Sequencing and characterization of lncRNAs in the breast muscle of Gushi and Arbor Acres chickens

Ren, Tuanhui; Li, Zhuanjian; Yu, Zhe; Han, Ruili; Wang, Yongcai; Yan, Fengbin; Sun, Guirong; Li, Hong; Kang, Xin

doi:10.1139/gen-2017-0114

Cited by 27 publications

(22 citation statements)

References 91 publications

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“…Once considered the noise in transcription, lncRNAs have been shown to play important roles in a wide range of biological processes (reviewed in Batista and Chang, 2013;Fatica and Bozzoni, 2014). Although there has been tremendous effort to identify lncRNAs in chicken development and diseases (Liu et al, 2018(Liu et al, , 2017Li et al, , 2016Li et al, , 2012Ren et al, 2018;Wu et al, 2018;Wang et al, 2017b;Zhang et al, 2017;Lin et al, 2016), there are very few reports to functionally annotate them (Roeszler et al, 2012;Arriaga-Canon et al, 2014;Cai et al, 2017;Fan et al, 2017). The nomenclature of the chicken lncRNAs has not reached a consensus and the current databases are still under constant improvement.…”

Section: Discussionmentioning

confidence: 99%

“…In recent years, there has been tremendous effort to profile and characterize lncRNAs in the chicken genome in development and diseases (Liu et al, 2018(Liu et al, , 2017Li et al, , 2016Li et al, , 2012Ren et al, 2018;Wu et al, 2018;Wang et al, 2017b;Zhang et al, 2017;Lin et al, 2016). The NONCODE database (www.noncode.org) lists a total of 13,085 lncRNA transcripts, corresponding to 9688 lncRNA genes in the chicken genome (Xie et al, 2014;Zhao et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

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Long noncoding RNAs regulate Wnt signaling during feather regeneration

et al. 2018

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Long non-coding RNAs (lncRNAs) are non-protein coding transcripts that are involved in a broad range of biological processes. Here, we examine the functional role of lncRNAs in feather regeneration. RNAseq profiling of the regenerating feather blastema revealed that Wnt signaling is among the most active pathways during feather regeneration, with Wnt ligands and their inhibitors showing distinct expression patterns. Co-expression analysis identified hundreds of lncRNAs with similar expression patterns to either the Wnt ligands (the Lwnt group) or their downstream target genes (the Twnt group). Among these, we randomly picked two lncRNAs in the Lwnt group and three lncRNAs in the Twnt group to validate their expression and function. Members in the Twnt group regulated feather regeneration and axis formation, whereas members in the Lwnt group showed no obvious phenotype. Further analysis confirmed that the three Twnt group members inhibit Wnt signal transduction and, at the same time, are downstream target genes of this pathway. Our results suggest that the feather regeneration model can be utilized to systematically annotate the functions of lncRNAs in the chicken genome.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Long noncoding RNAs regulate Wnt signaling during feather regeneration

et al. 2018

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“…In recent years, there are some reports about the lncRNA regulated muscle development in chickens [73]. lncRNA pouMU1 was most abundant in the leg muscle and breast muscle tissue, and low or no expression in other tissues.…”

Section: Regulation Of Muscle Development By Lncrnas In Poultrymentioning

confidence: 99%

Regulatory Mechanism and Application of lncRNAs in Poultry

Li¹,

Ren²,

Wen-ya³

et al. 2020

Poultry - An Advanced Learning

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Long noncoding RNA (lncRNAs) are transcripts greater than 200 nt in length with decreased coding potential and are widespread in all types of biological organisms. lncRNAs can interact with protein, DNA and RNA, respectively, which may participate in the multilevel regulation of transcriptional, posttranscriptional and epigenetic modifications. It is well known that lncRNA, which length is single-stranded non-coding RNA molecule, plays crucial roles in animal growth, development, cell proliferation and differentiation, and other life activities. In this research, we review the regulation mechanism and current research status of lncRNAs in chicken economic traits and disease, which would contribute to further understanding the regulatory mechanisms and application of lncRNAs in poultry.

