Identification of a novel antisense long non-coding RNA PLA2G16-AS that regulates the expression of PLA2G16 in pigs

Liu, Pengliang; Jin, Long; Zhao, Lirui; Long, Keren; Yang, Song; Tang, Qianzi; Ma, Jideng; Wang, Xun; Tang, Guoqing; Jiang, Yanzhi; Zhu, Li; Li, Xuewei; Li, Mingzhou

doi:10.1016/j.gene.2018.05.114

Cited by 12 publications

(14 citation statements)

References 38 publications

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“…Also, lncRNAs can connect to DNA, regulating the transcription process, or bind to proteins affecting their stability ( [38]). Antisense lncRNAs are known to regulate the transcription output RNA in mammals, affecting the mRNA expression [39,40] and stabilizing the mRNA [40]. Some antisense lncRNAs may act on their neighboring coding genes, reducing the complementary mRNA expression [41,42], while others clearly upregulate the expression of the corresponding mRNA and protein [43].…”

Section: Resultsmentioning

confidence: 99%

Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma

Mello

Freitas

Coutinho

et al. 2020

BioMed Research International

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Uterine corpus endometrial carcinoma (UCEC) is the second most common type of gynecological tumor. Several research studies have recently shown the potential of different ncRNAs as biomarkers for prognostics and diagnosis in different types of cancers, including UCEC. Thus, we hypothesized that long noncoding RNAs (lncRNAs) could serve as efficient factors to discriminate solid primary (TP) and normal adjacent (NT) tissues in UCEC with high accuracy. We performed an in silico differential expression analysis comparing TP and NT from a set of samples downloaded from the Cancer Genome Atlas (TCGA) database, targeting highly differentially expressed lncRNAs that could potentially serve as gene expression markers. All analyses were performed in R software. The receiver operator characteristics (ROC) analyses and both supervised and unsupervised machine learning indicated a set of 14 lncRNAs that may serve as biomarkers for UCEC. Functions and putative pathways were assessed through a coexpression network and target enrichment analysis.

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Section: Resultsmentioning

confidence: 99%

Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma

Mello

Freitas

Coutinho

et al. 2020

BioMed Research International

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“…For example, a NAT targeting the mouse gene encoding ubiquitin carboxy-terminal hydrolase L1 which is involved in brain function and neurodegenerative diseases, has been showed to regulate the synthesis of corresponding protein at the post-transcriptional level [12]. A phospholipase A2 group XVI locus (PLA2G16) NAT transcribed from porcine PLA2G16 promotes PLA2G16 transcription and might stimulate adipogenesis in pigs [31]. We previously identified a GHR-AS that enhanced GHR mRNA stability by forming an RNA-RNA duplex at the last exon of GHR mRNA in chicken LMH cells [16].…”

Section: Discussionmentioning

confidence: 99%

“…Antisense RNAs reportedly form duplexes with their sense mRNA partners [12,13,16,31,32], and these duplexes regulate the stability of the coding mRNA and thus, the protein level [2,33]. To determine whether GHR-AS-EST forms a duplex with GHR sense transcripts, including GHR mRNA, GHBP and 0.7-kb GHR, we carrried out an endogenous RNase protection assay using RNA extracted from liver and leg muscle tissues, LMH cells, and primary myoblasts.…”

Section: Ghr-as-est Upregulates Ghbp Expression By Forming An Rna Dupmentioning

confidence: 99%

“…To detect the RNA duplex formed by GHR sense and antisense RNAs, endogenous ribonuclease protection assay was performed as previously described [16,31,40], with minor modifications, using total RNA from chicken liver and leg muscle tissues, LMH cells and primary myoblasts. To remove genomic DNA and single-strand RNA, the total RNA was treated with DNase I (TaKaRa, Otsu, Japan) at 37°C for 30 min and then digested with RNase A (20 ng/μL; TaKaRa) 37°C for 1 h. Following the RNase A protection assay, we used RT-PCR to detect duplex formation.…”

Section: Endogenous Ribonuclease Protection Assaymentioning

confidence: 99%

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Identiﬁcation of a novel antisense RNA that regulates growth hormone receptor expression in chickens

et al. 2019

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Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules of gene expression. However, studies on NATs in the chicken are relatively rare. We identiﬁed a novel antisense transcript in the chicken, designated GHR-AS-EST , transcribed from the growth hormone receptor ( GHR ) locus, which encodes a well-known regulatory molecule of muscle development and fat deposition. GHR-AS-EST is predominantly expressed in the chicken liver and muscle tissues. GHR-AS-EST sequence conservation among vertebrates is weak. GHR-AS-EST forms an RNA–RNA duplex with GHBP to increase its stability, and regulates the expression of GHR sense transcripts at both the mRNA and protein levels. Further, GHR-AS-EST promotes cell proliferation by stimulating the expression of signaling factors in the JAK2/STAT pathway, and contributes to fat deposition via downregulating the expression of signaling factors in the JAK2/SOCS pathway in LMH hepatocellular carcinoma cells. We expect that the discovery of a NAT for a regulatory gene associated with cell proliferation and lipolysis will further our understanding of the molecular regulation of both muscle development and fat deposition.

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“…Coexpression network analysis identified potential lncRNAs (including MSTRG.131380 and MSTRG.62128) related to adipogenesis, which might contribute to the phenotypic changes in adipocytes at different stages of differentiation (Liu et al, 2018c). More recently, an antisense lncRNA PLA2G16-AS, transcribed from the phospholipase A2 group XVI locus (PLA2G16) in the porcine genome, was shown to be dominantly expressed in porcine adipose tissue (Liu et al, 2018b). By forming an RNA-RNA duplex, PLA2G16-AS stabilizes PLA2G16 mRNA and increases PLA2G16 expression at the RNA level.…”

Section: Pigmentioning

confidence: 99%

GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: Long noncoding RNAs in adipogenesis and adipose development of meat animals12

Wei

Zhang

et al. 2019

Journal of Animal Science

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Sequencing technology, especially next-generation RNA sequencing, has greatly facilitated the identification and annotation of long noncoding RNAs (lncRNAs). In mammals, a large number of lncRNAs have been identified, which regulate various biological processes. An increasing number of lncRNAs have been identified which could function as key regulators of adipogenesis (adipocyte formation), a key step of the development of adipose tissue. Because proper adipose tissue development is a key factor affecting animal growth efficiency, lean/fat ratio, and meat quality, summarizing the roles and recent advances of lncRNAs in adipogenesis is needed in order to develop strategies to effectively manage fat deposition. In this review, we updated lncRNAs contributed to the regulation of adipogenesis, focusing on their roles in fat development of farm animals.

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Identification of a novel antisense long non-coding RNA PLA2G16-AS that regulates the expression of PLA2G16 in pigs

Cited by 12 publications

References 38 publications

Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma

Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma

Identiﬁcation of a novel antisense RNA that regulates growth hormone receptor expression in chickens

GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: Long noncoding RNAs in adipogenesis and adipose development of meat animals12

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