Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing.

Salavati, Mazdak; Clark, Richard; Becker, Doreen; Kühn, Christa; Plastow, Graham; Dupont, Sébastien; Costa Monteiro Moreira, Gabriel; Charlier, Carole; Clark, Emily Louise

doi:10.1093/g3journal/jkad108

Article (Scientific journals)

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing.

Salavati, Mazdak; Clark, Richard; Becker, Doreen et al.

2023 • In G3: Genes, Genomes, Genetics

Peer reviewed

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https://hdl.handle.net/2268/305351

DOI
10.1093/g3journal/jkad108

PubMed
37216666

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Keywords :

BovReg; CAGE-Seq; EuroFAANG; FAANG; Transcription start site; cattle genome

Abstract :

[en] Understanding the genomic control of tissue-specific gene expression and regulation can help to inform the application of genomic technologies in farm animal breeding programs. The fine mapping of promoters (transcription start sites (TSS)) and enhancers (divergent amplifying segments of the genome local to TSS) in different populations of cattle across a wide diversity of tissues provides information to locate and understand the genomic drivers of breed- and tissue-specific characteristics. To this aim we used Cap Analysis Gene Expression (CAGE) sequencing, of 24 different tissues from three populations of cattle, to define TSS and their co-expressed short-range enhancers (<1 kb) in the ARS-UCD1.2_Btau5.0.1Y reference genome (1000bulls run9), and analysed tissue- and population specificity of expressed promoters. We identified 51,295 TSS and 2,328 TSS-Enhancer regions shared across the three populations (Dairy, Dairy - Beef cross and Canadian Kinsella composite cattle from 2 individuals, one of each sex, per population). Cross-species comparative analysis of CAGE data from seven other species, including sheep, revealed a set of TSS and TSS-Enhancers that were specific to cattle. The CAGE dataset will be combined with other transcriptomic information for the same tissues to create a new high-resolution map of transcript diversity across tissues and populations in cattle for the BovReg Project. Here we provide the CAGE dataset and annotation tracks for TSS and TSS-Enhancers in the cattle genome. This new annotation information will improve our understanding of the drivers of gene expression and regulation in cattle and help to inform the application of genomic technologies in breeding programs.

Disciplines :

Genetics & genetic processes

Author, co-author :

Salavati, Mazdak ; The Roslin Institute, University of Edinburgh, EH25 9RG, Edinburgh, UK

Clark, Richard; Genetics Core, Edinburgh Clinical Research Facility, University of Edinburgh, EH4 2XU, Edinburgh, UK

Becker, Doreen; Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany

Kühn, Christa; Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany ; Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany

Plastow, Graham; Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, T6G 2H1, Edmonton, Canada

Dupont, Sébastien ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA)

Costa Monteiro Moreira, Gabriel ; Université de Liège - ULiège > Département de gestion vétérinaire des Ressources Animales (DRA) ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics - Unit of Animal Genomics

Charlier, Carole ; Université de Liège - ULiège > GIGA > GIGA Medical Genomics

Clark, Emily Louise; The Roslin Institute, University of Edinburgh, EH25 9RG, Edinburgh, UK

Language :

English

Title :

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing.

Publication date :

22 May 2023

Journal title :

G3: Genes, Genomes, Genetics

eISSN :

2160-1836

Peer reviewed :

Peer reviewed

Available on ORBi :

since 21 July 2023

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