Author
Listed:
- Matthias Hörtenhuber
(Karolinska Institutet)
- Marjo K. Hytönen
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
- Abdul Kadir Mukarram
(Karolinska Institutet)
- Meharji Arumilli
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
- César L. Araujo
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
- Ileana Quintero
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
- Pernilla Syrjä
(University of Helsinki)
- Niina Airas
(University of Helsinki)
- Maria Kaukonen
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
- Kaisa Kyöstilä
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
- Julia Niskanen
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
- Tarja S. Jokinen
(University of Helsinki)
- Faezeh Mottaghitalab
(Karolinska Institutet)
- Işıl Takan
(Karolinska Institutet)
- Noora Salokorpi
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
- Amitha Raman
(Karolinska Institutet)
- Irene Stevens
(Karolinska Institutet
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
University of Helsinki)
- Shintaro Katayama
(Karolinska Institutet
University of Helsinki
University of Helsinki)
- Carsten O. Daub
(Karolinska Institutet
Karolinska Institutet)
- Juha Kere
(Karolinska Institutet
Folkhälsan Research Center
University of Helsinki)
- Hannes Lohi
(University of Helsinki
University of Helsinki
Folkhälsan Research Center)
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.
Suggested Citation
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 , 2024.
"The DoGA consortium expression atlas of promoters and genes in 100 canine tissues,"
Nature Communications, Nature, vol. 15(1), pages 1-12, December.
Handle:
RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-52798-1
DOI: 10.1038/s41467-024-52798-1
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