Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds

Wang, Jing; Ren, Qiaoling; Hua, Liushuai; Chen, Junfeng; Zhang, Jiaqing; Bai, Hongjie; Li, Haili; Xu, Bin; Shi, Zhihai; Cao, Hai Xia; Xing, Baosong; X, Bai

doi:10.3390/ijms20051107

Cited by 93 publications

(85 citation statements)

References 68 publications

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“…More and more studies revealed that ncRNAs played regulatory roles by ceRNA network on the basis of ceRNA hypothesis [21], and utilizing ceRNA network analysis have identified a lot of regulatory factors including lncRNAs, miRNAs and cirRNAs associated with some animal economic traits such as hair follicle cycle of cashmere goat and poultry meat quality [27,47]. Although some studies also have paid attention on ceRNA regulatory mechanism in muscle of pig [2,48], little information is available in ceRNA regulatory pork quality formation. In this study, fat-type SS with higher pork quality and lean-type YY with faster growth as two typical pig breeds were used to investigate the regulatory mechanism of pork quality formation by transcriptome analysis including screening differentially expressed RNA and constructing ceRNA network.…”

Section: Discussionmentioning

confidence: 99%

“…With the rapid progression of sequencing technology in recent years, advances were produced in regulatory mechanism of pork quality formation, especially non-coding RNAs (ncRNA) [2,14,15]. For example, miR-23a was identified to associate with the composite of slow myosin heavy chain isoforms [16], and miR-17-5p was found to reduce preadipocyte differentiation by inhibiting some targets such as FABP4 and PPARG [17].…”

mentioning

confidence: 99%

“…Wang et al found that lnc_000679-miR221-5p-WNT3, lnc_000181-miR34a-GATA3 and lnc_000344-miR214-3p-SMAD3 were identified to play roles in hair follicle biology of Cashmere goat [27]. It is worth mentioning that a recent study has investigated the differences in muscle traits between Chinese indigenous Huainan pigs and Western commercial DLY crossbreed pigs, and identified some differentially expressed RNAs and regulatory factors such as miR423-5p and miR-874 [2]. Despite this, little ceRNA knowledge is available in pork quality formation, and more studies are required.…”

mentioning

confidence: 99%

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Competitive endogenous RNA network reveals that miR-1343 play key regulatory roles in longissimus dorsi muscle between Saba and Yorkshire pigs

Hu¹,

Chen²,

Wang³

et al. 2019

Preprint

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Background Pork quality is an important economic trait in pig industry, and increasing data shows that Chinese indigenous and Western commercial pig breeds have significant differences in pork quality. However, the molecular regulatory mechanism of pork quality formation is still unclear. The aim of this study was to explore the transcriptional regulation mechanism of pork quality formation of Chinese Saba pig (SS) and Western Yorkshire pig (YY) breeds. Results A total of 31 DEmiRNAs, 902 DEmRNAs, 47 DElncRNAs and 198 DEcircRNAs were identified in longissimus dorsi muscles between SSs and YYs. On the basis of differentially expressed RNAs, two ceRNA networks including lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA were established, and two ceRNA networks showed that miR-1343 had the most links in two ceRNA networks, which demonstrated that miR-1343 might play key regulatory roles in longissimus dorsi muscle formation between SS and YY breeds. Conclusions The present study identified miR-1343 as key regulatory factor in pig longissimus dorsi muscle formation by ceRNA networks, which provides novel insights into molecular regulatory mechanism of pork quality formation between fat-type and lean-type pig breeds.

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Competitive endogenous RNA network reveals that miR-1343 play key regulatory roles in longissimus dorsi muscle between Saba and Yorkshire pigs

Hu¹,

Chen²,

Wang³

et al. 2019

Preprint

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“…Currently, ceRNET is mainly used to solve human cancer treatment, among which the typical representative is the construction of PTEN's ceRNET. In addition, ceRNET has also been applied to explore biological characteristics in animal and plant research (Qiu et al, 2018;Bai et al, 2019;He et al, 2019;Li et al, 2019;Wang et al, 2019a). It is reasonable to hypothesized that ceRNET would be an exactly effective methods to reflect the complete and accurate regulate process of the antler rapidly development.…”

Section: Introductionmentioning

confidence: 99%

Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development

Han

Wang

et al. 2020

Front. Genet.

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Deer antler is the only completely regenerable organ in mammals. During the rapid growth period, the antler proliferates even faster than cancerous tissue growth. However, the proliferation and development of antler have been in a stable and controllable growth cycle. In this study, we analyzed the time series expression data of nine samples from mesenchyme layer in three male sika deer in the early period of the antler with a saddle-like appearance (30 days), the rapid growth period of the antler with two branches (60 days), and the final period of the antler with three branches (90 days). Whole Transcriptome sequencing results show that in the 30 d versus 60 d group, 1,464 genes, 85 long noncoding RNAs (lncRNAs), and 61 miRNAs were identified as differentially expressed; 1,748 genes, 138 lncRNAs, and 78 miRNAs were identified as differentially expressed in 30d versus 90d group; and 816 differentially expressed genes (DEGs), 49 differentially expressed lncRNAs (DE lncRNAs), and 24 differentially expressed miRNA (DE miRNAs) were identified in 60d versus 90d group. A total of 182 miRNA-mRNA interaction pairs and 89 miRNA-lncRNA interaction pairs were screened from DEGs, DE miRNAs, and DE lncRNAs to construct the ceRNA regulatory network (ceRNET). In summary, we identified candidate mRNAs, miRNAs and lncRNAs that regulate the development of antler tip. It may lay the foundation for further investigating the molecular mechanism of antler rapid growth and development.

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“…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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Comprehensive Analysis of Differentially Expressed mRNA, lncRNA and circRNA and Their ceRNA Networks in the Longissimus Dorsi Muscle of Two Different Pig Breeds

Cited by 93 publications

References 68 publications

Competitive endogenous RNA network reveals that miR-1343 play key regulatory roles in longissimus dorsi muscle between Saba and Yorkshire pigs

Competitive endogenous RNA network reveals that miR-1343 play key regulatory roles in longissimus dorsi muscle between Saba and Yorkshire pigs

Whole Transcriptome Analysis of Mesenchyme Tissue in Sika Deer Antler Revealed the CeRNAs Regulatory Network Associated With Antler Development

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

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