Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle

Abstract

Background: A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome in beef cattle.

Results: Our transcriptome atlas was generated from 135 bovine tissues in adult beef cattle, covering 51 tissue types of major organ systems (e.g., muscular system, digestive system, immune system, reproductive system). Approximately 94.76% of sequencing reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We detected a total of 60,488 transcripts, and 32% of them were not reported before. We identified 2654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across tissues. Using weighted gene co-expression network analysis, we obtained 24 modules with 237 hub genes (HUBGs). Functional enrichment analysis showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were more conserved in terms of expression pattern as compared to TSGs and HUBGs among multiple species. Finally, we obtained a subset of tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and several functional pathways, which may be involved in production and health traits.

Conclusions: We generated a large-scale gene expression atlas across the major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs, and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between beef and dairy cattle also fill in the knowledge gaps about differential transcriptome regulation of bovine tissues underlying economically important traits.

Keywords: Beef cattle; Co-expression network; Differentially expressed genes; Gene expression; Housekeeping genes; Tissue-specific genes.

Fig. 1

Global framework of the current study. We used 51 tissues from male Chinese Simmental beef cattle to study the expression specificity patterns through multifaceted analyses (tissue-specific expression, differentially expressed gene analysis, co-expression analysis, expression pattern analysis, housekeeping gene expression, etc.). Then, we performed conservation analysis and RT-qPCR validation for several identified candidate genes. The panel at the top shows the tissue samples. Tissues belonging to the same organ system are labeled with the same color

Fig. 2

Gene expression profile among 51 tissue types. a Principal component analysis for all tissue types based on corrected expression data through log₂ (FPKM+1). Tissues are colored according to organ systems as the same as in Fig. 1. b Unbiased hierarchical clustering heat map based on Pearson’s correlation coefficient for all genes. Color intensity indicates the correlation between tissues, red indicates high correlation (1), and blue indicates low correlation (0.5)

Fig. 3

The expression pattern and hierarchical clustering of 2654 HKGs across 51 bovine tissues. a Clustering of expression patterns of housekeeping genes. Color intensity represents expression level estimated through log₁₀ normalized FPKM. Red indicates high expression and blue indicates low expression. b The HKGs are variably expressed and only 8.52% are constantly expressed HKGs. Among those constant HK genes, only 3.98% are highly expressed with FPKM larger than 50. c Functional annotation of low variable expression, medium variable expression, and high variable expression of HKGs. d Hierarchical clustering heatmap based on Pearson’s correlation coefficient for HKGs. The red color represents high correlation and the blue color represents low correlation

Fig. 4

Tissue-specific expression patterns between system categories. a Distribution of the number of tissue-specific genes in all system categories. b Examples of TSG in the circulatory system (MYL3), the digestive system (LOC100847998) and the endocrine system (NNAT). The x-axis represents tissue labeled with the same colors as in Fig. 1 and the y-axis is the FPKM value. c Network topology analysis of 477 TSGs based on the String database. Each node represents a tissue-specific protein-coding gene. The size of the node indicates the level of expression of tissue-specific protein-coding genes. The node colors represent ten system categories, and the gray means that the gene comes from the STRING database. The edges represent the co-expression relationship between tissue-specific protein-coding genes. d Functional annotation and enrichment distribution of tissue-specific gene sets in the system. The x-axis represents -log₁₀ (P value) and the y-axis represents GO term

Fig. 5

Clustered network graph of the transcriptome in bovine tissues. a Functional modules are represented in different colors. Each major branch represents a color-coded module that contains a group of highly connected genes. b Heatmap between 24 modules and 47 tissues. Boxes display Pearson correlation coefficients and their associated P values. Red indicates that the given tissue has a strong positive correlation relative to all other tissues. Green indicates that the given tissue has a strong negative correlation relative to other tissues. c, d, and e represents the cerebellum-red module, the muscle-pink module, and the liver-dark green module, respectively. Hub genes were marked with yellow. The size of each node represents the within module connectivity of the node to adjacent genes

Fig. 6

Different gene expression patterns between beef and dairy. a Overview of tissues collected from adult beef and dairy cattle for RNA-seq. b Venn diagram shows the shared and unique differentially expressed genes among heart, muscle, liver, lung, brain, and testis tissues between beef and dairy cattle. c. Symmetric heatmap generated based on the Spearman correlation coefficients of all differentially expressed genes in all paired wise tissues. d GO function annotation of DEGs in muscle tissue. BP represents biological process, CC represents cellular component, and MF represents molecular function