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- 저자 : Yuxun Zhou (검색결과 4 건)
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Genome wide methylation analysis to uncover genes related to recurrent pregnancy loss
Lixia Zhou,Yudong Pu,Yuxun Zhou,Bin Wang,Ye Chen,Yang Bai,Shuzhen He 한국유전학회 2021 Genes & Genomics Vol.43 No.4
Background Recurrent pregnancy loss (RPL) refers to two or more consecutive spontaneous abortion before 24 weeks of gestation, representing 1% of couples of childbearing age. Epigenetic factors including dysregulation of DNA methylation of some genes may play a role in RPL. Objective To identify RPL related genes modulated by DNA methylation expressed in decidua and blood. Methods Three decidua samples each from RPL patients and normal controls were recruited to perform genome-wide bisulfte sequencing (GWBS) and transcriptome sequencing. Based on the above results, 22.52 kb of diferential methylation regions (DMRs) from 17 genes were verifed by bisulfte sequencing PCR at specifc region (Hi-MethylSeq) in another 15 decidua (7RPL vs. 8 Controls) and 13 blood (5RPL vs. 8 Controls) samples. Results 23 genes showed signifcantly diferential cytosine methylation status and distinct expression level between PRL patients and healthy controls synergistically. Three signaling pathways were found to be shared between genes with both hypomethylated diferential methylation regions (DMR) and upregulated diferential gene expression (DGE). The results from Hi-MethylSeq showed that the hypermethylation of SGK1 in both blood and decidua samples in RPL patients, which was consistent to its lower expression in endometrium reported earlier. SGK3 and CREB5 also showed modulated methylation level in RPL decidua. Conclusion Our fnding supported that aberrant methylation of SGK1 and CREB5 could be a cause of the dysregulation of these gens in the endometrium, which is one of cause of reproductive failure. The function of SGK3 in reproduction system deserves further investigation.
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Multiplex PCR with the Blunt Hairpin Primers for Next Generation Sequencing
Ke Chen,Yuxun Zhou,Kai Li,Junhua Xiao 한국생물공학회 2017 Biotechnology and Bioprocess Engineering Vol.22 No.3
The multiplex PCR is one of the important methods to enrich the target DNAs for next generation sequencing. The non-specific amplification and interaction between the primers are the pivotal challenges of multiplex PCR. Here, we introduce the novel blunt hairpin primers for effective reducing the primer dimers and mispriming events. We also used a pair of auxiliary primers to enhance PCR efficiency. We simultaneously amplified 89 target regions from 44 samples and sequenced all amplicons on ion torrent PGM platform. Among all the filtrated amplicons (3438 different amplicons), 99.7, 97.6, 90.1 and 72.8% had sequencing depths fell within 200, 100, 50 and 25-fold range. The sequencing depth variations among all the samples were less than 27-fold. We also amplified multiplex regions with blunt hairpin, stick hairpin and normal linear primers, and the blunt hairpin primers could significantly reduce the amount of primer dimers and unspecific products.These results show that multiplex PCR with the blunt hairpin primers is a flexible, specific and economical target-region captured approach for the next generation sequencing.
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Gideon Omariba,Li Tong,Maochun Wang,Kai Li,Yuxun Zhou,Junhua Xiao 한국유전학회 2018 Genes & Genomics Vol.40 No.3
Puberty onset is a milestone in sexual development. A tumor suppress gene (TSG) network had been reported to be involved in the regulation of female puberty onset. The observations in rodents and primates showed a potential link between microRNAs and puberty onset. To figure out what miRNAs play roles in this important biological process, profilings of microRNAs in the hypothalamus of female mice from three different pubertal stages, juvenile [postnatal day (P10)], early pubertal (P25) and pubertal (P30) were performed on the Affymetrix GeneChip miRNA 3.0 Arrays, the cerebral cortex (CTX) was used as a control tissue. 20 miRNAs were shown to be differentially expressed in hypothalamus (fold change > 1.5, P < 0.05), but not in CTX during the transition from juvenile to pubertal. Four of them were validated by real-time quantitative RT-PCR (qRTPCR) method. 1018 genes were predicted as the targets of these miRNAs. Further bioinformatics analysis suggested that these target genes were involved in many important signaling pathways, especially in the cancer related pathways. We also found that about 90% of these target genes were expressed in the hypothalamus, as well as in the immortalized GnRH-producing GT1-7 cells, which provided additional evidence that these miRNAs could be female puberty onset related. Here we present a novel comprehensive data set of miRNA gene expression during the puberty onset; and it provides an important recourse for the future functional characterization of individual miRNAs and their targets in mouse hypothalamus and in GT1-7 cells.
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A Multiplex Sensitive Quantification of MicroRNAs Based on Competitive PCR
Maochun Wang,Li Tong,Sijia Wang,Kai Li,Junhua Xiao,Yuxun Zhou 한국생물공학회 2017 Biotechnology and Bioprocess Engineering Vol.22 No.1
MicroRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in animals and plants by targeting mRNAs for cleavage or gene silencing. Although quantitative real-time PCR (qRT-PCR) had been widely used for miRNAs quantification, a multiplex quantification method is demanding. In this study, we successfully detected 2 miRNAs (miR-505-3p and miR- 21a-5p) and an internal control (miR-16-5p) with only one reaction based on competitive PCR (cPCR) with high sensitivity. For each miRNA, two stem-loop reverse transcription (RT) primers were designed to produce two different templates: the competitor cDNA and the target cDNA, which had similar sequences except for 3 nucleotides different in length. RNA from a control sample was reverse transcribed with the competitive RT primers of multiple genes. Samples for test were reverse transcribed with target RT primers to obtain target cDNAs. Target cDNA was mixed with competitor cDNA to be used as the template for a multiplex fluorescent cPCR reaction. The cPCR products were separated on polyacrylamide gel electrophoresis with ABI 377 DNA sequencer and each fluorescent peak was quantified by its intensity. In this method, we compared the expression level of miR-505-3p in two tissues (thalamus and tail) between C57BL/6J and C3H/HeJ mice. The results showed that in the thalamus, which had high abundance of miR-505-3p, both cPCR and SYBR Green based qRT-PCR provided a sensitive quantification outcome. However, in the tail, which had extremely low level of miR-505-3p, it could be steadily detected by cPCR even after 8 times dilution with a relatively high sensitivity, while qRT-PCR can’t detect any product only after 2 times dilution. The variation as low as 12.2% between samples could be clarified by cPCR, which could not be accomplished by qRT-PCR. This method enables multiplex, accurate and sensitive quantification of miRNAs with fewer precious RNA samples than qRT-PCR.
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