Prediction of novel pre-microRNAs with high accuracy through boosting and SVM

Zhang, Yuanwei; Yang, Yifan; Zhang, Huan; Jiang, Xiaohua; Xu, Bo; Xue, Yu; Cao, Yunxia; Zhai, Qian; Zhai, Yongmei; Xu, Mingqing; Cooke, Howard J.; Shi, Qinghua

doi:10.1093/bioinformatics/btr148

Cited by 25 publications

(20 citation statements)

References 15 publications

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“…Most recently, microRNA expression profiles have been established in ovaries in human (Zhang et al 2011), mice (Choi et al 2007, Ro et al 2007, Ahn et al 2010, Zhang et al 2013, and cattle (Tripurani et al 2010 around the time of primordial follicle assembly. All these studies suggested important roles of microRNAs in the developing ovaries.…”

Section: Discussionmentioning

confidence: 99%

“…The small size of microRNAs, combined with their target recognition, provides microRNAs with the capacity and versatility to act as global gene regulators in a wide array of biological processes including cell proliferation and apoptosis (Bartel 2009, Krol et al 2010, Huntzinger & Izaurralde 2011. Many microRNAs are present in ovaries around the time of primordial follicle assembly in mammals (Choi et al 2007, Ahn et al 2010, Tripurani et al 2010, Torley et al 2011, Zhang et al 2011. Female mice lacking Dicer1 (Dicer), a gene required for the biogenesis of vast majority of microRNAs, show abnormal follicle morphology (Lei et al 2010, Baley & Li 2012.…”

Section: Introductionmentioning

confidence: 99%

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microRNA 376a regulates follicle assembly by targeting Pcna in fetal and neonatal mouse ovaries

Zhang¹,

Jiang²,

Zhang³

et al. 2014

Reproduction

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In mammals, the primordial follicle pool, providing all oocytes available to a female throughout her reproductive life, is established perinatally. Dysregulation of primordial follicle assembly results in female reproductive diseases, such as premature ovarian insufficiency and infertility. Female mice lacking Dicer1 (Dicer), a gene required for biogenesis of microRNAs, show abnormal morphology of follicles and infertility. However, the contribution of individual microRNAs to primordial follicle assembly remains largely unknown. Here, we report that microRNA 376a (miR-376a) regulates primordial follicle assembly by modulating the expression of proliferating cell nuclear antigen (Pcna), a gene we previously reported to regulate primordial follicle assembly by regulating oocyte apoptosis in mouse ovaries. miR-376a was shown to be negatively correlated with Pcna mRNA expression in fetal and neonatal mouse ovaries and to directly bind to Pcna mRNA 3 0 untranslated region. Cultured 18.5 days postcoitum mouse ovaries transfected with miR-376a exhibited decreased Pcna expression both in protein and mRNA levels. Moreover, miR-376a overexpression significantly increased primordial follicles and reduced apoptosis of oocytes, which was very similar to those in ovaries co-transfected with miR-376a and siRNAs targeting Pcna. Taken together, our results demonstrate that miR-376a regulates primordial follicle assembly by modulating the expression of Pcna. To our knowledge, this is the first microRNA-target mRNA pair that has been reported to regulate mammalian primordial follicle assembly and further our understanding of the regulation of primordial follicle assembly.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

microRNA 376a regulates follicle assembly by targeting Pcna in fetal and neonatal mouse ovaries

Zhang¹,

Jiang²,

Zhang³

et al. 2014

Reproduction

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“…The development of next-generation sequencing (NGS) techniques has facilitated and improved the identification of miRNAs due to their high sensitivity [24]. Although high-throughput miRNA profiling has been carried out in ovarian somatic cells [25]–[27], comparative miRNA expression profiling of CRCs and COCs has not yet been conducted.…”

Section: Introductionmentioning

confidence: 99%

Research Resources: Comparative MicroRNA Profiles in Human Corona Radiata Cells and Cumulus Oophorus Cells Detected by Next-Generation Small RNA Sequencing

