The DoGA consortium expression atlas of promoters and genes in 100 canine tissues

Matthias Hörtenhuber, Marjo K. Hytönen, Abdul Kadir Mukarram, Meharji Arumilli, César L. Araujo, Ileana Quintero, Pernilla Syrjä, Niina Airas, Maria Kaukonen, Kaisa Kyöstilä, Julia Niskanen, Tarja S. Jokinen, Faezeh Mottaghitalab, Işıl Takan, Noora Salokorpi, Amitha Raman, Irene Stevens, Antti Iivanainen, Masahito Yoshihara, Oleg Gusev, Danika Bannasch, Antti Sukura, Jeffrey J. Schoenebeck, Sini Ezer, Shintaro Katayama, Carsten O. Daub (), Juha Kere () and Hannes Lohi ()
Additional contact information
Matthias Hörtenhuber: Karolinska Institutet
Marjo K. Hytönen: University of Helsinki
Abdul Kadir Mukarram: Karolinska Institutet
Meharji Arumilli: University of Helsinki
César L. Araujo: University of Helsinki
Ileana Quintero: University of Helsinki
Pernilla Syrjä: University of Helsinki
Niina Airas: University of Helsinki
Maria Kaukonen: University of Helsinki
Kaisa Kyöstilä: University of Helsinki
Julia Niskanen: University of Helsinki
Tarja S. Jokinen: University of Helsinki
Faezeh Mottaghitalab: Karolinska Institutet
Işıl Takan: Karolinska Institutet
Noora Salokorpi: University of Helsinki
Amitha Raman: Karolinska Institutet
Irene Stevens: Karolinska Institutet
Antti Iivanainen: University of Helsinki
Masahito Yoshihara: Karolinska Institutet
Oleg Gusev: Intractable Disease Research Center, Graduate School of Medicine, Juntendo University
Danika Bannasch: University of California
Antti Sukura: University of Helsinki
Jeffrey J. Schoenebeck: University of Edinburgh
Sini Ezer: Folkhälsan Research Center
Shintaro Katayama: Karolinska Institutet
Carsten O. Daub: Karolinska Institutet
Juha Kere: Karolinska Institutet
Hannes Lohi: University of Helsinki

Nature Communications, 2024, vol. 15, issue 1, 1-12

Abstract: Abstract The dog, Canis lupus familiaris, is an important model for studying human diseases. Unlike many model organisms, the dog genome has a comparatively poor functional annotation, which hampers gene discovery for development, morphology, disease, and behavior. To fill this gap, we established a comprehensive tissue biobank for both the dog and wolf samples. The biobank consists of 5485 samples representing 132 tissues from 13 dogs, 12 dog embryos, and 24 wolves. In a subset of 100 tissues from nine dogs and 12 embryos, we characterized gene expression activity for each promoter, including alternative and novel, i.e., previously not annotated, promoter regions, using the 5’ targeting RNA sequencing technology STRT2-seq. We identified over 100,000 promoter region candidates in the recent canine genome assembly, CanFam4, including over 45,000 highly reproducible sites with gene expression and respective tissue enrichment levels. We provide a promoter and gene expression atlas with interactive, open data resources, including a data coordination center and genome browser track hubs. We demonstrated the applicability of Dog Genome Annotation (DoGA) data and resources using multiple examples spanning canine embryonic development, morphology and behavior, and diseases across species.

Date: 2024
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DOI: 10.1038/s41467-024-52798-1

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