Lnc<scp>RNA</scp>net: a comprehensive <i>Sus scrofa</i> lnc<scp>RNA</scp> database

Liang, Guo Hua; Yang, Yuxin; Li, H.; Yu, Huan; Li, X.; Tang, Zhonglin; Li, K.

doi:10.1111/age.12720

Cited by 13 publications

(16 citation statements)

References 20 publications

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“…Therefore, understanding the underlying mechanisms of myogenesis is particularly important. Although thousands of lncRNAs have been identified [38,50], a minority of functional lncRNAs, such as TncRNA [51], lncMD [52], H19 [52][53][54][55][56], and lncIRS1 [57], are involved in mammal myogenesis. MEG3, a differentially expressed lncRNA during postnatal skeletal muscle development in pigs, has four crucial polymorphism sites associated with back fat thickness [39].…”

Section: Discussionmentioning

confidence: 99%

MEG3 Promotes Differentiation of Porcine Satellite Cells by Sponging miR-423-5p to Relieve Inhibiting Effect on SRF

Cheng

Long

Shi

et al. 2020

Cells

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Although thousands of long noncoding RNAs (lncRNAs) have been identified in porcine growth and development, the regulation mechanisms of functional lncRNAs have not been well explored. In this study, using 5′- and 3′-rapid amplification of cDNA ends (RACE) assays, we obtained two different variants of lncRNA maternally expressed gene 3 (MEG3), namely, MEG3 v1 and MEG3 v2, that were both highly expressed in porcine skeletal muscle and in the early stage of the differentiation of porcine satellite cells. Moreover, we identified the core transcript MEG3 v2. Functional analyses showed that MEG3 overexpression could effectively arrest myoblasts in the G1 phase, inhibit DNA replication, and promote myoblast differentiation, whereas MEG3 knockdown resulted in the opposite effects. Interestingly, the expression of serum response factor (SRF), a crucial transcription factor for myogenesis process, remarkably increased and decreased in mRNA and protein levels with the respective overexpression and knockdown of MEG3. Dual luciferase reporter assay showed that MEG3 could attenuate the decrease of luciferase activity of SRF induced by miR-423-5p in a dose-dependent manner. MEG3 overexpression could relieve the inhibitory effect on SRF and myoblast differentiation induced by miR-423-5p. In addition, results of RNA immunoprecipitation analysis suggested that MEG3 could act as a ceRNA for miR-423-5p. Our findings initially established a novel connection among MEG3, miR-423-5p, and SRF in porcine satellite cell differentiation. This novel role of MEG3 may shed new light on understanding of molecular regulation of lncRNA in porcine myogenesis.

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Section: Discussionmentioning

confidence: 99%

MEG3 Promotes Differentiation of Porcine Satellite Cells by Sponging miR-423-5p to Relieve Inhibiting Effect on SRF

Cheng

Long

Shi

et al. 2020

Cells

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“…With the rapid adoption of RNA-seq technologies, thousands of lncRNA in the genome have been discovered in various species, their functions in various biological processes have been demonstrated (Geng et al, 2013; Gong et al, 2015b; Volders et al, 2015; Liang et al, 2018). However, compared with those of human and mouse, the lncRNA resources in pig are relatively limited (Quek et al, 2015; Liang et al, 2018). In this study, we identified a total of 8,166 novel lncRNAs, greatly expanding the genomic information of non-coding RNAs in pigs.…”

Section: Discussionmentioning

confidence: 99%

Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig

Yang

Zhou

et al. 2019

Front. Genet.

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Postnatal development and maturation of pineal gland is a highly dynamic period of tissue remodeling and phenotype maintenance, which is genetically controlled by programmed gene expression regulations. However, limited molecular characterization, particularly regarding long noncoding RNAs (lncRNA), is available for postnatal pineal at a whole transcriptome level. The present study first characterized the comprehensive pineal transcriptome profiles using strand-specific RNA-seq to illustrate the dynamic mRNA/lncRNA expression at three developmental stages (infancy, puberty, and adulthood). The results showed that 21,448 mRNAs and 8,166 novel lncRNAs were expressed in pig postnatal pineal gland. Among these genes, 3,573 mRNAs and 851 lncRNAs, including the 5-hydroxytryptamine receptors, exhibited significant dynamic regulation along maturation process, while the expression of homeobox genes didn’t show significant differences. Gene Ontology analysis revealed that the differentially expressed genes (DEGs) were significantly enriched in ion transport and synaptic transmission, highlighting the critical role of calcium signaling in postnatal pineal development. Additionally, co-expression analysis revealed the DEGs could be grouped into 12 clusters with distinct expression patterns. Many differential lncRNAs were functionally enriched in co-expressed clusters of genes related to ion transport, transcription regulation, DNA binding, and visual perception. Our study first provided an overview of postnatal pineal transcriptome dynamics in pig and demonstrated that dynamic lncRNA regulation of developmental transitions impact pineal physiology.

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“…The porcine translational research database is a manually curated, genomics- and proteomics-based research resource ( 45 ). Lastly, LncRNAnet is a comprehensive Sus scrofa long non-coding RNA database ( 46 ).…”

Section: Resultsmentioning

confidence: 99%

SPDB: a specialized database and web-based analysis platform for swine pathogens

Wang

Liu

et al. 2020

Database

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The rapid and accurate diagnosis of swine diseases is indispensable for reducing their negative impacts on the pork industry. Next-generation sequencing (NGS) is a promising diagnostic tool for swine diseases. To support the application of NGS in the diagnosis of swine disease, we established the Swine Pathogen Database (SPDB). The SPDB represents the first comprehensive and highly specialized database and analysis platform for swine pathogens. The current version features an online genome search tool, which now contains 26 148 genomes of swine, swine pathogens and phylogenetically related species. This database offers a comprehensive bioinformatics analysis pipeline for the identification of 4403 swine pathogens and their related species in clinical samples, based on targeted 16S rRNA gene sequencing and metagenomic NGS data. The SPDB provides a powerful and user-friendly service for veterinarians and researchers to support the applications of NGS in swine disease research. Database URL: http://spdatabase.com:2080/

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LncRNAnet: a comprehensive Sus scrofa lncRNA database

Cited by 13 publications

References 20 publications

MEG3 Promotes Differentiation of Porcine Satellite Cells by Sponging miR-423-5p to Relieve Inhibiting Effect on SRF

MEG3 Promotes Differentiation of Porcine Satellite Cells by Sponging miR-423-5p to Relieve Inhibiting Effect on SRF

Dynamic Transcriptome Analysis Reveals Potential Long Non-coding RNAs Governing Postnatal Pineal Development in Pig

SPDB: a specialized database and web-based analysis platform for swine pathogens

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