The DoGA consortium expression atlas of promoters and genes in 100 canine tissues
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...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2024-10-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-52798-1 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850203833601359872 |
|---|---|
| author | 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 DoGA Consortium Sini Ezer Shintaro Katayama Carsten O. Daub Juha Kere Hannes Lohi |
| author_facet | 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 DoGA Consortium Sini Ezer Shintaro Katayama Carsten O. Daub Juha Kere Hannes Lohi |
| author_sort | Matthias Hörtenhuber |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-7894452dee5b4ca9b19fbe1f626becc8 |
| institution | OA Journals |
| issn | 2041-1723 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-7894452dee5b4ca9b19fbe1f626becc82025-08-20T02:11:25ZengNature PortfolioNature Communications2041-17232024-10-0115111210.1038/s41467-024-52798-1The DoGA consortium expression atlas of promoters and genes in 100 canine tissuesMatthias Hörtenhuber0Marjo K. Hytönen1Abdul Kadir Mukarram2Meharji Arumilli3César L. Araujo4Ileana Quintero5Pernilla Syrjä6Niina Airas7Maria Kaukonen8Kaisa Kyöstilä9Julia Niskanen10Tarja S. Jokinen11Faezeh Mottaghitalab12Işıl Takan13Noora Salokorpi14Amitha Raman15Irene Stevens16Antti Iivanainen17Masahito Yoshihara18Oleg Gusev19Danika Bannasch20Antti Sukura21Jeffrey J. Schoenebeck22DoGA ConsortiumSini Ezer23Shintaro Katayama24Carsten O. Daub25Juha Kere26Hannes Lohi27Department of Medicine, Huddinge, Karolinska InstitutetDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Medicine, Huddinge, Karolinska InstitutetDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Equine and Small Animal Medicine, University of HelsinkiDepartment of Medicine, Huddinge, Karolinska InstitutetDepartment of Medicine, Huddinge, Karolinska InstitutetDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Medicine, Huddinge, Karolinska InstitutetDepartment of Medicine, Huddinge, Karolinska InstitutetDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Medicine, Huddinge, Karolinska InstitutetIntractable Disease Research Center, Graduate School of Medicine, Juntendo UniversityDepartment of Population Health and Reproduction, School of Veterinary Medicine, University of CaliforniaDepartment of Veterinary Biosciences, University of HelsinkiRoslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghFolkhälsan Research CenterDepartment of Medicine, Huddinge, Karolinska InstitutetDepartment of Medicine, Huddinge, Karolinska InstitutetDepartment of Medicine, Huddinge, Karolinska InstitutetDepartment of Veterinary Biosciences, University of HelsinkiAbstract 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.https://doi.org/10.1038/s41467-024-52798-1 |
| spellingShingle | 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 DoGA Consortium Sini Ezer Shintaro Katayama Carsten O. Daub Juha Kere Hannes Lohi The DoGA consortium expression atlas of promoters and genes in 100 canine tissues Nature Communications |
| title | The DoGA consortium expression atlas of promoters and genes in 100 canine tissues |
| title_full | The DoGA consortium expression atlas of promoters and genes in 100 canine tissues |
| title_fullStr | The DoGA consortium expression atlas of promoters and genes in 100 canine tissues |
| title_full_unstemmed | The DoGA consortium expression atlas of promoters and genes in 100 canine tissues |
| title_short | The DoGA consortium expression atlas of promoters and genes in 100 canine tissues |
| title_sort | doga consortium expression atlas of promoters and genes in 100 canine tissues |
| url | https://doi.org/10.1038/s41467-024-52798-1 |
| work_keys_str_mv | AT matthiashortenhuber thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT marjokhytonen thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT abdulkadirmukarram thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT meharjiarumilli thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT cesarlaraujo thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT ileanaquintero thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT pernillasyrja thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT niinaairas thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT mariakaukonen thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT kaisakyostila thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT julianiskanen thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT tarjasjokinen thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT faezehmottaghitalab thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT isıltakan thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT noorasalokorpi thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT amitharaman thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT irenestevens thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT anttiiivanainen thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT masahitoyoshihara thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT oleggusev thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT danikabannasch thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT anttisukura thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT jeffreyjschoenebeck thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT dogaconsortium thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT siniezer thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT shintarokatayama thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT carstenodaub thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT juhakere thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT hanneslohi thedogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT matthiashortenhuber dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT marjokhytonen dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT abdulkadirmukarram dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT meharjiarumilli dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT cesarlaraujo dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT ileanaquintero dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT pernillasyrja dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT niinaairas dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT mariakaukonen dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT kaisakyostila dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT julianiskanen dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT tarjasjokinen dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT faezehmottaghitalab dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT isıltakan dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT noorasalokorpi dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT amitharaman dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT irenestevens dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT anttiiivanainen dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT masahitoyoshihara dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT oleggusev dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT danikabannasch dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT anttisukura dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT jeffreyjschoenebeck dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT dogaconsortium dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT siniezer dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT shintarokatayama dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT carstenodaub dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT juhakere dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues AT hanneslohi dogaconsortiumexpressionatlasofpromotersandgenesin100caninetissues |