Identification and Characterization of lncRNA and mRNA in Testes of Landrace and Hezuo Boars

Zhang, Bo; Yan, Zunqiang; Wang, Pengfei; Yang, Qiaoli; Huang, Xiaoyu; Shi, Huidong; Tang, Yuran; Ji, Yanan; Zhang, Juanli; Gun, Shuangbao

doi:10.3390/ani11082263

Cited by 9 publications

(14 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…LncRNAs in Min pigs share similarities in structure and classification with their counterparts in mammals ( 27 – 29 ). The number of lncRNAs identified here is somewhat higher than that in other pig breeds such as Duroc, Landrace, and Guizhou miniature pigs ( 30 – 33 ), which might be caused by the rich genetic resource in Min pigs, and also by the different screening criteria used for lncRNA characterization.…”

Section: Discussionmentioning

confidence: 56%

Genome-wide characterization of lncRNAs and mRNAs in muscles with differential intramuscular fat contents

Sun

Zhang

et al. 2022

Front. Vet. Sci.

View full text Add to dashboard Cite

Meat quality is one of the most important traits in pig production. Long non-coding RNAs (lncRNAs) have been involved in diverse biological processes such as muscle development through regulating gene expression. However, studies on lncRNAs lag behind and a comparatively small number of lncRNAs have been identified in pigs. Also, the effects of lncRNAs on meat quality remain to be characterized. Here, we analyzed lncRNAs in longissimus thoracis (LT) and semitendinosus (ST) muscles, being different in meat quality, with RNA-sequencing technology. A total of 500 differentially expressed lncRNAs (DELs) and 2,094 protein-coding genes (DEGs) were identified. Through KEGG analysis on DELs, we first made clear that fat deposition might be the main reason resulting in the differential phenotype of LT and ST, for which cGMP–PKG and VEGF signaling pathways were the most important ones. In total, forty-one key DELs and 50 DEGs involved in the differential fat deposition were then characterized. One of the key genes, cAMP-response element binding protein 1, was selected to confirm its role in porcine adipogenesis with molecular biology methods and found that it promotes the differentiation of porcine preadipocytes, consistent with its higher expression level and intramuscular fat contents in LT than that in ST muscle. Furthermore, through integrated analysis of DELs and DEGs, transcription factors important for differential fat deposition were characterized among which BCL6 has the most target DEGs while MEF2A was targeted by the most DELs. The results provide candidate genes crucial for meat quality, which will contribute to improving meat quality with molecular-breeding strategies.

show abstract

Section: Discussionmentioning

confidence: 56%

Genome-wide characterization of lncRNAs and mRNAs in muscles with differential intramuscular fat contents

Sun

Zhang

et al. 2022

Front. Vet. Sci.

View full text Add to dashboard Cite

show abstract

“…The mRNA expression data of 12 samples from our previous study were used for a pairwise integrated analysis ( 31 ). To explore miRNAs related to precocious puberty in HZ boars, we screened 158 DE miRNAs from the Ha and Hb, Hb and Lb groups.…”

Section: Resultsmentioning

confidence: 99%

“…It can improve the utilization of female animals, shorten the generation interval of excellent females, and accelerate the genetic breeding process. Our previous works have shown that HZ boars have reached sexual maturity at 4 months of age ( 31 ). To explore potential regulatory mechanisms of early sexual maturation in HZ boars, the serum hormones (T, E 2 , FSH, and LH) of HZ and LC boars at 30, 90, 120, 180, and 240 days were measured and compared, and the miRNAs in the testes of HZ and LC boars at 30 and 120 days were identified and comparatively analyzed using small RNA-Seq.…”

Section: Discussionmentioning

confidence: 99%

“…The differentially expressed miRNAs were analyzed in targeted association with the 984 mRNAs screened in our previous study ( 31 ), pairs with Pearson correlation coefficient < −0.7 and p -value < 0.05 were selected as co-expressed negative miRNA-mRNA pairs and a miRNA-mRNA interaction network was constructed. The interaction analysis was visualized by Cytoscape software ( 32 ).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Integrated analysis of miRNA and mRNA expression profiles in testes of Landrace and Hezuo boars

Zhang

Yan²,

Gao³

et al. 2022

Front. Vet. Sci.

