui Manuel Dos Santos Malhó, Professor Catedrático, Faculdade de Ciências da Universidade de Lisboa Vogais: ● Doutor Manfred Schartl, Full Professor, Biology Faculty da University of Wuerzburg, Alemanha (Orientador) ● Doutor Vasco Temudo e Melo Cabral Barreto, Investigador Principal, Centro de Estudos de Doenças Crónicas da Universidade Nova de Lisboa ● Doutora Carla Patrícia Cândido de Sousa Santos, Investigadora, ISPA – Instituto Universitário de Doenças Psicológicas, Sociais e da Vida ● Doutor Rui Miguel Duque de Brito, Professor Coordenador com Agregação, Escola Superior de Tecnologias de Saúde de Lisboa do Instituto Politécnico de Lisboa ● Doutora Maria João Ivens Collares Pereira, Professora Catedrática Aposentada, Faculdade de Ciências da Universidade de Lisboa ● Doutor Vitor Martins Conde e Sousa, Professor Auxiliar Convidado, Faculdade de Ciências da Universidade de Lisboa Documento especialmente elaborado para a obtenção do grau de doutor Bolsa Individual de Doutoramento SFRH/BD/61217/2009 Fundação para a Ciência e a Tecnologia 2018 Nota prévia Para a elaboração da presente dissertação, e nos termos do nº 2 do artigo 25º do Regulamento de Estudos de Pós-Graduação da Universidade de Lisboa, publicado no Diário da República, 2.ª série N.º 155 — 11 de Agosto de 2017, foram usados integralmente artigos científicos publicados (4) ou submetidos para publicação (1) em revistas internacionais indexadas. Tendo os trabalhos referidos sido efetuados em colaboração, a autora da dissertação esclarece que participou integralmente na conceção e execução do trabalho experimental, na análise e interpretação dos resultados e na redação de todos os manuscritos, mesmo do único em que não é primeira autora. Lisboa, Outubro de 2018 Isa Maria Nunes de Matos i ACKNOWLEDGEMENTS Foram muitas as pessoas que ao longo destes anos fizeram parte desta viagem. A todas agradeço o papel que tiveram. Quero, no entanto, agradecer especialmente a algumas delas. À Professora Doutora Maria Manuela Coelho pelo apoio, confiança, motivação, paciência e carinho. Por me ter recebido no seu laboratório e ter estado sempre ao meu lado a festejar as pequenas vitorias e a amparar as quedas. Agradeço também por me ter confiado o “seu alburnoides”, o seu projeto e as suas ideias, mas deixando sempre espaço para as minhas iniciativas e planos menos convencionais. To Professor Doctor Manfred Schartl, for the scientific guidance and support, always. For opening the doors of his lab, make available his resources and knowledge to make this project happen. Thanks for the patience and understanding of my many flaws. It was a personal and professional privilege to work and learn from you. À Professora Maria João Collares-Pereira, pela disponibilidade em partilhar todo o seu enorme conhecimento sobre este fascinante modelo que é o S. alburnoides, sempre com simpatia e boa disposição. Aos “Meus Migueis”, quero agradecer a loucura do dia-dia, a emoção e a festa que foram estes anos partilhados. Sem vocês… não sei…. À minha Su, que melhor que ninguém sabe como isto é. Contigo por perto foi mais fácil. Agora é a tua vez! À Tia Inês, que apesar de ser de “letras” (ninguém é perfeito!) sempre se interessou pelo meu trabalho. Obrigado por teres ouvido as minhas “histórias dos peixes”. À minha família (em especial à minha Mãe, ao meu Pai, à Ana ao Pedro e à Avó). Vocês são as bases de tudo. Ao meu Ricardo, o companheiro de todas as horas! Hoje e sempre “Apaga as luzes”! ii Resumo Os indivíduos resultantes de hibridação são muitas vezes inviáveis ou inférteis, pelo que, durante décadas, foram vistos como ocorrências pouco frequentes e meros erros irrelevantes para o processo evolutivo. No entanto, esta perspectiva redutora tem vindo progressivamente a ser abandonada e actualmente, a hibridação e a poliploidia, fenómenos que aparecem muitas vezes associados, são aceites como processos evolutivamente relevantes. Em relação ás plantas, a ocorrência de (alo)poliploides dentro deste grupo é bastante frequente, e estas sempre foram reconhecidas como sendo bastante tolerantes a alterações de ploidia e à hibridação. Assim, os efeitos destes processos na expressão génica e na regulação das cópias de cada genoma têm sido amplamente estudados neste grupo. No entanto, a existência e importância da (alo)poliploidia em animais foi, por muitos anos, negligenciada e consequentemente, pouco se sabe sobre os seus efeitos na expressão génica e nos mecanismos da sua regulação em vertebrados (allo)poliplóides. Posto isto, esta tese apresenta-se, como um avanço na informação disponível sobre o tema da regulação da expressão génica em animais, contribuindo para desvendar as causas e os mecanismos que levam a que alguns genomas poliploides híbridos superem eficazmente o “choque genómico” resultante do aumento do número de cromossomas e da combinação de genomas divergentes. Os estudos aqui englobados são também a continuação e o amadurecimento de descobertas e resultados anteriores, uma vez que a sua génese baseou-se numa interessante teoria de “diploidização funcional” da expressão génica em alotriploides do complexo Squalius alburnoides mediante silenciamento alélico. Este complexo de peixes alopoliploides, endémico da Península Ibérica, foi assim o primeiro modelo a ser estudado neste âmbito, pois apresenta características que o tornam particularmente interessante. O complexo resulta da hibridação interespecífica e não recíproca entre fêmeas de Squalius pyrenaicus (genoma P) e de uma espécie que se pensar estar actualmente extinta, próxima de Anaecypris hispanica (genoma iii A). Inclui formas diploides e poliploides mantidas por diferentes modos de reprodução potenciando um sistema de trocas genéticas em que as diferentes formas diploides e poliploides se cruzam e contribuem activamente para a manutenção da diversidade e do potencial evolutivo da espécie. Apresenta ainda como caraterística um acentuado desvio na distribuição dos sexos, com uma predominância de fêmeas triplóides e ainda a ocorrência de uma linhagem aparentemente constituída exclusivamente por machos. O objectivo geral deste trabalho foi ajudar a esclarecer como se processa a expressão génica em alotriploides de S. alburnoides, bem como de mecanismos ligados à sua regulação. Em concreto, pretendeu-se esclarecer se os mecanismos de compensação da dosagem e o silenciamento alélico, anteriormente descritos recorrendo à análise de um número muito limitado de genes, são fenómenos com extensão genómica ou se estão limitados, específica ou aleatoriamente, a subgrupos de genes. No que respeita ao silenciamento alélico, pretendeu-se ainda esclarecer se existe enviesamento da expressão, favorecendo um ou outro complemento genómico, e, se sim, perceber a sua magnitude e a sua extensão no genoma. Sendo o silenciamento alélico o limite máximo do enviesamento da expressão alélica, e também o mecanismo de compensação de dosagem anteriormente proposto, este foi um tópico que mereceu uma análise mais aprofundada. O primeiro passo dado no âmbito desta investigação foi a verificação da ocorrência do fenómeno de mosaicismo de ploidia em S. alburnoides, um fenómeno nunca antes descrito neste complexo híbrido, mas bastante frequente em alopoliploides. A ocorrência de mosaicos de ploidia poderia explicar as diferenças de expressão alélica existentes entre indivíduos triploides e/ou entre órgãos do mesmo indivíduo triploide. Para explorar esta hipótese foram desenvolvidos protocolos de citometria de fluxo e sorting de células de forma a identificar indivíduos mosaicos de ploidia e isolar as populações com ploidia diferente permitindo que fossem analisadas de forma independente quanto ao seu padrão de expressão alélica. Apesar da ocorrência do fenómeno de mosaicismo de ploidia em triploides de S. alburnoides, esta não explica os padrões de expressão alélica obtidos. iv Embora o complexo S. alburnoides tenha sido usado como principal modelo de estudo, seguiu-se também uma abordagem multiespécies para comparar a expressão génica e a sua regulação entre peixes diploides e triploides, pois outro objectivo desta tese foi determinar se os mecanismos de regulação da expressão génica previamente especulados para S. alburnoides eram uma característica particular deste complexo ou se apresentavam uma ocorrência mais difundida entre vertebrados alopoliploides. Assim, recorrendo a indivíduos diploides e triploides de Oryzias latipes, Poecilia formosa e S. alburnoides, incluindo híbridos tri-genómicos produzidos em laboratório, foram feitas sequenciações de RNA de nova geração, “de novo assembly” de transcriptomas, comparação de níveis de expressão génica e de expressão alélica específica e determinação de níveis globais de metilação. Em relação ao complexo S. alburnoides, verificou-se que, apesar dos triploides serem afectados por uma significativa regulação negativa da expressão génica, esta não corresponde a
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