Hepatic microRNAome reveals potential microRNA-mRNA pairs association with lipid metabolism in pigs

Liu, Jingge; Chen, Ning; Li, Bo-jiang; Li, Rongyang; Wu, Wang Jun

doi:10.5713/ajas.18.0438

Cited by 7 publications

(8 citation statements)

References 32 publications

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“…According to size distribution analysis, 22-nt RNAs were the most abundant, followed by 21 and 23-nt RNAs. The characteristics of the length distribution were consistent with the typical size of miRNAs produced by Dicer processing and were consistent with previous results [39,56]. These findings indicate that the depth and quality of our sequencing data are satisfactory.…”

Section: Discussionsupporting

confidence: 91%

“…Before data analysis, the raw data were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA), to remove adapter dimers, junk, low complexity, and repeats. Subsequently, unique sequences with lengths of 18-40 nucleotides were mapped to porcine precursors in miRbase 21.0 by BLAST search to identify known miRNAs and novel 3p-and 5p-derived miRNAs ftp://mirbase.org/pub/mirbase/ (accessed on 12 December 2019) [39]. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs).…”

Section: Library Construction Mirna Sequencing and Data Analysismentioning

confidence: 99%

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The Effect of RBP4 on microRNA Expression Profiles in Porcine Granulosa Cells

Zhao

Rao

Qiu

et al. 2021

Animals

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Retinol binding protein 4 (RBP4) is a transporter of vitamin A that is secreted mainly by hepatocytes and adipocytes. It affects diverse pathophysiological processes, such as obesity, insulin resistance, and cardiovascular diseases. MicroRNAs (miRNAs) have been reported to play indispensable roles in regulating various developmental processes via the post-transcriptional repression of target genes in mammals. However, the functional link between RBP4 and changes in miRNA expression in porcine granulosa cells (GCs) remains to be investigated. To examine how increased expression of RBP4 affects miRNA expression, porcine GCs were infected with RBP4-targeted lentivirus for 72 h, and whole-genome miRNA profiling (miRNA sequencing) was performed. The sequencing data were validated using real-time quantitative polymerase chain reaction (RT-qPCR) analysis. As a result, we obtained 2783 known and 776 novel miRNAs. In the experimental group, 10 and seven miRNAs were significantly downregulated and upregulated, respectively, compared with the control group. Ontology analysis of the biological processes of these miRNAs indicated their involvement in a variety of biological functions. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these miRNAs were involved mainly in the chemokine signaling pathway, peroxisome proliferators-activated receptors (PPAR) signaling pathway, insulin resistance pathway, nuclear factor-kappa B(NF-kappa B) signaling pathway, and steroid hormone biosynthesis. Our results indicate that RBP4 can regulate the expression of miRNAs in porcine GCs, with consequent physiological effects. In summary, this study profiling miRNA expression in RBP4-overexpressing porcine GCs provides an important reference point for future studies on the regulatory roles of miRNAs in the porcine reproductive system.

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Section: Discussionsupporting

confidence: 91%

Section: Library Construction Mirna Sequencing and Data Analysismentioning

confidence: 99%

The Effect of RBP4 on microRNA Expression Profiles in Porcine Granulosa Cells

Zhao

Rao

Qiu

et al. 2021

Animals

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“…The rst nucleotide bias of known 20 nt, 22 nt, 24 nt miRNAs is U which was similar to others [12]. While, the rst nucleotide bias of known 21nt and 23nt miRNA and novel miRNA was different from other researches [7,8]. The length of predicted novel miRNA was largely aggregated in 22 nt, while the length of known miRNA was mainly clustered in 23 nt which was different from other reports [26].…”

Section: Discussionsupporting

confidence: 64%

“…MicroRNAs (miRNA) are a kind of 22~nt small non-coding RNAs that direct posttranscriptional repression of mRNA targets in mammals [6]. In recent years, a large number of miRNAs have been identi ed in eukaryotic organisms from nematodes to humans [7][8][9]. Moreover, miRNAs have been regarded as key regulators because they play a critical role in various biological processes, such as animal development, cell proliferation, and differentiation, transcriptional regulation, and homeostasis [10].…”

Section: Introductionmentioning

confidence: 99%

MicroRNA Profiling Reveals an Abundant ssc-miRNA-148a-3p that Promotes Proliferation and Differentiation during Intramuscular Adipogenesis in Chinese Guizhou Congjiang Pigs Breeds by targeting PPARGC1A

