Integrative analysis of transcriptomic data related to the liver of laying hens: from physiological basics to newly identified functions

Abstract

BackgroundAt sexual maturity, the liver of laying hens undergoes many metabolic changes to support vitellogenesis. In published transcriptomic approaches, hundreds of genes were reported to be overexpressed in laying hens and functional gene annotation using gene ontology tools have essentially revealed an enrichment in lipid and protein metabolisms. We reanalyzed some data from a previously published article comparing 38-week old versus 10-week old hens to give a more integrative view of the functions stimulated in the liver at sexual maturity and to move beyond current physiological knowledge. Functions were defined based on information available in Uniprot database and published literature.ResultsOf the 516 genes previously shown to be overexpressed in the liver of laying hens, 475 were intracellular (1.23–50.72 fold changes), while only 36 were predicted to be secreted (1.35–66.93 fold changes) and 5 had no related information on their cellular location. Besides lipogenesis and protein metabolism, we demonstrated that the liver of laying hens overexpresses several clock genes (which supports the circadian control of liver metabolic functions) and was likely to be involved in a liver/brain/liver circuit (neurotransmitter transport), in thyroid and steroid hormones metabolisms. Many genes were associated with anatomical structure development, organ homeostasis but also regulation of blood pressure. As expected, several secreted proteins are incorporated in yolky follicles but we also evidenced that some proteins are likely participating in fertilization (ZP1, MFGE8, LINC00954, OVOCH1) and in thyroid hormone maturation (CPQ). We also proposed that secreted proteins (PHOSPHO1, FGF23, BMP7 but also vitamin-binding proteins) may contribute to the development of peripheral organs including the formation of medullar bones to provide labile calcium for eggshell formation. Thirteen genes are uniquely found in chicken/bird but not in human species, which strengthens that some of these genes may be specifically related to avian reproduction.ConclusionsThis study gives additional hypotheses on some molecular actors and mechanisms that are involved in basic physiological function of the liver at sexual maturity of hen. It also revealed some additional functions that accompany reproductive capacities of laying hens, and that are usually underestimated when using classical gene ontology approaches.

Comparative Analysis of Metabolites in the Liver of Muscovy Ducks at Different Egg-Laying Stages Using Nontargeted Ultra-High-Performance Liquid Chromatography-Electrospray Mass Spectrometry-Based Metabolomics

“…Nucleotides are not only the basic constituent units of DNA and RNA but also the precursors for nucleic acid synthesis in the body. The guanine monophosphate synthase ( GMPS ) and cytidine/uridine monophosphate kinase 1 ( CMPK1 ) genes were significantly upregulated during the egg-laying stage to promote pyrimidine synthesis . Therefore, a significant upregulation in the FT/TT group and downregulation in the ST/FT group of pyrimidine metabolism (apla00240) were observed in this study.…”

A Comprehensive Proteome and Acetyl-Proteome Atlas Reveals Molecular Mechanisms Adapting to the Physiological Changes From Pre-laying to Peak-Laying Stage in Liver of Hens (Gallus gallus)

“…In hens, with reaching the peak-laying period, the liver undergoes a serial of great physiological changes to meet the needs for egg-laying. The most notable ones are the enhanced lipid metabolism in both catabolic and anabolic directions in liver ( 40 ) and the activated protein synthesis and energy metabolism ( 35 ). However, the detailed regulatory mechanisms regarding the adaption of the physiological changes from pre-laying to peak-laying stage in liver of hens remain unknown.…”

“…Comparative transcriptome analysis suggested that differentially expressed genes (DEGs) were significantly enriched in oxidation reduction, sterol and cholesterol metabolic processes, and lipid biosynthetic processes between the liver of peak-laying hens at 30 weeks old (30 w) and the liver of pre-laying hens at 20 w (32). Integrative analysis of transcriptomic data related to the liver of laying hens further revealed the important roles of liver in lipid metabolism and linked it with egg yolk formation and egg fertilization as well (33)(34)(35). However, the roles of lysine acetylation modification of proteins in liver lipid metabolism in chicken are rarely reported until now.…”

Expression characteristics and regulatory mechanism of Apela gene in liver of chicken (Gallus gallus)

“…Especially during the transition from the sexually immature to laying phases, the liver of laying hens undergoes many metabolic changes to support vitellogenesis [20,21]. In the process, many lipid-metabolic genes, including those involved in lipogenesis, holding, breaking down and transporter functional genes, are sharply up-regulated or down-regulated to help achieve these metabolic changes [22]. Meanwhile, estrogen, as an important inducer of certain liver genes, rises significantly in the sexually mature hens compared to the sexually immature hens [23].…”