Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development

Zhao, Weimin; Mu, Yulian; Ma, Lei; Wang, Chen; Tang, Zhonglin; Yang, Shulin; Zhou, Rong; Hu, Xiaoju; Li, Menghua; Li, Kui

doi:10.1038/srep08957

Cited by 99 publications

(112 citation statements)

References 60 publications

(89 reference statements)

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“…2 Additionally, lncRNAs are more tissue-specific than protein-coding RNAs, with expression levels that not only vary from tissue to tissue, but also change in different parts of the same tissue. [3][4][5][6] Moreover, lncRNA expression exhibits strong temporal and spatial specificity, and the expression of the same lncRNA differs considerably during different developmental stages in the same | 4723 XU et al tissue or organ. [7][8][9][10] Abnormal lncRNA expression is closely related to many diseases, including cancer.…”

Section: Introductionmentioning

confidence: 99%

Improved characterization of the relationship between long intergenic non‐coding RNA Linc00152 and the occurrence and development of malignancies

Guo

Jiang

et al. 2019

Cancer Medicine

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Linc00152, located on chromosome 2p11.2, is a long intergenic non‐coding RNA molecule with 828 nucleotides that is highly expressed in many types of human tumor tissues, especially in malignant tumors of the digestive system. Linc00152 promotes the occurrence and development of tumors by increasing tumor cell proliferation, invasion, metastasis, and apoptosis. Additionally, linc00152 contributes to the carcinogenesis of several cancers, including gastric cancer, liver cancer, hepatocellular carcinoma, gallbladder cancer, clear cell renal cell carcinoma, and colorectal cancer, by disturbing various signaling pathways (eg PI3K/AKT, mTOR, IL‐1, and NOTCH 1 signaling pathways). High linc00152 expression levels are associated with chemoresistance as well as poor prognosis and shorter survival. Continual advances made in the relevant research have indicated that linc00152 may be useful as a new tumor molecular biomarker, applicable for tumor diagnosis, targeted therapy, and prognosis assessment. This review summarizes the progress in the research into the relationship between linc00152 and the occurrence and development of malignancies based on molecular functions, regulatory mechanisms, and clinical applications.

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Section: Introductionmentioning

confidence: 99%

Improved characterization of the relationship between long intergenic non‐coding RNA Linc00152 and the occurrence and development of malignancies

Guo

Jiang

et al. 2019

Cancer Medicine

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“…Widely used reference genes for expression analyses include GAPDH , ACTB , and HPRT (Blaha et al, 2015; Boosani, Dhar & Agrawal, 2015; Wang et al, 2016; Zhang et al, 2016b; Zhao et al, 2015). These genes are reported to have consistent expression levels under various conditions such as different organs and different developmental stages (Tang et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs

Niu

Yang

Zhang

et al. 2016

PeerJ

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The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB) in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods). We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases.

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“…; Zhao et al. ). It has been also demonstrated that some lncRNA encode peptides with muscle‐specific expression which affect muscle contractility (Anderson et al.…”

Section: Discussionmentioning

confidence: 98%

“…The 2310014F06Rik is a bidirectional promoter long noncoding RNA (lncRNA) gene preferentially expressed in skeletal muscle. Several lncRNAs have been implicated in gene regulation during skeletal muscle differentiation (Li et al 2012;Lu et al 2013;Zhao et al 2015). It has been also demonstrated that some lncRNA encode peptides with muscle-specific expression which affect muscle contractility (Anderson et al 2015;Nelson et al 2016).…”

Section: Discussionmentioning

confidence: 99%

Replication and discovery of musculoskeletal QTLs in LG/J and SM/J advanced intercross lines

et al. 2018

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The genetics underlying variation in health-related musculoskeletal phenotypes can be investigated in a mouse model. Quantitative trait loci (QTLs) affecting musculoskeletal traits in the LG/J and SM/J strain lineage remain to be refined and corroborated. The aim of this study was to map muscle and bone traits in males (n = 506) of the 50th filial generation of advanced intercross lines (LG/SM AIL) derived from the two strains. Genetic contribution to variation in all musculoskeletal traits was confirmed; the SNP heritability of muscle mass ranged between 0.46 and 0.56; and the SNP heritability of tibia length was 0.40. We used two analytical software, GEMMA and QTLRel, to map the underlying QTLs. GEMMA required substantially less computation and recovered all the QTLs identified by QTLRel. Seven significant QTLs were identified for muscle weight (Chr 1, 7, 11, 12, 13, 15, and 16), and two for tibia length, (Chr 1 and 13). Each QTL explained 4-5% of phenotypic variation. One muscle and both bone loci replicated previous findings; the remaining six were novel. Positional candidates for the replicated QTLs were prioritized based on in silico analyses and gene expression in muscle tissue. In summary, we replicated existing QTLs and identified novel QTLs affecting muscle weight, and replicated bone length QTLs in LG/SM AIL males. Heritability estimates substantially exceed the cumulative effect of the QTLs, hence a richer genetic architecture contributing to muscle and bone variability could be uncovered with a larger sample size.

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Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development

Cited by 99 publications

References 60 publications

Improved characterization of the relationship between long intergenic non‐coding RNA Linc00152 and the occurrence and development of malignancies

Improved characterization of the relationship between long intergenic non‐coding RNA Linc00152 and the occurrence and development of malignancies

Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs

Replication and discovery of musculoskeletal QTLs in LG/J and SM/J advanced intercross lines

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