Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss)

Wang, Jian; Fu, Liyuan; Koganti, Prasanthi P.; Wang, Lei; Hand, Jacqelyn M.; Ma, Hao; Yao, Jianbo

doi:10.1007/s10126-016-9689-5

Cited by 51 publications

(30 citation statements)

References 60 publications

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“…As expected, lncRNAs showed a significant lower expression level than PCGs by comparing the fragments per kilobase of exon per million fragments mapped (FPKM) values (Fig. 2d), which has also been observed in other species such as rainbow trout [15] and pacific oyster [16]. In conclusion, lncRNAs in NMR displayed higher GC content but shorter length, less exon numbers and lower expression level in comparison with PCGs (Fig.…”

Section: Resultssupporting

confidence: 80%

Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance

Jiang

Cheng

et al. 2016

Epigenetics & Chromatin

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BackgroundLong noncoding RNAs (lncRNAs) are a class of ubiquitous noncoding RNAs and have been found to act as tumor suppressors or oncogenes, which dramatically altered our understanding of cancer. Naked mole rat (NMR, Heterocephalus glaber) is an exceptionally long-lived and cancer-resistant rodent; however, whether lncRNAs play roles in cancer resistance in this seductive species remains unknown.ResultsIn this study, we developed a pipeline and identified a total of 4422 lncRNAs across the NMR genome based on 12 published transcriptomes. Systematic analysis revealed that NMR lncRNAs share many common characteristics with other vertebrate species, such as tissue specificity and low expression. BLASTN against with 1057 human cancer-related lncRNAs showed that only 5 NMR lncRNAs displayed homology, demonstrating the low sequence conservation between NMR lncRNAs and human cancer-related lncRNAs. Further correlation analysis of lncRNAs and protein-coding genes indicated that a total of 1295 lncRNAs were intensively coexpressed (r ≥ 0.9 or r ≤ −0.9, cP value ≤ 0.01) with potential tumor-suppressor genes in NMR, and 194 lncRNAs exhibited strong correlation (r ≥ 0.8 or r ≤ −0.8, cP value ≤ 0.01) with four high-molecular-mass hyaluronan related genes that were previously identified to play key roles in cancer resistance of NMR.ConclusionIn this study, we provide the first comprehensive genome-wide analysis of NMR lncRNAs and their possible associations with cancer resistance. Our results suggest that lncRNAs may have important effects on anticancer mechanism in NMR.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0101-5) contains supplementary material, which is available to authorized users.

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Section: Resultssupporting

confidence: 80%

Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance

Jiang

Cheng

et al. 2016

Epigenetics & Chromatin

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“…The pipeline reported in our previous study 21 was used to identify all lncRNAs from the expressed transcriptome reference. Two biological replicates (CTRL3 & EST4) at 24 hour time point were identified as outliers based upon multidimensional distance scaling analysis and therefore were excluded.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive analysis of lncRNAs and mRNAs in skeletal muscle of rainbow trout (Oncorhynchus mykiss) exposed to estradiol

Wang

Koganti

Yao

et al. 2017

Sci Rep

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Estradiol (E2) is a steroid hormone that negatively affects muscle growth in rainbow trout (Oncorhynchus mykiss), but the mechanisms directing with this response are not fully understood. To better characterize the effects of E2 in muscle, we identified differentially regulated mRNAs and lncRNAs in juvenile rainbow trout exposed to E2. Here, we performed next-generation RNA sequencing and comprehensive bioinformatics analyses to characterize the transcriptome profiles, including mRNAs and long noncoding RNAs (lncRNAs), in skeletal muscle of rainbow trout injected with E2. A total of 226 lncRNAs and 253 mRNAs were identified as differentially regulated. We identified crucial pathways, including several signal transduction pathways, hormone response, oxidative response and protein, carbon and fatty acid metabolism pathways. Subsequently, a functional lncRNA-mRNA co-expression network was constructed, which consisted of 681 co-expression relationships between 164 lncRNAs and 201 mRNAs. Moreover, a lncRNA-pathway network was constructed. A total of 65 key lncRNAs were identified that regulate 20 significantly enriched pathways. Overall, our analysis provides insights into mRNA and lncRNA networks in rainbow trout skeletal muscle and their regulation by E2 while understanding the molecular mechanism of lncRNAs.

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“…We predicted the PTGs of lincRNAs in two ways. For PTGs that were potentially regulated by lincRNAs in cis , we defined a lincRNA PTG as protein-coding genes that were transcribed nearby (<10 kb) lincRNAs [ 32 , 33 ], and we identified this kind of PTGs by BEDTools 2.17.0 [ 34 ]. For PTGs that were potentially regulated by lincRNAs in trans, we referred to Liao’s study and constructed a lincRNA–mRNA co-expression network based on the Pearson correlation coefficient ( r ) between each pair of lincRNA and protein-coding gene.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig

Zou,

Li,

Deng

et al. 2017

Genes

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There are major differences between Yorkshire (lean-type) and Wannanhua pig (fat-type) in terms of growth performance and meat quality. Long intergenic noncoding RNAs (lincRNAs) are a class of regulators that are involved in numerous biological processes and widely identified in many species. However, the role of lincRNAs in pig is largely unknown, and the mechanisms by which they affect growth and meat quality are elusive. In this study, we used published data to identify 759 lincRNAs in porcine longissimus dorsi muscle. These putative lincRNAs shared many features with mammalian lincRNAs, such as shorter length and fewer exons. Gene ontology and pathway analysis indicated that many potential target genes (PTGs) of lincRNAs were involved in muscle growth-related and meat quality-related biological processes. Moreover, we constructed a co-expression network between differentially expressed lincRNAs (DELs) and their PTGs, and found a potential mechanism that most DELs can use to upregulate their PTGs, which may finally contribute to the growth and meat quality differences between the two breeds through an unknown manner. This work details some lincRNAs and their PTGs related to muscle growth or meat quality, and facilitates future research on the roles of lincRNAs in these two types of pig, as well as molecular-assisted breeding for pig.

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Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss)

Cited by 51 publications

References 60 publications

Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance

Insights into long noncoding RNAs of naked mole rat (Heterocephalus glaber) and their potential association with cancer resistance

Comprehensive analysis of lncRNAs and mRNAs in skeletal muscle of rainbow trout (Oncorhynchus mykiss) exposed to estradiol

Transcriptome Analysis Reveals Long Intergenic Noncoding RNAs Contributed to Growth and Meat Quality Differences between Yorkshire and Wannanhua Pig

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