New porcine microRNA genes found by homology search

Kim, Hee-Jeong KimH.-J.; Cui, Xiang-Shun; Kim, Eun-Jung KimE.-J.; Kim, Wun-Jae KimW.-J.; Kim, Nam-Hyung KimN.-H.

doi:10.1139/g06-120

Cited by 35 publications

(27 citation statements)

References 12 publications

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“…Choi et al (2007) identified 177 miRNAs in the newborn mouse ovary and found that four miRNAs were downregulated approximately twofold in the mouse with a knockdown in an ovarian homeobox gene, a transcription factor necessary for oocyte differentiation. In 2006, Kim et al (2006) identified 58 miRNAs in the pig genome and confirmed the expression of two of these miRNAs in the porcine ovary using northern blot analysis. Ro et al (2007) identified 122 miRNAs in the ovaries of 2-week-old and adult mice.…”

Section: Introductionmentioning

confidence: 88%

Differentially expressed plasma microRNAs in premature ovarian failure patients and the potential regulatory function of mir-23a in granulosa cell apoptosis

Yang

Zhou²,

Peng³

et al. 2012

Reproduction

161

122

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Recent studies implicate the regulatory function of microRNAs (miRNAs) in oocyte maturation and ovarian follicular development. Differentially expressed miRNAs are found in the plasma of premature ovarian failure (POF) patients and normal cycling women. In this study, miRNA-regulated signaling pathways and related genes were described using Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis. The effect of mir-23a on granulosa cell apoptosis was also studied by examining the protein expression of X-linked inhibitor of apoptosis protein (XIAP) and caspase-3, followed by subsequent counting of apoptotic cells after Hoechst 33258 staining. Both GO analysis and pathway analysis suggested that many signaling pathways, including the AKT signaling pathway, steroid hormone receptor signaling pathways, and others, were regulated by this group of differentially expressed miRNAs. A decrease in XIAP expression (mRNA and protein level) and caspase-3 protein levels and an increase in cleaved caspase-3 protein were observed in human ovarian granulosa cells transfected with pre-mir-23a, along with an increased occurrence of apoptosis. In conclusion, differentially expressed miRNAs in the plasma of POF patients may have regulatory effects on proliferation and apoptosis of granulosa cells by affecting different signaling pathways. Mir-23a may play important roles in regulating apoptosis via decreasing XIAP expression in human ovarian granulosa cells.

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Section: Introductionmentioning

confidence: 88%

Differentially expressed plasma microRNAs in premature ovarian failure patients and the potential regulatory function of mir-23a in granulosa cell apoptosis

Yang

Zhou²,

Peng³

et al. 2012

Reproduction

161

122

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“…Only reads with more than 15 bp were chosen for further analysis. These reads were mapped to miRBase V.20 (http://www.mirbase.org/) and were annotated by using BLAST (Kim et al, 2006). Reads mapped to mature miRNA were saved.…”

Section: Mirna Data and Preprocessingmentioning

confidence: 99%

Integrated miRNA-mRNA analysis of Epstein-Barr virus-positive nasopharyngeal carcinoma

2015

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ABSTRACT. This study aims to identify the crucial miRNAs in Epstein-Barr virus-positive nasopharyngeal carcinoma (NPC) and their target genes. Gene expression profile data (GSE12452) that included 31 NPC and 10 normal nasopharyngeal tissue specimens were downloaded. Differentially expressed genes (DEGs) were identified using significance analysis of microarrays. The underlying function of DEGs was predicted via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. The miRNA sequencing dataset GSE14738 was also downloaded, and expression levels of miRNA were calculated by the number of reads mapped to each miRNA. The selected miRNAs were integrated into the miRecords 6029 Integrated miRNA-mRNA analysis of NPC ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (2): 6028-6036 (2015) database to obtain their target genes. Target genes associated with DEGs were used to construct the interaction network via Cytoscape. A total of 1437 DEGs between NPC and control were identified, most of which were enriched in cell cycle and extracellular matrix-receptor interaction signaling pathways. Furthermore, 112 miRNAs were considered upregulated in NPC samples. A total of 2228 relationships between 39 miRNAs and 1247 target genes were obtained, of which 182 relationships between 32 miRNAs and 97 target genes were chosen to construct an interaction network. The interactions between DEGs and the let-7 or miR-29 families appeared strongest in this network, where CDC25A, COL3A1, and COL1A1 were regulated by several let-7 family members, while COL4A1 and COL5A2 were regulated by several miR-29 family members. The let-7 and miR-29 families may be related to the development of NPC by regulating the genes involved in cell cycle and ECM-receptor interaction.

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“…Initial research has focused on expanding the current miRNA database (miRBase) to include sequences for livestock species through evaluation of miRNA transcriptome profiles and homology searches (Kim et al, 2006;Coutinho et al, 2007;Gu et al, 2007;Feng et al, 2008;Shao et al, 2008). In addition, new sequencing technologies have advanced this effort by identifying new miRNA sequences through deep sequencing of the miRNA transcriptome in chicken models (Burnside et al, 2008;Glazov et al, 2008).…”

Section: Role Of Microrna In Production Livestockmentioning

confidence: 99%

MicroRNA: Mechanism of gene regulation and application to livestock1

McDaneld

2009

Journal of Animal Science

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New porcine microRNA genes found by homology search

Cited by 35 publications

References 12 publications

Differentially expressed plasma microRNAs in premature ovarian failure patients and the potential regulatory function of mir-23a in granulosa cell apoptosis

Differentially expressed plasma microRNAs in premature ovarian failure patients and the potential regulatory function of mir-23a in granulosa cell apoptosis

Integrated miRNA-mRNA analysis of Epstein-Barr virus-positive nasopharyngeal carcinoma

MicroRNA: Mechanism of gene regulation and application to livestock1

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