Identification of Conserved and Novel microRNAs in Cashmere Goat Skin by Deep Sequencing

Liu, Zhihong; Xiao, Hong‐Mei; Li, Huipeng; Zhao, Yanhong; Lai, Shuangying; Yu, Xinheng; Cai, Ting; Du, Chenguang; Zhang, Wenguang; Li, Jinquan

doi:10.1371/journal.pone.0050001

Cited by 61 publications

(44 citation statements)

References 37 publications

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“…Liu et al identified the miRNAs in goat skin by Deep Sequencing (Liu et al 2012). They found that 68 miRNAs were conserved in goat and had been reported in NCBI.…”

Section: Discussionmentioning

confidence: 99%

Identification of Conserved and Novel microRNAs in Cerebral Ischemia-Reperfusion Injury of Rat Using Deep Sequencing

et al. 2014

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MicroRNAs are a class of noncoding small RNAs that regulate gene expression by inhibiting target genes at post-transcriptional levels. MicroRNAs have been highlighted in many organs and tissues, including the brain. To identify special microRNAs involved in ischemia-reperfusion injury, we performed a comprehensive small RNA profiling in rat model and the control using Illumina high-throughput sequencing. A total of 9,444,562 and 10,290,391 clean reads were sequenced from two small RNA libraries constructed, respectively. Three hundred fifty-eight known microRNAs were identified, in which 78 microRNAs exhibited significantly differential expression between model and control. In addition, 62 and 68 novel miRNAs were found in model and control, respectively. Comparative analysis showed that 24 novel microRNAs were differentially expressed with greater than six-fold change. The GO annotation suggested that predicted targets of microRNAs were enriched into the category of metabolic process, cell part, cell-extracellular communications, and so on. KEGG pathway analysis suggested that these genes were involved in many important pathways, mainly including signaling transduction, MAPK signaling pathway, NF-κB signaling pathway, and neurotrophin signaling pathway. Our findings provided a deeper understanding to the regulatory mechanism of microRNAs underlying cerebral ischemia, therefore benefitting the improvement of the protection and treatment strategies of this disease.

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“…Liu et al identified the miRNAs in goat skin by Deep Sequencing (Liu et al 2012). They found that 68 miRNAs were conserved in goat and had been reported in NCBI.…”

Section: Discussionmentioning

confidence: 99%

Identification of Conserved and Novel microRNAs in Cerebral Ischemia-Reperfusion Injury of Rat Using Deep Sequencing

et al. 2014

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“…With the successful applications of high-throughput sequencing technologies, a large number of miRNAs regulating the development of the mammary glands, skin growth, and the hair follicle formation cycle have been identified in goats [18–20]. However, the number of goat miRNA sequences in miRBase is much lower compared to the data deposition of miRNAs for pig and cattle.…”

Section: Introductionmentioning

confidence: 99%

Identification and Expression Profiling of miRNAome in Goat longissimus dorsi Muscle from Prenatal Stages to a Neonatal Stage

et al. 2016

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Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, such as microRNAs (miRNAs). In the current study, we made use of the deep sequencing data from Jianzhou Da’er goat longissimus dorsi sampled on days 45, 60, and 105 of gestation, as well as day three after birth to identify miRNAs that regulate goat skeletal myogenesis, and examine their temporal expression profiles. A total of 410 known goat miRNAs, 752 miRNA homologs and 88 novel miRNAs were identified across four stages. Besides three myomiRs, the abundance of 17 miRNAs, including chi-miR-424, chi-miR-542-3p and chi-miR-136-5p was more than 10,000 reads per million mapped reads (RPM), on average. Furthermore, 50 miRNAs with more than 100 RPM clustered at the imprinted DLK1–DIO3 locus on chromosome 21 and showed similar expression patterns, indicating that these miRNAs played important roles in skeletal myogenesis of goats. Based on pairwise comparisons, 221 differentially expressed (DE), known miRNAs were identified across four stages. GO and KEGG analyses of the genes targeted by the DE miRNAs revealed the significantly enriched processes and pathways to be consistent with temporal changes of skeletal muscle development across all sampled stages. However, follow-up experimental studies were required to explore functions of these miRNAs and targets underlying skeletal myogenesis.

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“…The miR-184 inhibition argonaute 2 protein expression [22] and the growth of hair follicles [23]. And miRNA-199b has an important role in skin and hair follicle development [24,25]. The miR-1623 target genes that played important roles in Wnt/β-catenin pathway [19].…”

Section: Discussionmentioning

confidence: 99%

High-Throughput Sequencing Reveals miRNAs Affecting Follicle Development in Chicken

Zhang¹

2017

IJGG

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Abstract:As the derivative of chicken skin, hair follicle is capable of self-renew. Its proliferation and differentiation result in hair formation. MicroRNAs (miRNAs) can effectively regulate gene expression at the post-transcriptional level and play a critical role in tissue growth, development. In this study, we used next generation sequencing technology sequenced miRNAs of the hair follicle derived from the 13 day-old chicken (Gallus gallus) embryos in which from Kirin chicken and Huaixiang chicken that feathers having morphogenesis with significantly different curling. A population of conserved miRNAs was identified. These conserved miRNAs were derived from 638 homologous hairpin precursors across 5 animal species. We identified a total of 645 miRNAs in the chicken embryos. Among them, 11 differentially expressed miRNAs were identified (>±2 Fold, p value <0.05) by comparing Kirin chicken and Huaixiang chicken. Several gene ontology (GO) biology processes and the WNT, BMP and TGF-β signaling pathways were found to be differentially expressed miRNAs as part of hair follicle development process. The miR-1623 has an effect on WNT4 and involved in hair follicle cell development. This study has identified miRNAs that associated with the chick embryonic hair follicle development and identified some target miRNAs for further research into their role played in feather growth.

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Identification of Conserved and Novel microRNAs in Cashmere Goat Skin by Deep Sequencing

Cited by 61 publications

References 37 publications

Identification of Conserved and Novel microRNAs in Cerebral Ischemia-Reperfusion Injury of Rat Using Deep Sequencing

Identification of Conserved and Novel microRNAs in Cerebral Ischemia-Reperfusion Injury of Rat Using Deep Sequencing

Identification and Expression Profiling of miRNAome in Goat longissimus dorsi Muscle from Prenatal Stages to a Neonatal Stage

High-Throughput Sequencing Reveals miRNAs Affecting Follicle Development in Chicken

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