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Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers

Author

Listed:
  • Renata Bordeira-Carriço

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto)

  • Joana Teixeira

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto
    Doctoral program in Molecular and Cell Biology (MCbiology), ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto)

  • Marta Duque

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto
    Doctoral program in Molecular and Cell Biology (MCbiology), ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto)

  • Mafalda Galhardo

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto
    Instituto de Ciências, Tecnologias e Agroambiente (CIBIO), Universidade do Porto)

  • Diogo Ribeiro

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto)

  • Rafael D. Acemel

    (Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide)

  • Panos. N. Firbas

    (Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide)

  • Juan J. Tena

    (Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide)

  • Ana Eufrásio

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto
    Doctoral program in Molecular and Cell Biology (MCbiology), ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto)

  • Joana Marques

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto)

  • Fábio J. Ferreira

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto
    Doctoral program in Areas of Basic and Applied Biology (GABBA), Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto)

  • Telmo Freitas

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto)

  • Fátima Carneiro

    (Faculdade de Medicina da Universidade do Porto (FMUP)
    Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP))

  • José Luís Goméz-Skarmeta

    (Centro Andaluz de Biología del Desarrollo (CABD), Universidad Pablo de Olavide)

  • José Bessa

    (Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto
    Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto)

Abstract

The pancreas is a central organ for human diseases. Most alleles uncovered by genome-wide association studies of pancreatic dysfunction traits overlap with non-coding sequences of DNA. Many contain epigenetic marks of cis-regulatory elements active in pancreatic cells, suggesting that alterations in these sequences contribute to pancreatic diseases. Animal models greatly help to understand the role of non-coding alterations in disease. However, interspecies identification of equivalent cis-regulatory elements faces fundamental challenges, including lack of sequence conservation. Here we combine epigenetic assays with reporter assays in zebrafish and human pancreatic cells to identify interspecies functionally equivalent cis-regulatory elements, regardless of sequence conservation. Among other potential disease-relevant enhancers, we identify a zebrafish ptf1a distal-enhancer whose deletion causes pancreatic agenesis, a phenotype previously found to be induced by mutations in a distal-enhancer of PTF1A in humans, further supporting the causality of this condition in vivo. This approach helps to uncover interspecies functionally equivalent cis-regulatory elements and their potential role in human disease.

Suggested Citation

  • Renata Bordeira-Carriço & Joana Teixeira & Marta Duque & Mafalda Galhardo & Diogo Ribeiro & Rafael D. Acemel & Panos. N. Firbas & Juan J. Tena & Ana Eufrásio & Joana Marques & Fábio J. Ferreira & Telm, 2022. "Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29551-7
    DOI: 10.1038/s41467-022-29551-7
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    References listed on IDEAS

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    2. Alvaro Rada-Iglesias & Ruchi Bajpai & Tomek Swigut & Samantha A. Brugmann & Ryan A. Flynn & Joanna Wysocka, 2011. "A unique chromatin signature uncovers early developmental enhancers in humans," Nature, Nature, vol. 470(7333), pages 279-283, February.
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