Genomic structure, chromosomal localization and expression profile of a porcine long non‐coding RNA isolated from long SAGE libraries

Ren, Hong; Li, Yan Hui; Tang, Zhonglin; Yang, S. L.; Mu, Yulian; Cui, Wentao; Hong, Ai; Du, Lixin; Wang, L; Li, K

doi:10.1111/j.1365-2052.2009.01868.x

Cited by 19 publications

(11 citation statements)

References 28 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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“…Some lncRNA identification efforts have focused on maize [ 30 ] and one of the primary malaria-causing parasite species, Plasmodium falciparum [ 31 ]. For farm animals, work has begun more recently to identify lncRNAs in chickens [ 32 – 37 ], cattle [ 38 – 43 ], pigs [ 33 , 44 – 48 ], sheep [ 49 – 52 ], goats [ 53 – 56 ], and horses [ 57 ]. A recent review of lncRNA in livestock species provides a comprehensive overview of the current progress in the field [ 58 ].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

et al. 2018

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BackgroundNumerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in farm animal species. While previous studies in chickens, cattle, and pigs identified lncRNAs in specific developmental stages or differentially expressed under specific conditions in a limited number of tissues, more comprehensive identification of lncRNAs in these species is needed. The goal of the FAANG Consortium (Functional Annotation of Animal Genomes) is to functionally annotate animal genomes, including the annotation of lncRNAs. As one of the FAANG pilot projects, lncRNAs were identified across eight tissues in two adult male biological replicates from chickens, cattle, and pigs.ResultsComprehensive lncRNA annotations for the chicken, cattle, and pig genomes were generated by utilizing RNA-seq from eight tissue types from two biological replicates per species at the adult developmental stage. A total of 9393 lncRNAs in chickens, 7235 lncRNAs in cattle, and 14,429 lncRNAs in pigs were identified. Including novel isoforms and lncRNAs from novel loci, 5288 novel lncRNAs were identified in chickens, 3732 in cattle, and 4870 in pigs. These transcripts match previously known patterns of lncRNAs, such as generally lower expression levels than mRNAs and higher tissue specificity. An analysis of lncRNA conservation across species identified a set of conserved lncRNAs with potential functions associated with chromatin structure and gene regulation. Tissue-specific lncRNAs were identified. Genes proximal to tissue-specific lncRNAs were enriched for GO terms associated with the tissue of origin, such as leukocyte activation in spleen.ConclusionsLncRNAs were identified in three important farm animal species using eight tissues from adult individuals. About half of the identified lncRNAs were not previously reported in the NCBI annotations for these species. While lncRNAs are less conserved than protein-coding genes, a set of positionally conserved lncRNAs were identified among chickens, cattle, and pigs with potential functions related to chromatin structure and gene regulation. Tissue-specific lncRNAs have potential regulatory functions on genes enriched for tissue-specific GO terms. Future work will include epigenetic data from ChIP-seq experiments to further refine these annotations.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5037-7) contains supplementary material, which is available to authorized users.

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“…The domestic pig (Sus scrofa) is a major animal protein source for human and has significant advantages over other biomedical models [ 20 , 21 ]. Some lncRNAs are known to be associated with complex and economically relevant traits in pigs [ 22 – 24 ]. TncRNA, a porcine lncRNA isolated from long SAGE libraries, may perform complex and critical functions in pig fetal development [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Systematic Identification and Molecular Characteristics of Long Noncoding RNAs in Pig Tissues

Yang

Zhou

Zhu

et al. 2017

BioMed Research International

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Long noncoding RNAs (lncRNAs) are non-protein-coding RNAs that are involved in a variety of biological processes. The pig is an important farm animal and an ideal biomedical model. In this study, we performed a genome-wide scan for lncRNAs in multiple tissue types from pigs. A total of 118 million paired-end 90 nt clean reads were obtained via strand-specific RNA sequencing, 80.4% of which were aligned to the pig reference genome. We developed a stringent bioinformatics pipeline to identify 2,139 high-quality multiexonic lncRNAs. The characteristic analysis revealed that the novel lncRNAs showed relatively shorter transcript length, fewer exons, and lower expression levels in comparison with protein-coding genes (PCGs). The guanine-cytosine (GC) content of the protein-coding exons and introns was significantly higher than that of the lncRNAs. Moreover, the single nucleotide polymorphism (SNP) density of lncRNAs was significantly higher than that of PCGs. Conservation analysis revealed that most lncRNAs were evolutionarily conserved among pigs, humans, and mice, such as CUFF.253988.1, which shares homology with human long noncoding RNA MALAT1. The findings of our study significantly increase the number of known lncRNAs in pigs.

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Genomic structure, chromosomal localization and expression profile of a porcine long non‐coding RNA isolated from long SAGE libraries

Cited by 19 publications

References 28 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

Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species

Systematic Identification and Molecular Characteristics of Long Noncoding RNAs in Pig Tissues

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