Tong

Zhang

et al. 2014

PLoS ONE

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During folliculogenesis, cumulus cells surrounding the oocyte differentiate into corona radiata cells (CRCs) and cumulus oophorus cells (COCs), which are involved in gonadal steroidogenesis and the development of germ cells. Several studies suggested that microRNAs (miRNAs) play an important regulatory role at the post-transcriptional level in cumulus cells. However, comparative miRNA profiles and associated processes in human CRCs and COCs have not been reported before. In this study, miRNA profiles were obtained from CRCs and COCs using next generation sequencing in women undergoing controlled ovarian stimulation for IVF. A total of 785 and 799 annotated miRNAs were identified in CRCs and COCs, while high expression levels of six novel miRNAs were detected both in CRCs and in COCs. In addition, different expression patterns in CRCs and COCs were detected in 72 annotated miRNAs. To confirm the miRNA profile in COCs and CRCs, quantitative real-time PCR was used to validate the expression of annotated miRNAs, differentially expressed miRNAs, and novel miRNAs. The miRNAs in the let-7 family were found to be involved in the regulation of a broad range of biological processes in both cumulus cell populations, which was accompanied by a large amount of miRNA editing. Bioinformatics analysis showed that amino acid and energy metabolism were targeted significantly by miRNAs that were differentially expressed between CRCs and COCs. Our work extends the current knowledge of the regulatory role of miRNAs and their targeted pathways in folliculogenesis, and provides novel candidates for molecular biomarkers in the research of female infertility.

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“…All real-time PCRs were performed by Applied Biosystems StepOne TM realtime PCR System (Applied Bio systems, USA) using Faststart universal SYBR Green Master (Roche), according to our previous report. 61 Clone formation assay 5 £ 10 4 A2780 cells were seeded in 24-well plate and 24 h after transfection, 1000 or 150 cells were seeded in each 6-well plate and treated with or without 5 Gy IR at 72 h after transfection, respectively. The detail protocol for clone formation assay was performed following previous report.…”

Section: Construction Of Luciferase Reporter Vectorsmentioning

confidence: 99%

miR-214-mediated downregulation of RNF8 induces chromosomal instability in ovarian cancer cells

et al. 2014

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Defective DNA damage response (DDR) is frequently associated with carcinogenesis. Abrogation of DDR leads to chromosomal instability, a most common characteristic of tumors. However, the molecular mechanisms underlying regulation of DDR are still elusive. The ubiquitin ligase RNF8 mediates the ubiquitination of gH2AX and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DDR and inhibits chromosomal instability. Though RNF8 is a key player involved in DDR, regulation of its expression is still poorly understood. Here, we show that miR-214 could abrogate DDR by repressing RNF8 expression through direct binding to 3 0 -untranslated region (3 0 UTR) of RNF8 mRNA in human ovarian cancer cells. Antagonizing miR-214 by expressing its inhibitors in A2780 cells significantly increased RNF8 expression and thus promoted DNA damage repair. Consistent with the role of miR-214 in regulating RNF8 expression, the impaired DNA repair induced by miR-214 overexpression can be rescued by overexpressing RNF8 mRNA lacking the 3 0 UTR. Together, our results indicate that down-regulation of RNF8 mediated by miR-214 impedes DNA damage response to induce chromosomal instability in ovarian cancers, which may facilitate the understanding of mechanisms underlying chromosomal instability.

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Prediction of novel pre-microRNAs with high accuracy through boosting and SVM

Abstract: miRD is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/rpg/mird/mird.php.

Cited by 25 publications

References 15 publications

microRNA 376a regulates follicle assembly by targeting Pcna in fetal and neonatal mouse ovaries

microRNA 376a regulates follicle assembly by targeting Pcna in fetal and neonatal mouse ovaries

Research Resources: Comparative MicroRNA Profiles in Human Corona Radiata Cells and Cumulus Oophorus Cells Detected by Next-Generation Small RNA Sequencing

miR-214-mediated downregulation of RNF8 induces chromosomal instability in ovarian cancer cells

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