Differentially Expressed MiRNAs of Goat Submandibular Glands Among Three Developmental Stages Are Involved in Immune Functions

Wang, Aili; Ji, Zhibin; Xuan, Rong; Zhao, Xiaodong; Hou, Lei; Li, Qing; Chu, Yunpeng; Chao, Tianle; Wang, Jianmin

doi:10.3389/fgene.2021.678194

Cited by 6 publications

(4 citation statements)

References 92 publications

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“…In this study, coimmunoprecipitation sequencing and general transcription sequencing data were combined to analyze the correlation between m 6 A modification and the expression of mammary gland development and lactation-related genes based on mRNA in the mammary gland tissue of dairy goats. Previous studies have found that m 6 A modification characteristics and patterns are highly consistent in the same species but different in various species ( Dominissini et al, 2012 ; Meyer et al, 2012 ; Wang A et al, 2021 ). Based on this technology, we investigated the characteristics and patterns of m 6 A modification, including the degree of m 6 A modification, the distribution position of m 6 A in the transcript, and the m 6 A methylation sequence motif, in the mRNA transcriptome of dairy goats.…”

Section: Discussionmentioning

confidence: 90%

Identification and functional analysis of m6A in the mammary gland tissues of dairy goats at the early and peak lactation stages

Wang

Zhang

Xuan

et al. 2022

Front. Cell Dev. Biol.

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N6-methyladenosine (m6A) is the most common reversible epigenetic RNA modification in the mRNA of all higher eukaryotic organisms and plays an important role in the regulation of gene expression and cell function. In this study, m6A-modified methylated RNA immunoprecipitation sequencing (MeRIP-seq) and transcriptome sequencing (RNA-seq) were used to identify the key genes with m6A modification during mammary gland development and lactation in dairy goats. The results showed that m6A methylation occurred at 3,927 loci, which were significantly enriched in the 3′ untranslated region (3′UTR) and the termination codon region. In the early stage and peak stage of lactation, m6A methylation occurred extensively in mammary tissues, and a total of 725 differentially expressed m6A-modified genes were obtained, all negatively correlated with mRNA expression. In addition, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that different methylated genes were mainly involved in the growth and apoptosis of mammary epithelial cells through signaling pathways, such as the mitogen-activated protein kinase (MAPK) and phospholipase D pathways, and then affected the development and lactation of mammary gland. All in all, we identified and analyzed the methylation events related to the development and lactation regulation of mammary gland at the early and peak lactation stages, and provided a theoretical basis to reveal the physiological regulatory system of mammary gland development and lactation in dairy goats.

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Section: Discussionmentioning

confidence: 90%

Identification and functional analysis of m6A in the mammary gland tissues of dairy goats at the early and peak lactation stages

Wang

Zhang

Xuan

et al. 2022

Front. Cell Dev. Biol.

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“…The expression dynamics of miRNAs in three stages of anthers were analyzed using TPM values (Supplementary Table S 2 ). About 40% miRNAs exhibited high-levels of expression (≥ 50 TPM) [ 23 ]: about 9% of these showed TPM values between 50 and 100, about 13% miRNAs had TPM values between 101 and 500, and about 17% had TPM values > 501 (Fig. 2 F).…”