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“…Pathway analysis indicated that IMPA might inhibit a differentiation via the JNK/MAPK pathway and promote lipid deposition via the PPAR pathway. Ren et al (2018) collected six-week-old pectoral muscles of slow-growing (Gushi, GS) and fast-growing (Arbor Acres, AA) chicken breeds for transcriptome sequencing. A total of 4815 differentially expressed lncRNAs (long non-coding RNAs) were screened.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages

Zhang

et al. 2020

PeerJ

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Background. The meat quality of yellow feathered broilers is better than the quality of its production. Growth traits are important in the broiler industry. The exploration of regulation mechanisms for the skeletal muscle would help to increase the growth performance of chickens. At present, some progress has been made by researchers, but the molecular mechanisms of the skeletal muscle still remain unclear and need to be improved. Methods. In this study, the breast muscles of fast-and slow-growing female Jinghai yellow chickens (F4F, F8F, F4S, F8S) and slow-growing male Jinghai yellow chickens (M4S, M8S) aged four and eight weeks were selected for transcriptome sequencing (RNA-seq). All analyses of differentially expressed genes (DEGs) and functional enrichment were performed. Finally, we selected nine DEGs to verify the accuracy of the sequencing by qPCR. Results. The differential gene expression analysis resulted in 364, 219 and 111 DEGs (adjusted P-value ≤ 0.05) for the three comparison groups, F8FvsF4F, F8SvsF4S, and M8SvsM4S, respectively. Three common DEGs (ADAMTS20, ARHGAP19, and Novel00254) were found, and they were all highly expressed at four weeks of age. In addition, some other genes related to growth and development, such as ANXA1, COL1A1, MYH15, TGFB3 and ACTC1, were obtained. The most common DEGs (n = 58) were found between the two comparison groups F8FvsF4F and F8SvsF4S, and they might play important roles in the growth of female chickens. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway also showed some significant enrichment pathways, for instance, extracellular matrix (ECM)-receptor interaction, focal adhesion, cell cycle, and DNA replication. The two pathways that were significantly enriched in the F8FvsF4F group were all contained in that of F8SvsF4S. The same two pathways were ECM-receptor interaction and focal adhesion, and they had great influence on the growth of chickens. However, many differences existed between male and female chickens in regards to common DEGs and KEGG pathways. The results would help to reveal the regulation mechanism of the growth and development of chickens and serve as a guideline to propose an experimental design on gene function with the DEGs and pathways. M. 2017. Sound analysis to model weight of broiler chickens. Francisco CL, Jorge AM, Dalpaisilva M, Carani FR, Cabeço LC, Silva SR. 2011. Muscle fiber type characterization and myosin heavy chain (MyHC) isoform expression in Mediterranean buffaloes. Meat Science 88(3):535-541 DOI 10.1016/j.meatsci.2011.02.007. Friedrich RE, Scheuer HA, Holtje W. 2019. The effect of bisphosphonate medication on orthodontics and orthognathic surgery in patients with osteogenesis imperfecta. GMS Interdisciplinary Plastic and Reconstructive Surgery DGPW 8:Doc06 . 2019. Synergistic effects of recombinant Lentiviral-mediated BMP2 and TGF-beta3 on the osteogenic differentiation of rat bone marrow mesenchymal stem cells in vitro. Cytokine 120:1-8 Noda M. 2016. Collagens VI and XII form complexes mediating osteoblast interact...

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Sequencing and characterization of lncRNAs in the breast muscle of Gushi and Arbor Acres chickens

Cited by 27 publications

References 91 publications

Long noncoding RNAs regulate Wnt signaling during feather regeneration

Long noncoding RNAs regulate Wnt signaling during feather regeneration

Regulatory Mechanism and Application of lncRNAs in Poultry

Transcriptome for the breast muscle of Jinghai yellow chicken at early growth stages

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