Screening of Key Genes in Tail Fat Deposition and Analysis of lncRNA-miRNA-mRNA Network in Sheep

doi:10.7668/hbnxb.20195458

Abstract

Abstract:

The objective of this study was to identify differentially expressed mRNAs,miRNAs,and lncRNAs between different tail types of sheep in their tail fat tissues,and to construct a critical ceRNA(competing endogenous RNAs)regulatory network involved in the regulation of fat deposition in the tails of sheep.Three 2-year-old(24-month-old)Dorper sheep and three Tianjin large-tail sheep were randomly selected.Tail fat tissues were collected for H&E staining and whole transcriptome sequencing.Bioinformatics approaches were employed to screen for differentially expressed RNAs,predict target genes,and conduct functional enrichment analyses.The regulatory network and targeting relationships were further analyzed from the perspective of lipid deposition regulation.The results demonstrated that the tail fat cell area of Tianjin large-tail sheep was significantly larger than that of Dorper sheep.There were a total of 1 156 differentially expressed mRNAs between the tail fat tissues of Dorper sheep and Tianjin large-tail sheep(with 403 upregulated and 753 downregulated),72 differentially expressed miRNAs(46 upregulated and 26 downregulated),and 392 differentially expressed lncRNAs(142 upregulated and 250 downregulated).Additionally,216 target genes were predicted from the differentially expressed lncRNAs.These target genes were involved in biological processes related to lipid metabolism,such as the tetrahydrofolate metabolic process,GAIT complex,and coenzyme catabolic process,as well as signaling pathways like glycerolipid metabolism,biotin metabolism,fat digestion and absorption,and the phosphatidylinositol signaling system.The study successfully constructed a ceRNA network closely associated with sheep tail fat deposition by predicting the targeting relationships between differentially expressed mRNAs and lncRNAs and miRNAs.Among them,24 lncRNAs and 6 miRNAs were predicted to regulate genes closely related to lipid metabolism,including PROX1,LPL,and LRP1B.In summary,PROX1,LPL,and LRP1B play a key role in the deposition of tail fat in sheep.This study predicts that four lncRNAs,including MSTRG.9916.7,positively regulate fat metabolism through PROX1,while MSTRG.7563.1 and MSTRG.4729.1 positively regulate fat metabolism through LPL.

Key words: Dorper sheep, Tianjin large-tail sheep, Tail fat, RNA-seq, ceRNA

CLC Number:

S826.89

ZHANG Yuxin, ZHANG Long, GUO Yanyan, SHI Xiaodi, LI Boyu, RUAN Weibin, YAO Dawei, ZHANG Xiaosheng. Screening of Key Genes in Tail Fat Deposition and Analysis of lncRNA-miRNA-mRNA Network in Sheep[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(3): 190-198. doi: 10.7668/hbnxb.20195458.

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Figures/Tables 7

Fig.1 Comparison of tail adipocyte area of DS and TJLTS Different capital letters indicate extremely significant differences in cell area(P<0.01).A—B.H&E staining of DS tail fat sections(20×);C—D.H&E staining of TJLTS tail fat sections(20×);E.The difference of adipocyte area between DS and TJLTS.

Tab.1 Overview of RNA sequencing of tail adipocytes in DS and TJLTS

样本 Sample	总测序数据条数/条 Total reads	干净数据条数/条 Clean reads	干净数据占比/% Clean reads rate	Q30/%
DS-1	11 481 551 700	11 025 543 442	96.03	90.74
DS-2	11 514 227 100	11 094 165 042	96.35	91.24
DS-3	11 252 444 700	10 822 169 237	96.18	90.85
TJLTS-1	12 610 019 100	12 106 135 122	96.00	91.32
TJLTS-2	12 387 500 400	12 045 289 806	97.24	93.16
TJLTS-3	11 762 612 400	11 445 769 722	97.31	93.35

Fig2. Correlation heatmap of gene expression in tail adipose tissue of DS and TJLTS The sample correlation is measured by Pearson correlation coeficient.

Fig.3 Volcano plot for differentially expressed mRNAs(A),miRNAs(B)and lncRNAs(C)

Fig.4 Functional analysis of target genes of lncRNA A.Bar diagram of GO pathway enrichment analysis of differentially expressed target gene of lncRNA:1.Protein maturation by iron-sulfur cluster transfer,2.Endothelial cell morphogenesis,3.2 iron,2 sulfur cluster binding,4.Iron-sulfur transferase activity,5.D-amino acid metabolic process,6.Tetrahydrofolate metabolic GAIT process,7.GAIT complex,8.Endodermal digestive tract morphogenesis,9.Binding,10.Coenzyme catabolic process,11.Mitochondrial matrix,12.Thianmine kinase activity,13.Regulation of translation,14.ATP-dependent 5'—3' DNA belicase activity,15.Posttranscriptional regulation of gene expression,16.5'—3' DNA helicase activity,17.Folic acid-containing compound metabolic process,18.Retrograde protein transport,ER to cytosol,19.Protein lipoylation,20.[4Fe-4S]cluster assembly;B.Bubble diagram of KEGG pathway enrichment analysis of differentially expressed target gene of lncRNA:1.One carbon pool by folate,2.Penicillin and cephalosporin biosynthesis,3.D-Arginine and D-ornithine metabolism,4.Proteasome,5.Amebiasis,6.Glycerolipid metabolism,7.Biotin metabolism,8.Hepatitis C,9.Retrograde endocannabinoid signaling,10.IL-17 signaling pathway,11.Phosphatidylinositol signaling system,12.Type Ⅱ diabetes mellitus,13.Glycine,serine and threonine metabilism,14.Protein processing in endoplasmic reticulum,15.Fat digestion and absorption,16.Measles,17.Transcriptional misregulation in cancer,18.TNF signaling pathway.

Fig.5 Functional analysis of target genes of miRNA A.Bar diagram of GO pathway enrichment analysis of differentially expressed target gene of miRNA:1.Cell,2.Cell part,3.Intracellular,4.Intracellular part,5.Binding,6.Intracellular organelle,7.Organelle,8.Protein binding,9.Cytoplasm,10.Membrane-bounded organelle,11.Intracellular membrane-bounded organelle,12.Cellular component organi zation,13.Organelle part,14.Developmental process,15.Cellular component organization or biogenesis,16.Intracellular organelle part,17.Single-organism developmental process,18.Single-multicellular organism process,19.System development,20.Metabolic precess;B.Bubble diagram of KEGG pathway enrichment analysis of differentially expressed target gene of miRNA:1.Metabolic pathways,2.Phosphatidylinositol signaling system,3.Axon guidance,4.Pathways in cancer,5.MAPK signaling pathway,6.CAMP signaling pathway,7.Rap1 signaling pathway,8.Inositol phosphate metabolism,9.Tight junction,10.Adherens junction,11.Endocytosis,12.Hippo signaling pathway,13.Oxytocin signaling pathway,14.Ras signaling pathway,15.Notch signaling pathway,16.Calcium signaling pathway,17.Adipocylokine signaling pathway,18.Phospholipase D signaling pathway.

Fig.6 The construction of ceRNA networks

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