Section: Resultsmentioning

confidence: 99%

Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

Kong

Zhuo

et al. 2022

BMC Genomics

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Background Explored the molecular science of anther development is important for improving productivity and overall yield of crops. Although the role of regulatory RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), in regulating anther development has been established, their identities and functions in Camellia oleifera, an important industrial crop, have yet not been clearly explored. Here, we report the identification and characterization of genes, lncRNAs and miRNAs during three stages of the tropical C. oleifera anther development by single-molecule real-time sequencing, RNA sequencing and small RNA sequencing, respectively. Results These stages, viz. the pollen mother cells stage, tetrad stage and uninucleate pollen stage, were identified by analyzing paraffin sections of floral buds during rapid expansion periods. A total of 18,393 transcripts, 414 putative lncRNAs and 372 miRNAs were identified, of which 5,324 genes, 115 lncRNAs, and 44 miRNAs were differentially accumulated across three developmental stages. Of these, 44 and 92 genes were predicted be regulated by 37 and 30 differentially accumulated lncRNAs and miRNAs, respectively. Additionally, 42 differentially accumulated lncRNAs were predicted as targets of 27 miRNAs. Gene ontology enrichment indicated that potential target genes of lncRNAs were enriched in photosystem II, regulation of autophagy and carbohydrate phosphatase activity, which are essential for anther development. Functional annotation of genes targeted by miRNAs indicated that they are relevant to transcription and metabolic processes that play important roles in microspore development. An interaction network was built with 2 lncRNAs, 6 miRNAs and 10 mRNAs. Among these, miR396 and miR156 family were up-regulated, while their targets, genes (GROWTH REGULATING FACTORS and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE genes) and lncRNAs, were down-regulated. Further, the trans-regulated targets of these lncRNAs, like wall-associated kinase2 and phosphomannose isomerase1, are involved in pollen wall formation during anther development. Conclusions This study unravels lncRNAs, miRNAs and miRNA-lncRNA-mRNA networks involved in development of anthers of the tropical C. oleifera lays a theoretical foundation for further elucidation of regulatory roles of lncRNAs and miRNAs in anther development.

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“…Avian skeletal muscle growth is comprised of distinct and precisely regulated periods of embryonic and post-hatch muscle development [52]. Studies have shown that lncRNA and miRNA expression is usually tissue specific or affects specific developmental stages [53,54]. Therefore, we questioned whether the function of the constructed ceRNA network possesses development specific to regulating pigeon muscle development.…”

Section: Discussionmentioning

confidence: 99%

Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development

Zhang

Chen

Han³

et al. 2021

Genes

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Growing evidence has demonstrated the emerging role of long non-coding RNA as competitive endogenous RNA (ceRNA) in regulating skeletal muscle development. However, the mechanism of ceRNA regulated by lncRNA in pigeon skeletal muscle development remains unclear. To reveal the function and regulatory mechanisms of lncRNA, we first analyzed the expression profiles of lncRNA, microRNA (miRNA), and mRNA during the development of pigeon skeletal muscle using high-throughput sequencing. We then constructed a lncRNA–miRNA–mRNA ceRNA network based on differentially expressed (DE) lncRNAs, miRNAs, and mRNAs according to the ceRNA hypothesis. Functional enrichment and short time-series expression miner (STEM) analysis were performed to explore the function of the ceRNA network. Hub lncRNA–miRNA–mRNA interactions were identified by connectivity degree and validated using dual-luciferase activity assay. The results showed that a total of 1625 DE lncRNAs, 11,311 DE mRNAs, and 573 DE miRNAs were identified. A ceRNA network containing 9120 lncRNA–miRNA–mRNA interactions was constructed. STEM analysis indicated that the function of the lncRNA-associated ceRNA network might be developmental specific. Functional enrichment analysis identified potential pathways regulating pigeon skeletal muscle development, such as cell cycle and MAPK signaling. Based on the connectivity degree, lncRNAs TCONS_00066712, TCONS_00026594, TCONS_00001557, TCONS_00001553, and TCONS_00003307 were identified as hub genes in the ceRNA network. lncRNA TCONS_00026594 might regulate the FSHD region gene 1 (FRG1)/ SRC proto-oncogene, non-receptor tyrosine kinase (SRC) by sponge adsorption of cli-miR-1a-3p to affect the development of pigeon skeletal muscle. Our findings provide a data basis for in-depth elucidation of the lncRNA-associated ceRNA mechanism underlying pigeon skeletal muscle development.

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Differentially Expressed MiRNAs of Goat Submandibular Glands Among Three Developmental Stages Are Involved in Immune Functions

Cited by 6 publications

References 92 publications

Identification and functional analysis of m6A in the mammary gland tissues of dairy goats at the early and peak lactation stages

Identification and functional analysis of m6A in the mammary gland tissues of dairy goats at the early and peak lactation stages

Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera

Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development

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