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

Animals Dogs / genetics Promoter Regions, Genetic / genetics Genome Wolves / genetics Molecular Sequence Annotation Organ Specificity Gene Expression Profiling / methods

Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
21 Oct 2024
Historique:
received: 14 03 2023
accepted: 13 09 2024
medline: 22 10 2024
pubmed: 22 10 2024
entrez: 21 10 2024
Statut: epublish

Résumé

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.

Identifiants

DOI: 10.1038/s41467-024-52798-1 PMID: 39433728
pubmed: 39433728
doi: 10.1038/s41467-024-52798-1
pii: 10.1038/s41467-024-52798-1
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

9082

Investigateurs

Carsten Daub (C)
César L Araujo (CL)
Ileana B Quintero (IB)
Milla Salonen (M)
Riika Sarviaho (R)
Sruthi Hundi (S)
Jenni Puurunen (J)
Sini Sulkama (S)
Sini Karjalainen (S)
Henna Pekkarinen (H)
Ilona Kareinen (I)
Anna Knuuttila (A)
Hanna-Maaria Javela (HM)
Laura Tuomisto (L)
Heli Nordgren (H)
Karoliina Hagner (K)
Tarja Jokinen (T)
Kaarel Krjutskov (K)
Auli Saarinen (A)
Rasha Fahad Aljelaify (RF)
Fiona Ross (F)
Irene Stevens (I)
Jeffrey J Schoenebeck (JJ)
Heini Niinimäki (H)
Marko Haapakoski (M)

Informations de copyright

© 2024. The Author(s).

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Auteurs

Matthias Hörtenhuber (M)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden.
ORCID: 0000-0002-5599-5565

Marjo K Hytönen (MK)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
Folkhälsan Research Center, 00290, Helsinki, Finland.
ORCID: 0000-0003-1976-5874

Abdul Kadir Mukarram (AK)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden.

Meharji Arumilli (M)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
Folkhälsan Research Center, 00290, Helsinki, Finland.

César L Araujo (CL)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
Folkhälsan Research Center, 00290, Helsinki, Finland.

Ileana Quintero (I)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
Folkhälsan Research Center, 00290, Helsinki, Finland.
ORCID: 0000-0001-7040-1289

Pernilla Syrjä (P)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.

Niina Airas (N)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.

Maria Kaukonen (M)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
Folkhälsan Research Center, 00290, Helsinki, Finland.
ORCID: 0000-0002-2146-4694

Kaisa Kyöstilä (K)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
Folkhälsan Research Center, 00290, Helsinki, Finland.

Julia Niskanen (J)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
Folkhälsan Research Center, 00290, Helsinki, Finland.
ORCID: 0000-0002-2871-6890

Tarja S Jokinen (TS)

Department of Equine and Small Animal Medicine, University of Helsinki, Helsinki, Finland.
ORCID: 0000-0001-6389-0109

Faezeh Mottaghitalab (F)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden.
ORCID: 0000-0001-6495-6667

Işıl Takan (I)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden.
ORCID: 0000-0002-0269-6625

Noora Salokorpi (N)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland.
Folkhälsan Research Center, 00290, Helsinki, Finland.

Amitha Raman (A)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden.

Irene Stevens (I)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden.
Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
ORCID: 0000-0003-3823-1499

Antti Iivanainen (A)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
ORCID: 0000-0003-1002-3225

Masahito Yoshihara (M)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden.
ORCID: 0000-0002-8915-9282

Oleg Gusev (O)

Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, 113-8421, Tokyo, Japan.
ORCID: 0000-0002-6203-9758

Danika Bannasch (D)

Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, US.
ORCID: 0000-0002-7614-7207

Antti Sukura (A)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
ORCID: 0000-0002-8992-1695

Jeffrey J Schoenebeck (JJ)

Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland.
ORCID: 0000-0003-4964-2138

Sini Ezer (S)

Folkhälsan Research Center, 00290, Helsinki, Finland.
Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.

Shintaro Katayama (S)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden.
Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland.
Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.
ORCID: 0000-0001-7581-5157

Carsten O Daub (CO)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden. carsten.daub@ki.se.
Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden. carsten.daub@ki.se.
ORCID: 0000-0002-3295-8729

Juha Kere (J)

Department of Medicine, Huddinge, Karolinska Institutet, Huddinge, Sweden. juha.kere@helsinki.fi.
Folkhälsan Research Center, 00290, Helsinki, Finland. juha.kere@helsinki.fi.
Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland. juha.kere@helsinki.fi.
ORCID: 0000-0003-1974-0271

Hannes Lohi (H)

Department of Veterinary Biosciences, University of Helsinki, 00014, Helsinki, Finland. hannes.lohi@helsinki.fi.
Department of Medical and Clinical Genetics, University of Helsinki, 00014, Helsinki, Finland. hannes.lohi@helsinki.fi.
Folkhälsan Research Center, 00290, Helsinki, Finland. hannes.lohi@helsinki.fi.
ORCID: 0000-0003-1087-5532

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › The DoGA consortium expression atlas of...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Carnivora › Pinnipedia › Canidae › Chiens › The DoGA consortium expression atlas of...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Composants de génome › Gènes › Composants de gène › Éléments de régulation transcriptionnelle › Régions promotrices (génétique) › The DoGA consortium expression atlas of...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › The DoGA consortium expression atlas of...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Carnivora › Pinnipedia › Canidae › Loups › The DoGA consortium expression atlas of...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › The DoGA consortium expression atlas of...
questionsmedicales.fr › Phénomènes physiologiques › Spécificité d'organe › The DoGA consortium expression atlas of...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › The DoGA consortium expression atlas of...