Identification and characterization of long non-coding RNA in prenatal and postnatal skeletal muscle of sheep

Li, Cunyuan; Li, Xiaoyue; Liu, Zhijin; Ni, Wei; Zhang, Xiangyu; Hazi, Wureli; Ma, Qiman; Zhang, Yunfeng; Cao, Yang; Qi, Jiangjiao; Yao, Yang; Liu, Feng; Wang, Dawei; Hou, Xiaoxu; Yu, Shuting; Liu, Li; Zhang, Mengdan; Hu, Shengwei

doi:10.1016/j.ygeno.2018.01.009

Cited by 18 publications

(12 citation statements)

References 63 publications

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“…2.6 Prediction of long non-coding RNAs and their targetgenes As described by Li et al (33), three criteria were used to identify long non-coding RNAs: 1) the transcripts that have no hits with known protein-coding genes on the same strand; 2) the transcripts have no coding potential according to the result of Coding Potential Calculator (CPC) (34), and Coding-Non-Coding Index (CNCI) (35); 3) the transcripts have no hits with known protein domains in Pfam database (36). The transcripts complied with all of three criteria were considered as reliable lncRNAs.…”

Section: Differentially Expressed Genes Identi Cation and Functional Enrichment Analysismentioning

confidence: 99%

Comparative Transcriptome Analysis Provides Insights into Response of Ulva compressa to Fluctuating Salinity Conditions

Xing

Cao

et al. 2021

Journal of Phycology

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Background: Ulva compressa, known as the green tide forming species, was reported that can adapt to hypo-salinity conditions such as estuaries and brackish lakes. To understand the underlying molecular mechanisms of hypo-salinity stress tolerance, a genome-wide gene expression pro les in U. compressa was performed using digital gene expression pro le (DGE).Results: The RNA-seq data were analyzed based on the comparison of differently expressed genes involved in speci c pathways under hypo-salinity and recovery conditions. Under the long-term hypo-salinity stress, the recovery of photosynthesis and energy metabolism could provide su cient energy for the tolerance under long-term hypo-saline stress. Multiple strategies were performed to maintain the osmotic homeostasis. Additionally, several long non-coding RNA were detected as differently expressed genes during the stress, which could play important roles in the osmotolerance.Conclusions: Our work will serve as an essential foundation for the understanding of the tolerance mechanism of U. compressa under the uctuating salinity conditions.

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Section: Differentially Expressed Genes Identi Cation and Functional Enrichment Analysismentioning

confidence: 99%

Comparative Transcriptome Analysis Provides Insights into Response of Ulva compressa to Fluctuating Salinity Conditions

Xing

Cao

et al. 2021

Journal of Phycology

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“…Therefore, improving the quality of meat products and maintaining a high growth rate has become the focus of research. Muscle development is generally classi ed into two stages, embryonic period and after birth [2]. In the embryonic stage, muscle progenitor cells undergo differentiation and proliferation to form myoblasts, which then fuse to form multinucleated myotubes.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Ren

Liu

Wang

et al. 2020

Preprint

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Background: Muscle is the predominant portion of any meat product, and growth performance and product quality are the core of modern breeding. The embryonic period is highly critical for muscle development, the number, shape and structure of muscle fibers are determined at the embryonic stage. Herein, we performed transcriptome analysis to reveal the law of muscle development in the embryonic stage of Chengkou Mountain Chicken at embryonic days (E) 12, 16, 19, 21. Results: Diameter and area of muscle fibers exhibited significant difference at different embryonic times(P<0.01). A total of 16,330 mRNAs transcripts were detected, including 109 novel mRNAs transcripts. By comparing different embryonic muscle development time points, 2,251 (E12vsE16), 4,324 (E12vsE19), and 5,224 (E12vsE21), 1,274 (E16vsE19), 2,735 (E16vsE21) and 857 (E19vsE21) differentially expressed mRNAs were identified. It is worth noting that 6,726 mRNAs were differentially expressed. The time-series expression profile of differentially expressed genes (DEGs) showed that the rising and falling expression trends were significantly enriched. The downward trend was the most important and was enriched in 3,963 DEGs. GO enrichment analysis provided three significantly enriched categories of the down-trending genes, including 91 cellular components, 53 molecular functions, and 248 biological processes. Through KEGG analysis, we explored the pathway of downtrend genes. A total of 183 KEGG pathways were enriched, including 17 significant pathways, such as extracellular matrix-receptor interactions. Similarly, numerous pathways related to muscle development were found, including the Wnt signaling pathway (P<0.05), MAPK signalingpathway, TGF-beta signaling pathway, and mTOR signaling pathway. Among the differentially expressed genes, we selected those involved in developing 4-time points; notably, up-regulated genes included MYH1F, SLC25A12, and HADHB, whereas the down-regulated genes included STMN1, VASH2, and TUBAL3. Conclusion: Our study explored the embryonic muscle development of the Chengkou Mountain Chicken. A large number of DEGs related to muscle development have been identified ,and validation of key genes for embryonic development and preliminary explanation of their role in muscle development. Overall, this study broadened our current understanding of the phenotypic mechanism for myofiber formation and provides valuable information for improving chicken quality.

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“…In this context, regulatory functions of lncRNAs in lipid metabolism have been already demonstrated in different organisms, including human (Chen 2016; Gao et al 2018), mouse (Sun et al 2013a), pig (Palmieri 2014; Zhou et al 2015), bovine (Zhou et al 2014) and chicken (Muret et al 2017). There are a few transcriptome studies with a focus on the investigation of potential regulatory roles of lncRNAs in specific sheep tissues using RNA-seq, such as skeletal muscle (Li et al 2018), skin (Yue et al 2016), ovaries (Miao et al 2016a, 2016b) and testis (Zhang et al 2017). These studies reinforce that lncRNAs are widely involved during sheep development, like other mammals.…”

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confidence: 99%

Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds

Bakhtiarizadeh¹,

Salami

2019

G3 Genes|Genomes|Genetics

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Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep.

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Identification and characterization of long non-coding RNA in prenatal and postnatal skeletal muscle of sheep

Cited by 18 publications

References 63 publications

Comparative Transcriptome Analysis Provides Insights into Response of Ulva compressa to Fluctuating Salinity Conditions

Comparative Transcriptome Analysis Provides Insights into Response of Ulva compressa to Fluctuating Salinity Conditions

Transcriptome Analysis of Embryonic Muscle Development in Chengkou Mountain Chicken

Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds

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