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Hörtenhuber M, Hytönen MK, Mukarram AK, Arumilli M, Araujo CL, Quintero I, Syrjä P, Airas N, Kaukonen M, Kyöstilä K, Niskanen J, Jokinen TS, Mottaghitalab F, Takan I, Salokorpi N, Raman A, Stevens I, Iivanainen A, Yoshihara M, Gusev O, Bannasch D, Sukura A, Schoenebeck JJ, DoGA Consortium , Ezer S, Katayama S, Daub CO, Kere J, Lohi H
Nat Commun 15 (1) 9082 [2024-10-21; online 2024-10-21]
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.
PubMed 39433728
DOI 10.1038/s41467-024-52798-1
Crossref 10.1038/s41467-024-52798-1
pmc: PMC11494170
pii: 10.1038/s41467-024-52798-1
BioProject: PRJNA907518
SRA: SRR22520740
SRA: SRR22520741
SRA: SRR22520742
SRA: SRR22520743
SRA: SRR22520744
SRA: SRR22520745
SRA: SRR22520746
SRA: SRR22520747
SRA: SRR22520748