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 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.

Fig. 1. Overview of the Dog Genome Annotation (DoGA) project.

This includes the DoGA biobank, DoGA Data Coordination Center (DCC) Database, and public resources and tools, such as functional annotations from STRT2-seq and CAGE-seq analyses (manuscript in preparation). * Indicates free living wolves.

Fig. 2. Overview of tissues in the biobank and expressed promoters and genes in tissues collected from different organ systems based on STRT2-seq.

Bold tissue names have been sequenced with STRT2-seq. In brackets, we indicate the number of enriched robust promoters, genes, and their tissue-enriched orthologs in the Human Protein Atlas for the specific tissue and organ system. Dashes indicate no orthologue tissue was included in the Human Protein Atlas.

Fig. 3. DoGA promoter classes, their expression profiles and their enriched expression in tissues and organ systems.

a Overview of our different promoter classes and their sizes. b The UMAP plot of the STRT2-seq tissue samples based on the expression of the robust promoter set. Each dot represents one sample and was color-coded based on their organ system of origin in the metadata. Overlapping causes the darkening of dots. The neuronal tissue cluster consists of CNS samples as well as retinal tissue. c The number of tissue-enriched robust promoters in each tissue (right) and the number of organ-system-enriched robust promoters in each organ system (left).

Fig. 4. Tissue-level expression profiles of disease-associated genes, promoter usage in cardiac tissues, and gene expression during embryonic development are use-case examples of the DoGA data.

a log-normalized expression of genes associated with eye-development-related diseases across all tissues. b Alternative promoter usage for RGS3 in cardiac muscle tissues. c Expression profiles of genes enriched during embryonic development compared to adult samples. We highlighted one gene enriched in the early stage (AIPL1) and one later stage (CBX2). d The expression of robust promoters overlapping with SNPs is associated with “Sorry when wrong” behavior.