Identification and Expression Profiling of miRNAome in Goat longissimus dorsi Muscle from Prenatal Stages to a Neonatal Stage

Guo, Jiazhong; Zhao, Wei; Zhan, Siyuan; Li, Li; Zhong, Tao; Wang, Linjie; Dong, Yao; Zhang, Hongping

doi:10.1371/journal.pone.0165764

Cited by 25 publications

(27 citation statements)

References 54 publications

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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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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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“…Overexpression of miR3405p is known to reduce the expression of Nrf2 protein in the postexercise skeletal muscle of mice [83]. miR-424 and miR-542-3p are among the most abundant miRNAs in goat muscles [20]. Meanwhile, Garros et al stated that miR-542 overexpression caused muscle wasting in mice, and reduced mitochondrial function [84].…”

Section: Discussionmentioning

confidence: 99%

“…Except for linear transcripts like miRNA, lncRNAs, and mRNAs, numerous circular RNAs (circRNAs) responsible for skeletal muscle development have been identi ed through the introduction of high throughput sequencing technology [19][20][21]. circRNAs are newly discovered non-coding RNA molecules with a closed-loop structure and acting as gene regulators in most organisms [22,23].…”

Section: Introductionmentioning

confidence: 99%

CDR1as related miRNA-mRNA networks in differentiating goat skeletal muscle satellite cells

Kyei

Liu

et al. 2020

Preprint

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Background: Myogenesis is a complex process controlled by several coding and non-coding RNAs (ncRNAs) such as circular RNAs (circRNAs) that well-known function as endogenous microRNAs (miRNAs) sponges. Over the past few years, numerous circRNAs have been known and their roles in biological processes have begun to be understood. Cerebellar Degeneration-Related protein 1 antisense (CDR1as), the most spotlighted circRNA as miR-7 sponge that has been blooming circRNAs’ research for a decade, and can potentially sponge several miRNAs in disease and muscle physiology. Nevertheless, the linear-RNAs-differed character that the acute interventions for circRNAs do not affect miRNAs levels, and has retarded the transcriptome-wide discovery of miRNAs sponged by. Therefore, the purpose of this study was to provide the transcriptomic effect of CDR1as during muscle differentiation.Methods: siCDR1as and siDICER1 were transfected into goat skeletal muscle satellite cells (SMSCs). RNA-seq technology and bioinformatics tools were used to analyze genes that are deregulated by siCDR1as and siDICER1. quantitative PCR was used to verify the expression levels of the differentially expressed mRNAs and miRNAs. Results: Here, to systematically identify miRNAs targeting CDR1as, we employed the critical enzyme DICER1 that governs the biogenesis of miRNAs. The deficiency of either DICER1 or CDR1as inhibited myogenic differentiation of SMSCs, and knockdown of DICER1 decreased the expression of CDR1as. Moreover, we screened for the targeted messenger RNAs (mRNAs) and miRNAs in SMSCs transfected with siDICER1 or siCDR1as respectively and found out that some well-known muscle-related pathways such as phosphoinositide 3-kinase (PI3K)-AKT signaling pathway, Rap1 signaling pathway, and MAPK signaling pathway were enriched in all groups. Further, regarding the miRNAs identified in siDICER1 and siCDR1as together with the sequence complementary information, we identified 11 miRNAs including miR-1, miR-206, and miR-27a-5p which are more likely to be novel targets for CDR1as. Conclusion: In summary, our study provides a perspective on the potential functions and relationship between CDR1as and DICER1 during muscle development.

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“…The clean reads were aligned with Silva, GtRNAdb, Rfam, and Repbase databases, respectively, to filter rRNA, tRNA, snRNA, snoRNA, other ncRNA, and repeat sequences using the Bowtie v.1.1.0 software ( Langmead et al, 2009 ). The derived reads were used to detect known goat miRNAs by aligned to the goat miRNA precursors present in the miRBase v21 2 as described in our previous study ( Guo et al, 2016a ). Clear reads were also mapped to the goat reference genome (CHIR_1.0, NCBI) using the Bowtie aligner.…”

Section: Methodsmentioning

confidence: 99%

Identification and Characterization of MicroRNAs in the Goat (Capra hircus) Rumen during Embryonic Development

Zhong

Xiao

et al. 2017

Front. Genet.

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The rumen is an important digestive organ in ruminants. Numerous regulatory factors including microRNAs (miRNAs) are involved in embryonic organ development. In the present study, miRNAs expressed in the rumens of goats (Capra hircus) and their potential roles in the pathways involved in rumen development were identified using high-throughput sequencing. Histological morphology revealed a distinct difference in each layer of rumen during the period from embryonic day 60 (E60) to embryonic day 135 (E135). We determined the expression profiles of miRNAs in the goat rumen, and identified 423 known miRNAs and 559 potentially novel miRNAs in the E60 and E135 embryonic rumen, respectively. Bioinformatics analysis annotated the 42 differentially expressed miRNAs and the top 10 most highly expressed miRNAs of the two libraries to 48 and 38 gene ontology categories, as well as to 168 and 71 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. The expression patterns of eight randomly selected miRNAs were validated by stem-loop quantitative reverse transcription PCR, suggesting that the sequencing data were reliable. We profiled the genome-wide expression of rumen-expressed miRNAs at different prenatal stages of rumen tissues, revealing that a subset of miRNAs might play important roles in the formation of the rumen layers. Taken together, these findings will aid the investigation of dominant rumen-related miRNA sets and help understand the genetic control of rumen development in goats.

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Identification and Expression Profiling of miRNAome in Goat longissimus dorsi Muscle from Prenatal Stages to a Neonatal Stage

Cited by 25 publications

References 54 publications

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

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

CDR1as related miRNA-mRNA networks in differentiating goat skeletal muscle satellite cells

Identification and Characterization of MicroRNAs in the Goat (Capra hircus) Rumen during Embryonic Development

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