LncRNA profiling of skeletal muscles in Large White pigs and Mashen pigs during development1,2

Gao, Pengfei; Guo, Xiaohong; Du, Min; Cao, Guo Qing; Yang, Qinping; Pu, Zhening; Wang, Z. Y.; Zhang, Q.; Li, M.; Jin, Y. S.; Wang, X. J.; Liu, H.

doi:10.2527/jas2016.1297

Cited by 24 publications

(16 citation statements)

References 49 publications

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“…Interestingly, roughly, 2% of the mammalian genome are genes encoding proteins, suggesting that non-coding RNA constitutes the majority of the mammalian transcriptome [ 11 ], which do not code for proteins but serve regulatory roles [ 12 ]. Regarding their length, lncRNAs ranged in size from 200 bp to 100 kb, and have been involved in many biological processes and diseases such as lymphoma in both humans and dogs [ 13 ], prostate cancer [ 14 ], skeletal muscle development in pig [ 15 ] etc. However, the regulatory roles and functions of lncRNAs in the ETEC-F4ac adhesion phenotype in small intestine epithelial cells in piglets remain unclear.…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Augustino

Liu

et al. 2020

BMC Genomics

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Background Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which do not code for proteins, have been widely investigated in various physiological and pathological contexts by high-throughput sequencing techniques and bioinformatics analysis. However, little is known about the regulatory mechanisms by which lncRNAs regulate genes that are associated with Enterotoxigenic Escherichia coli F4 fimbriae (ETEC-F4ac) adhesion phenotype in small intestine epithelial cells of Large White piglets. To address this, we used RNA sequencing to profile lncRNAs and mRNAs of small intestine epithelial cells in Large White piglets differing in their ETEC-F4 adhesion phenotypes and ITGB5 genotypes. Eight male piglets were used in this study and were divided into two groups on the basis of their adhesion phenotype and ITGB5 genotypes, a candidate gene for F4ac receptor. Non-adhesive group (n = 4) with CC genotype and adhesive group (n = 4) with TT genotype. Results In total, 78 differentially expressed lncRNAs (DE-lncRNA) and 223 differentially expressed mRNAs (log2 |FC| > 1, P < 0.05) were identified in the comparison of non-adhesive vs. adhesive small intestine epithelial cells. Furthermore, cis- and trans-regulatory target genes of DE-lncRNAs were identified, then interaction networks of lncRNAs and their cis- and trans-target differentially expressed genes (DEGs) were constructed separately. A total of 194 cis-targets were involved in the lncRNAs-cis genes interaction network and 61 trans-targets, were involved in lncRNA-trans gene interaction network that we constructed. We determined that cis-target genes were involved in alcoholism, systemic lupus erythematosus, viral carcinogenesis and malaria. Whereas trans-target DEGs were engaged in three important pathways related to the ETEC-F4 adhesion phenotype namely cGMP-PKG signaling pathway, focal adhesion, and adherens junction. The trans-target DEGs which directly involved in these pathways are KCNMB1 in cGMP-PKG signaling pathway, GRB2 in focal adhesion pathway and ACTN4 in focal adhesion and adherens junction pathways. Conclusion The findings of the current study provides an insight into biological functions and epigenetic regulatory mechanism of lncRNAs on porcine small intestine epithelial cells adhesion to ETEC-F4-ac and piglets’ diarrhea susceptibility/resistance.

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Section: Discussionmentioning

confidence: 99%

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Augustino

Liu

et al. 2020

BMC Genomics

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“…Furthermore, many viruses, such as influenza virus, enterovirus, and porcine reproductive and respiratory syndrome virus (PRRSV), can alter the expression of lncRNAs (Winterling et al, 2014; Yin et al, 2013; Zeng et al, 2018). Dysregulation of lncRNAs may also lead to diseases in pigs (Gao et al, 2017; Zhou et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing

Fang

Yang

Wang

et al. 2019

PeerJ

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Porcine circovirus-associated disease (PCVAD), which is induced by porcine circovirus type 2 (PCV2), is responsible for severe economic losses. Recently, the role of noncoding RNAs, and in particular microRNAs, in PCV2 infection has received great attention. However, the role of long noncoding RNA (lncRNA) in PCV2 infection is unclear. Here, for the first time, we describe the expression profiles of lncRNAs in an intestinal porcine epithelial cell line (IPEC-J2) after PCV2 infection, and analyze the features of differently expressed lncRNAs and their potential target genes. After strict filtering of approximately 150 million reads, we identified 13,520 lncRNAs, including 199 lncRNAs that were differentially expressed in non-infected and PCV2-infected cells. Furthermore, trans analysis found lncRNA-regulated target genes enriched for specific Gene Ontology terms (P < 0.05), such as DNA binding, RNA binding, and transcription factor activity, which are closely associated with PCV2 infection. In addition, we analyzed the predicted target genes of differentially expressed lncRNAs, including SOD2, TNFAIP3, and ARG1, all of which are involved in infectious diseases. Our study identifies many candidate lncRNAs involved in PCV2 infection and provides new insight into the mechanisms underlying the pathogenesis of PCVAD.

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“…LncRNA and other small ncRNAs, such as miRNA, piRNA and siRNA, have been explored the effect on growth development, reproduction, metabolism and diseases research via participation in regulating transcription levels, post-transcription levels and protein levels. Some research has investigated the role of lncRNA on growth development in muscles [41], heart [42], brain [43], spinal cord neuron [44] and cancer cells [45]. In addition, hypothalamic-pituitary-gonadal (HPG) axis plays an important role in reproduction, and there are many studies focus on hypothalamus [46,47], testis [48] and ovary [49] during different development stages.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation

Yang

Wang

et al. 2020

Genes

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Long noncoding RNA (lncRNA) plays a crucial role in the hypothalamic-pituitary-testis (HPT) axis associated with sheep reproduction. The pituitary plays a connecting role in the HPT axis. However, little is known of their expression pattern and potential roles in the pituitary gland. To explore the potential lncRNAs that regulate the male sheep pituitary development and sexual maturation, we constructed immature and mature sheep pituitary cDNA libraries (three-month-old, TM, and nine-month-old, NM, respectively, n = 3) for lncRNA and mRNA high-throughput sequencing. Firstly, the expression of lncRNA and mRNA were comparatively analyzed. 2417 known lncRNAs and 1256 new lncRNAs were identified. Then, 193 differentially expressed (DE) lncRNAs and 1407 DE mRNAs were found in the pituitary between the two groups. Moreover, mRNA-lncRNA interaction network was constructed according to the target gene prediction of lncRNA and functional enrichment analysis. Five candidate lncRNAs and their targeted genes HSD17B12, DCBLD2, PDPK1, GPX3 and DLL1 that enriched in growth and reproduction related pathways were further filtered. Lastly, the interaction of candidate lncRNA TCONS_00066406 and its targeted gene HSD17B12 were validated in in vitro of sheep pituitary cells. Our study provided a systematic presentation of lncRNAs and mRNAs in male sheep pituitary, which revealed the potential role of lncRNA in male reproduction.

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LncRNA profiling of skeletal muscles in Large White pigs and Mashen pigs during development1,2

Cited by 24 publications

References 49 publications

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

Genome-wide analysis of long non-coding RNA expression profile in porcine circovirus 2-infected intestinal porcine epithelial cell line by RNA sequencing

Genome-Wide Analysis and Function Prediction of Long Noncoding RNAs in Sheep Pituitary Gland Associated with Sexual Maturation

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