Exploration of exosomal microRNA expression profiles in pigeon ‘Milk’ during the lactation period

Ma, Yao; Feng, Siyuan; Wang, Xun; Qazi, Izhar Hyder; Long, Keren; Luo, Yi; Li, Guojun; Ning, Chunyou; Wang, Yixin; Hu, Silu; Li, Xiaokai; Lan, Dan; Hu, Yaodong; Tang, Qianzi; Ma, Jideng; Jin, Long; Jiang, Anan; Li, Mingzhou

doi:10.1186/s12864-018-5201-0

Cited by 18 publications

(13 citation statements)

References 56 publications

(75 reference statements)

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“…It has been well evidenced that exosomes are presented in porcine milk, and miRNAs ( Chen et al, 2014 ; Ma et al, 2018 ) and mRNAs ( Chen et al, 2017 ) were identified from these extracellular vesicles. In the present study, we identified a total of 3,275 lncRNAs and 61 circRNAs in PME.…”

Section: Discussionmentioning

confidence: 99%

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes

et al. 2020

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RNA in milk exosomes can be absorbed in the mammalian intestinal tract and function in gene expression regulations. Our previous work demonstrated that porcine milk exosomes (PME) contain large amounts of miRNAs and mRNAs. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are of particular interest, given their key role in diverse biological processes of animals. However, the expression profiles and the potential functions of lncRNAs and circRNAs in PME are still unknown. In the present study, we isolated PME by ultracentrifugation and performed a comprehensive analysis of lncRNA and circRNA in PME by using RNA sequencing. As a result, 2,466 novel lncRNAs, 809 annotated lncRNAs, and 61 circRNAs were identified in PME. The lncRNAs shared similar characteristics with other mammals in terms of length, exon number, and open reading frames. However, lncRNAs showed a higher level compared with mRNAs. Eight lncRNAs and five circRNAs in PME were selected for PCR identification. A functional enrichment analysis on the target genes of lncRNAs indicated that these genes were involved in cellular macromolecule metabolic, RNA metabolic, and immune processes. The circRNAs host genes were enriched in nucleic acid binding and adherence junction. We also evaluated the potential interaction targets between miRNAs and PME lncRNAs or circRNAs, and the results showed that the PME lncRNAs and the circRNAs have a high density of miRNA target sites. The top 20 highly expressed lncRNAs were found to interact with the proliferation-related miRNAs, and the circRNAs potentially targeted many miRNAs that are associated with the intestinal barrier. This study is the first to provide a resource for lncRNA and circRNA research of porcine milk. Moreover, the potential interaction between lncRNA/circRNA and miRNA is revealed. The present study expands our knowledge of non-coding RNAs in milk, and additional research is necessary to confirm their exactly physiological functions.

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Section: Discussionmentioning

confidence: 99%

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes

et al. 2020

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“…Since muscle development was accompanied by the differential expression of related genes in different growth periods and our data were also collected at different time points, we used STEM software, which is widely used to study dynamic biological processes (Guo et al, 2016;Ma et al, 2018;Zhan et al, 2018), to investigate the dynamic genetic changes during breast muscle development. We experimented with various numbers of profiles and found that five profiles (combining with three clusters) best captured the expression patterns of DEGs (Figure 2 and Table S3).…”

Section: Discussionmentioning

confidence: 99%

Dynamic Transcriptomic Analysis of Breast Muscle Development From the Embryonic to Post-hatching Periods in Chickens

Liu

Lei

et al. 2020

Front. Genet.

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Skeletal muscle development and growth are closely associated with efficiency of poultry meat production and its quality. We performed whole transcriptome profiling based on RNA sequencing of breast muscle tissue obtained from Shouguang chickens at embryonic days (E) 12 and 17 to post-hatching days (D) 1, 14, 56, and 98. A total of 9,447 differentially expressed genes (DEGs) were filtered (Q < 0.01, fold change > 2). Time series expression profile clustering analysis identified five significantly different expression profiles that were divided into three clusters. DEGs from cluster I with downregulated pattern were significantly enriched in cell proliferation processes such as cell cycle, mitotic nuclear division, and DNA replication. DEGs from cluster II with upregulated pattern were significantly enriched in metabolic processes such as glycolysis/gluconeogenesis, insulin signaling pathway, calcium signaling pathway, and biosynthesis of amino acids. DEGs from cluster III, with a pattern that increased from E17 to D1 and then decreased from D1 to D14, mainly contributed to lipid metabolism. Therefore, this study may help us explain the mechanisms underlying the phenotype that myofiber hyperplasia occurs predominantly during embryogenesis and hypertrophy occurs mainly after birth at the transcriptional level. Moreover, lipid metabolism may contribute to the early muscle development and growth. These findings add to our knowledge of muscle development in chickens.

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“…The bioinformatics pipeline for miRNA discovery and profiling was carried out as previously described, with some improvements ( Ma et al., 2018 ). To identify the pigeon miRNA, the initial sequence was subjected to a series of stringent filters (such as removing low-quality reads, repeated sequences, and adapter sequences), and the output was called clean data.…”

Section: Methodsmentioning

confidence: 99%

MicroRNA expression profiling reveals potential roles for microRNA in the liver during pigeon (Columba livia) development

et al. 2020

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The liver is the central organ for metabolism and influence the growth and development of the animals. To date, little is known about the microRNA ( miRNA ) in pigeon livers, particularly in different developmental stages. A comprehensive investigation into miRNA transcriptomes in livers across 3 pigeon developmental stages (1, 14, 28 d old) and an adult stage (2 y old) was performed by small RNA sequencing. We identified 312 known miRNA, 433 conserved miRNA, and 192 novel miRNA in pigeon livers. A set of differentially expressed ( DE ) miRNA in livers were screened out during pigeon development. This set of miRNA might be involved in hepatospecific phenotype and liver development. A Short Time-series Expression Miner analysis indicated significant expression variations in DE miRNA during liver development of pigeons. These DE miRNA with different expression patterns might play essential roles in response to growth factor, cell morphogenesis, and gland development, etc. Protein–protein interaction network and Molecular Complex Detection analysis identified several vital target genes (e.g., TNRC6B, FRS2, PTCH1 , etc.) of DE miRNA, which is closely linked in liver development and enriched in PI3K cascade and regulation of growth. Our results expanded the repertoire of pigeon miRNA and may be of help in better understanding the mechanism of squab's rapid development from the perspective of liver development.

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Exploration of exosomal microRNA expression profiles in pigeon ‘Milk’ during the lactation period

Cited by 18 publications

References 56 publications

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes

Exploration of Long Non-coding RNAs and Circular RNAs in Porcine Milk Exosomes

Dynamic Transcriptomic Analysis of Breast Muscle Development From the Embryonic to Post-hatching Periods in Chickens

MicroRNA expression profiling reveals potential roles for microRNA in the liver during pigeon (Columba livia) development

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