Transcriptome Profile Analysis Reveals an Estrogen Induced LncRNA Associated with Lipid Metabolism and Carcass Traits in Chickens (Gallus Gallus)

Abstract

Background/Aims: Accumulating evidences have demonstrated that long noncoding RNAs (lncRNA) play important roles in hepatic lipid metabolism in mammals. However, no systematic screening of the potential lncRNAs in the livers of laying hens has been performed, and few studies have been reported concerning the effects of the lncRNAs on lipid metabolism in the livers of chickens during egg-laying period. The purpose of this study was to compare the difference in lncRNA expression in the livers of pre-laying and peak-laying hens at the age of 20 and 30 weeks old by transcriptome sequencing and to investigate the interaction networks among lncRNAs, mRNAs and miRNAs. Moreover, the regulatory mechanism and biological function of lncLTR, a significantly differentially expressed lncRNA in the liver between pre- and peak-laying hens, was explored in vitro and in vivo. Methods: Bioinformatics analyses were conducted to identify the differentially expressed (DE) lncRNAs between the two groups of hens. The target genes of the DE lncRNA were predicated for further functional enrichment. An integrated analysis was performed among the DE lncRNA datasets, DE mRNAs and DE miRNA datasets obtained from the same samples to predict the interaction relationship. In addition, in vivo and in vitro trials were carried out to determine the expression regulation of lncLTR, and polymorphism association analysis was conducted to detect the biological role of ncLTR. Results: A total of 124 DE lncRNAs with a P-value ≤ 0.05 were identified. Among them, 44 lncRNAs including 30 known and 14 novel lncRNAs were significant differentially expressed (SDE) with FDR ≤ 0.05. Thirty-two lncRNAs were upregulated and 12 were downregulated in peak-laying group compared with pre-laying group. The functional enrichment results revealed that target genes of some lncRNAs are involved in the lipid metabolism process. Integrated analysis suggested that some of the genes involved in lipid metabolism might be regulated by both the lncRNA and the miRNA. In addition, an upregulated lncRNA, designated lncLTR, was demonstrated to be induced by estrogen via ERβ signaling. The c242. G>A SNP in lncLTR was significantly associated with chicken carcass weight, evisceration weight, semi-evisceration weight, head weight, double-wing weight, claw weight traits, and blood biochemical index, especially for the blood triglyceride content. Conclusion: A series of lncRNAs associated with lipid metabolism in the livers of chickens were identified by transcriptome sequencing and functional analysis, providing a valuable data resource for further studies on chicken hepatic metabolism activities. LncLTR was regulated by estrogen via ERβ signaling and associated with chicken carcass trait and blood triglyceride content.

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

“…HIV, porcine circovirus 2, HSV-1, rabies virus, avian leukosis virus J, bovine viral diarrhea virus) and parasites (e.g. Echinococcus granulosus, Cryptosporidium parvum, Cryptosporidium baileyi) in animals and humans [28,33,[66][67][68][69][70][71][72][73]. The expression profiles of host circRNAs were also elucidated after infections of avian leukosis virus J [74], bovine viral diarrhea virus [75], human cytomegalovirus [76], Orf virus [30], porcine endemic diarrhea virus [29], HIV [77], transmissible gastroenteritis virus [78], Mycobacterium tuberculosis [79], Clostridium perfringens [80] and C. baileyi [33].…”

Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver

“…FLRL8, FLRL3, and FLRL7 have been demonstrated to show an underlying effect on the Peroxisome Proliferators-activated Receptors (PPAR) signaling pathway by interaction with candidate genes related to lipogenesis and lipid transport, such as FABP5, LPL, and FADS2 [22]. There are few investigations in animals with the one exception that Li et al has identified, a metabolism-related lncRNA (lncLTR), which is regulated by estrogen and associated with plasma triglyceride in hens [24].…”

Long noncoding RNAs in lipid metabolism: literature review and conservation analysis across species

“…(lnc)Liver, CBRH-7919↘CYP7A1, ABCA1 & ↘TG, Chol.[65]lncHR1AC023161.1 d (h: 1tr; 420 bp; 2ex)lncHR1mOv. (lnc)Liver↘SREBP1c, FASN, ACACA & ↘TG[66]lnc-KDM5D-4–LINCxxxx a hKD (lnc)HepG2↗LPIN2 & ↗Lipid droplet formation[67]lnc-leptin–lnc-leptin a mKD (lnc)Primary adipocyte↘LEP[68]lncLSTRC730036E19Rik (m: 1tr; 1102 bp; 5ex)lncLSTRmKD (lnc)Liver↗APOC2, ↘CYP8B1 & ↘TG, Glucose[69]lncLTRNONGGAG001747.2 (c: 1tr; 776 bp; NA)lncLTR a cGWAS (serum TG content)–SNP in lncLTR locus[70]lncSHGLB4GALT1-AS1 d (h: 3tr; 3752 bp; 4ex)lncSHGL a mKD, Ov. (lnc)Liver↗ACACB, ↘FASN, SREBP1 & ↘FA, lipolyse[71]lncSREBF1SMCR2 (h:1tr; 564 bp; 4ex)SMCR2 a hCo-effects (LXR agonist)THP-1↗lnc[62]LNMICCAC009902.2 (h: 2tr; 620 bp; 2ex)LNMICC a hKD, Ov.…”