Self Cite

View full text Add to dashboard Cite

Precocious puberty is closely related to testicular development and spermatogenesis, and there is increasing evidence that miRNAs are involved in regulation of testicular development and spermatogenesis. However, little is known about the regulation of microRNAs (miRNAs) during precocious maturation in Hezuo (HZ) boars. In this study, serum Testosterone (T), Estradiol (E2), Follicle-stimulating hormone (FSH) and Luteinizing hormone (LH) levels were detected in HZ and Landrace (LC) boars in the postnatal period at 30, 90, 120, 180, and 240 days, and the testes of HZ and LC boars at 30 and 120 days were used for histological observation. In addition, we performed small RNA-Seq to identify miRNA at sexual immaturity (30-days-old) and maturity (120-days-old) of HZ boar testis (using LC boar as control) to reveal the key miRNA in regulation of precocious puberty. Hormone assay results showed that high levels of T, E2, FSH, and LH may be related to precocious sexual maturity of HZ boars, and that FSH may play an important function before sexual maturity. Histological observation showed that HZ boars developed earlier than LC boars and had reached sexual maturity at 120 days. Small RNA-Seq yielded a total of 359 exist miRNAs, 767 known miRNAs and 322 novel miRNAs in 12 samples; 549, 468, 133, and 247 differentially expressed (DE) miRNAs were identified between Ha vs. Hb, La vs. Lb, Ha vs. La, and Hb vs. Lb (log2 fold change >1 and p < 0.05). Enrichment analysis showed that target genes of these DE miRNAs were enriched in many gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways (such as PI3K-Akt, Hippo and Rap1 signaling pathways) were related to testicular development and spermatogenesis. Further screening, some miRNAs (such as ssc-miR-29b, ssc-miR-199b, ssc-miR-383, ssc-miR-149, ssc-miR-615, and ssc-miR-370) were possibly associated with precocious puberty. These results provide new light on miRNA regulatory mechanisms involved in precocious puberty.

show abstract

“…Long noncoding RNAs can regulate the expression of functional genes in a variety of ways. lncRNAs regulate the expression of neighboring functional genes through cis -mRNA and can also regulate distant target genes through trans -mRNA ( 18 ). In addition, lncRNAs could serve as miRNA sponges and thereby impair miRNA-mediated gene silencing ( 19 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Transcriptome Analysis Reveals the Role of lncRNA in Fatty Acid Metabolism in the Longissimus Thoracis Muscle of Tibetan Sheep at Different Ages

Bao

Zhao

et al. 2022

Front. Nutr.

View full text Add to dashboard Cite

Long noncoding RNA (lncRNA) plays an important regulatory role in mammalian adipogenesis and lipid metabolism. However, their function in the longissimus thoracis (LT) muscle of fatty acid metabolism of Tibetan sheep remains undefined. In this study, fatty acid and fat content in LT muscle of Tibetan sheep were determined, and RNA sequencing was performed to reveal the temporal regularity of lncRNA expression and the effect of lncRNA-miRNA-mRNA ceRNA regulatory network on lipid metabolism of LT muscle in Tibetan sheep at four growth stages (4-month-old, 4 m; 1.5-year-old, 1.5 y; 3.5-year-old, 3.5 y; 6-year-old, 6 y). The results indicated that the intramuscular fat (IMF) content was highest at 1.5 y. Moreover, the monounsaturated fatty acid (MUFA) content in 1.5 y of Tibetan sheep is significantly higher than those of the other groups (P < 0.05), and it was also rich in a variety of polyunsaturated fatty acids (PUFA). A total of 360 differentially expressed lncRNAs (DE lncRNAs) were identified from contiguous period transcriptome comparative groups of 4 m vs. 1.5 y, 1.5 y vs. 3.5 y, 3.5 y vs. 6 y, and 4 m vs. 6 y, respectively. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis found that the target genes in lncRNA trans-mRNA were significantly related to the protein digestion, absorption, and fatty acid biosynthesis pathways (P < 0.05), which demonstrated that DE lncRNA trans-regulated the target genes, and further regulated the growth and development of the LT muscle and intramuscular fatty acid metabolism in Tibetan sheep. We further analyzed the role of the lncRNA-miRNA-mRNA regulatory network in the lipid metabolism of Tibetan sheep. Additionally, GPD2, LIPE (lipase E hormone-sensitive enzyme), TFDP2, CPT1A, ACACB, ADIPOQ, and other mRNA related to fatty acid and lipid metabolism and the corresponding lncRNA-miRNA regulatory pairs were identified. The enrichment analysis of mRNA in the regulatory network found that the AMPK signaling pathway was the most significantly enriched (P = 0.0000112361). Comprehensive transcriptome analysis found that the LIPE, ADIPOQ, ACACB, and CPT1A that were regulated by lncRNA might change the formation of energy metabolism in Tibetan sheep muscle through the AMPK signaling pathway, and oxidized muscle fibers are transformed into glycolytic muscle fibers, reduced IMF content, and the fatty acid profile also changed.

show abstract

Identification and Characterization of lncRNA and mRNA in Testes of Landrace and Hezuo Boars

Cited by 9 publications

References 72 publications

Genome-wide characterization of lncRNAs and mRNAs in muscles with differential intramuscular fat contents

Genome-wide characterization of lncRNAs and mRNAs in muscles with differential intramuscular fat contents

Integrated analysis of miRNA and mRNA expression profiles in testes of Landrace and Hezuo boars

Comprehensive Transcriptome Analysis Reveals the Role of lncRNA in Fatty Acid Metabolism in the Longissimus Thoracis Muscle of Tibetan Sheep at Different Ages

Contact Info

Product

Resources

About