Tan

Chen

Teng

et al. 2021

Preprint

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BackgroundIntramuscular fat development is regulated by a series of complicated processes, and non-coding RNA (ncRNA) such as microRNA (miRNA) plays a critical role during intramuscular preadipocyte proliferation and differentiation development in pigs. In present research, we detected the expression profiles of miRNA during different differentiation stages, namely, day 0 (D0), day 4 (D4), and day 8 (D8), of intramuscular preadipocytes from the longissimus dorsi muscle of Chinese Guizhou Congjiang pigs to provide first insights into their potential involvement in intramuscular preadipocyte development. And we investigated the function of miR-148a-3p in adipocyte proliferation, apoptosis, and differentiation. ResultsA total of 67, 95, and 16 differentially expressed (DE) miRNAs were detected between D4 and D0, between D8 and D0, and between D8 and D4, respectively. We further characterized the role of miR-148a-3p which was differentially expressed and highest expressed abundance in D0, D4, and D8. To explore the role of miR-148a-3p in porcine intramuscular preadipocyte, miR-148a-3p mimics and inhibitors were used to perform miR-148a-3p overexpression and knockdown, respectively. Overexpression of miRNA-148a-3p increased the number of intramuscular preadipocytes in the S/G2 phase of the cell cycle and decreased the proportion of cells in the G0/G1 phase. Moreover, it promoted proliferation by regulation of cyclin B, cyclin G1, cyclin D1, CDK2, CDK3, and CDK4 and inhibited apoptosis of intramuscular preadipocyte by regulating the expression of Caspase-3, Bax, and Bcl-2. Meanwhile, the mimics of miR-148a-3p dramatically promoted intramuscular preadipocyte differentiation and upregulated the expression levels of adipogenic marker genes PPARγ, FASN, FABP4, HSL, APOE, LPL, and CEBPα. Furthermore, miR-148a-3p promoted intramuscular preadipocyte differentiation via restraining the AMPK/ACC/CPT1C signaling pathway. PPARGC1A was identified as a target gene of miR-148a-3p by luciferase activity and western blotting assays. ConclusionOur study provides novel insights into the regulatory mechanisms underlying intramuscular preadipocyte development and identified amount of miRNAs whose regulatory potential will need to be explored in the future. Our results establish that miR-148a-3p promoted adipocyte differentiation by targeting PPARGC1A.

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“…Sequencing of high-quality miRNA was performed on the Illumina HiSeq 2,500 (Illumina, San Diego, CA, United States). A detailed description of alignment, mapping and normalization was processed as previously described ( Liu et al, 2019a ). DEseq2 was used to analyze the differentially expressed (DE) miRNAs.…”

Section: Methodsmentioning

confidence: 99%

Comparative miRNA expression profile analysis of porcine ovarian follicles: new insights into the initiation mechanism of follicular atresia

Liu,

Ning,

Zhang

et al. 2023

Front. Genet.

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Follicular atresia occurs in every stage of ovarian development, which is relevant to female fertility. In the past decade, increasing studies have confirmed that miRNAs, a class of short non-coding RNAs, play an important role in follicular atresia by post-transcription regulation of their target genes. However, the function of miRNAs on follicular atresia initiation is unknown. In the present study, high-throughput small RNA sequencing was performed to analyze differential miRNA expression profiles between healthy (HF) follicles and early atretic (EAF) follicles. A total of 237 conserved miRNA were detected, and the miR-143 is the highest expressed in follicles. Meanwhile, we also found wide sequence variations (isomiRs) in porcine ovarian miRNA, including in 5′un-translation region, core seed sequences and 3′untranslation region. Furthermore, we identified 22 differentially expressed miRNAs in EAF groups compared to HF group, of which 3 miRNAs were upregulated, as well as 19 miRNAs were downregulated, and then the RT-PCR was performed to validate these profiles. The target genes of these differentially expressed miRNAs were predicted by using miRwalk, miRDB, and Targetscan database, respectively. Moreover, the gene ontology and KEGG pathway enrichment established that the regulating functions and signaling pathways of these miRNAs contribute to follicular atresia initiation and cell fate. In conclusion, this study provides new insights into the changes of miRNAs in early atretic follicles to demonstrate their molecular regulation in ovarian follicular atretic initiation.

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Hepatic microRNAome reveals potential microRNA-mRNA pairs association with lipid metabolism in pigs

Abstract: Our study provides the main differences in the Large White at miRNA level between two different developmental stages. It supplies a valuable database for the further function and mechanism elucidation of miRNAs in porcine liver development and lipid metabolism.

Cited by 7 publications

References 32 publications

The Effect of RBP4 on microRNA Expression Profiles in Porcine Granulosa Cells

The Effect of RBP4 on microRNA Expression Profiles in Porcine Granulosa Cells

MicroRNA Profiling Reveals an Abundant ssc-miRNA-148a-3p that Promotes Proliferation and Differentiation during Intramuscular Adipogenesis in Chinese Guizhou Congjiang Pigs Breeds by targeting PPARGC1A

Comparative miRNA expression profile analysis of porcine ovarian follicles: new insights into the initiation mechanism of follicular atresia

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