Long non-coding RNAs and mRNAs profiling during spleen development in pig

Che, Tiandong; Li, Diyan; Jin, Long; Fu, Yuhua; Liu, Yingkai; Liu, Pengliang; Wang, Yixin; Tang, Qianzi; Ma, Jideng; Wang, Xun; Jiang, Anan; Li, Xuewei; Li, Mingzhou

doi:10.1371/journal.pone.0193552

Cited by 18 publications

(16 citation statements)

References 48 publications

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“…FEELnc, an alignment-free program that accurately annotates lncRNAs based on a random forest model trained with general features, and BLASTX (McGinnis and Madden, 2004) were used to identify and classify lncRNAs in this study. FEELnc (Wucher et al, 2017) has been shown to achieve similar or better classification performance on GENCODE (Harrow et al, 2012) and NONCODE (Bu et al, 2011) data sets when compared with five programs [PhyloCSF (Lin et al, 2011), CPC (Kong et al, 2007), CPAT (Wang et al, 2013), PLEK (Li et al, 2014), and CNCI (Sun et al, 2013)], and has previously been used to identify lncRNAs (Che et al, 2018; Donato et al, 2018; Wang et al, 2018). In this study, 2,623 novel lncRNAs were identified, of which 1,484 were classified.…”

Section: Discussionmentioning

confidence: 99%

Differentiation of Long Non-Coding RNA and mRNA Expression Profiles in Male and Female Aedes albopictus

Dong

et al. 2019

Front. Genet.

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The Asia tiger mosquito (Aedes albopictus) is an important vector of arboviruses, and females can transmit pathogens such as the dengue, zika, and chikungunya viruses. Understanding sex-related differences in this mosquito is fundamental for vector control. However, there are no reports of systematic characterization of long non-coding RNAs (lncRNAs) in male and female Ae. albopictus. To investigate the roles of coding and non-coding RNAs in both sexes of Ae. albopictus, RNA sequencing was performed on male and female samples. The results showed 305 differentially expressed protein-coding genes (DEGs) between males and females, of which 198 were highly expressed in males and 125 were highly expressed in females. Sex-associated gene ontology terms were enriched. Analysis with the FEELnc software identified 2,623 novel lncRNAs, of which 26 showed male high expression and 11 showed female high expression. Quantitative real-time PCR of randomly selected DEGs and lncRNAs supported the validity of the RNA sequencing results. Knocking down male high-expressed gene AALF000433 in male adults reduced the egg hatching rate. This study provides valuable data on sex-specific expression of protein-coding genes and lncRNAs in adult Ae. albopictus, which will guide further studies aimed at understanding sex development and determination mechanisms in this species.

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Section: Discussionmentioning

confidence: 99%

Differentiation of Long Non-Coding RNA and mRNA Expression Profiles in Male and Female Aedes albopictus

Dong

et al. 2019

Front. Genet.

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“…A large number of lincRNAs are present in the mammalian genomes (Carninci et al, 2005; Cabili et al, 2011). A small number of lincRNAs have been revealed in pigs; these lincRNAs play a key role in biological processes (Li et al, 2016; Che et al, 2018). In Zou’s study, some lincRNAs in longissimus dorsi muscle of Laiwu pigs may be involved in intramuscular fat-related biological processes, such as oxidative metabolism, lipid metabolism, and adipogenesis (Zou et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs

Shi

Chen

et al. 2019

Front. Genet.

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An increasing number of studies have shown that long intergenic non-coding RNAs (lincRNAs) are a very important class of non-coding RNAs that plays a vital role in many biological processes. Adipose tissue is an important place for storing energy, but few studies on lincRNAs were related to pig subcutaneous fat development. Here, we used published RNA-seq data from subcutaneous adipose tissue of Italian Large White pigs and identified 252 putative lincRNAs, wherein 34 were unannotated. These lincRNAs had relatively shorter length, lower number of exons, and lower expression level compared with protein-coding transcripts. Gene ontology and pathway analysis indicated that the adjacent genes of lincRNAs were involved in lipid metabolism. In addition, differentially expressed lincRNAs (DELs) between low and high backfat thickness pigs were identified. Through the detection of quantitative trait locus (QTL), DELs were mainly located in QTLs related to adipose development. Based on the expression correlation of DEL genes and their differentially expressed potential target genes, we constructed a co-expression network and a potential pathway of DEL’s effect on lipid metabolism. Our study identified and analyzed lincRNAs in subcutaneous adipose tissue, and results suggested that lincRNAs may be involved in the regulation of subcutaneous fat development. Our findings provided new insights into the biological function of porcine lincRNAs.

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“…lncRNAs have been identified in numerous porcine tissues, such as the skeletal muscles [38], lung [39], and spleen tissues [40], and play an important role in major mechanisms of gene expression, regulation, and cellular development. Despite the biological functions of lncRNAs, it is not yet clear whether lncRNAs are involved in the regulation of oxidative stress in the liver of piglets.…”

Section: Discussionmentioning

confidence: 99%

Diquat Determines a Deregulation of lncRNA and mRNA Expression in the Liver of Postweaned Piglets

Wang

Yang

et al. 2019

Oxidative Medicine and Cellular Longevity

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Oxidative stress is detrimental to animals and can depress the growth performance and regulate the gene expression of animals. However, it remains unclear how oxidative stress regulates the expression of long noncoding RNAs (lncRNAs) and mRNAs. Therefore, the purpose of this article was to explore the profiles of lncRNAs and mRNAs in the liver of piglets under oxidative stress. Here, we constructed a piglet oxidative stress model induced by diquat and evaluated the effects of oxidative stress on the growth performance and antioxidant enzyme activity of piglets. We also used RNA-Seq to examine the global expression of lncRNAs and mRNAs in piglets under oxidative stress. The targets of lncRNAs and mRNAs were enriched in gene ontology (GO) terms and signaling pathways. The results show that the growth performance and activities of antioxidant enzymes were decreased in piglets under oxidative stress. Moreover, eight lncRNAs (6 upregulated and 2 downregulated) and 30 mRNAs (8 upregulated and 22 downregulated) were differentially expressed in the oxidative stress group of piglets compared to the negative control group. According to biological processes in enriched GO terms, the oxoacid metabolic process, intramolecular oxidoreductase activity, and oxidation-reduction process play important roles in oxidative stress. Pathway analysis showed that the signaling pathways involved in insulin and glucose metabolism had a close relationship with oxidative stress. Further in vitro experiments showed that the expression of the upregulated gene GNMT was significantly increased in primary porcine hepatocytes after diquat stimulation. In contrast, the level of the downregulated gene GCK was significantly decreased at 12 h in primary porcine hepatocytes after diquat stimulation. Our results expand our knowledge of the lncRNAs and mRNAs transcribed in the livers of piglets under oxidative stress and provide a basis for future research on the molecular mechanisms mediating oxidative stress and tissue damage.

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Long non-coding RNAs and mRNAs profiling during spleen development in pig

Cited by 18 publications

References 48 publications

Differentiation of Long Non-Coding RNA and mRNA Expression Profiles in Male and Female Aedes albopictus

Differentiation of Long Non-Coding RNA and mRNA Expression Profiles in Male and Female Aedes albopictus

Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs

Diquat Determines a Deregulation of lncRNA and mRNA Expression in the Liver of Postweaned Piglets

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