Fragile X syndrome(FXS) patients carry the expansion of over 200 CGG repeats at the promoter of fragile X mental retardation 1(FMR1), leading to decreased or absent expression of its encoded fragile X mental retardati...Fragile X syndrome(FXS) patients carry the expansion of over 200 CGG repeats at the promoter of fragile X mental retardation 1(FMR1), leading to decreased or absent expression of its encoded fragile X mental retardation protein(FMRP). However, the global transcriptional alteration by FMRP deficiency has not been well characterized at single nucleotide resolution, i.e., RNA-seq. Here,we performed in-vitro neuronal differentiation of human induced pluripotent stem(iPS) cells that were derived from fibroblasts of a FXS patient(FXS-iPSC). We then performed RNA-seq and examined the transcriptional misregulation at each intermediate stage during in-vitro differentiation of FXS-iPSC into neurons. After thoroughly analyzing the transcriptomic data and integrating them with those from other platforms, we found up-regulation of many genes encoding TFs for neuronal differentiation(WNT1, BMP4,POU3F4, TFAP2 C, and PAX3), down-regulation of potassium channels(KCNA1, KCNC3, KCNG2, KCNIP4, KCNJ3, KCNK9,and KCNT1) and altered temporal regulation of SHANK1 and NNAT in FXS-iPSC derived neurons, indicating impaired neuronal differentiation and function in FXS patients. In conclusion, we demonstrated that the FMRP deficiency in FXS patients has significant impact on the gene expression patterns during development, which will help to discover potential targeting candidates for the cure of FXS symptoms.展开更多
The newly developed next-generation sequencing platforms, in combination with gcnome-scale amplification methods, provide a powerful tool to study genomics from a single cell. This mini-review summarizes the technolog...The newly developed next-generation sequencing platforms, in combination with gcnome-scale amplification methods, provide a powerful tool to study genomics from a single cell. This mini-review summarizes the technologies of single cell genomics and their applications in several areas of biomedical research including stem cells, cancer biology and reproductive medicine. Particularly, it highlights recent advances in single cell exome sequencing, RNA-seq, and genome sequencing. The application of these powerful techniques will shed new light on the fundamental principles of gene transcription and genome organization at single-cell level and improve our understanding of cellular heterogeneity and diversity in multicellular organisms展开更多
基金supported by National Program on Key Basic Research Project(2015CB964601,2015CB964702)Joint Research Fund for Overseas Chinese,Hong Kong and Macao Young Scholars(31428016)+3 种基金National Natural Science Foundation of China(Key Program 81430026)Scientific Research Foundation for the Returned Overseas Chinese Scholars,State Education Ministry(Xianmin Zhu)Shanghai Municipal Commission of Health and Family Planning(XBR2013094)Jiangsu Science and Technology Planning Project(BM2014052)
文摘Fragile X syndrome(FXS) patients carry the expansion of over 200 CGG repeats at the promoter of fragile X mental retardation 1(FMR1), leading to decreased or absent expression of its encoded fragile X mental retardation protein(FMRP). However, the global transcriptional alteration by FMRP deficiency has not been well characterized at single nucleotide resolution, i.e., RNA-seq. Here,we performed in-vitro neuronal differentiation of human induced pluripotent stem(iPS) cells that were derived from fibroblasts of a FXS patient(FXS-iPSC). We then performed RNA-seq and examined the transcriptional misregulation at each intermediate stage during in-vitro differentiation of FXS-iPSC into neurons. After thoroughly analyzing the transcriptomic data and integrating them with those from other platforms, we found up-regulation of many genes encoding TFs for neuronal differentiation(WNT1, BMP4,POU3F4, TFAP2 C, and PAX3), down-regulation of potassium channels(KCNA1, KCNC3, KCNG2, KCNIP4, KCNJ3, KCNK9,and KCNT1) and altered temporal regulation of SHANK1 and NNAT in FXS-iPSC derived neurons, indicating impaired neuronal differentiation and function in FXS patients. In conclusion, we demonstrated that the FMRP deficiency in FXS patients has significant impact on the gene expression patterns during development, which will help to discover potential targeting candidates for the cure of FXS symptoms.
基金This work was supported by ＂973＂ Programs （Nos. 2012CB966300, 2011CB966204 and 2011CB965102） from the Ministry of Science and Technology in China, the International Science and Technology Cooperation Program of China （No. 2011DFB30010）, the National Natural Science Foundation of China （Grant Nos. 81271258, 31301184）, and the Natural Science Foundation of Jiangsu Province of China （No. DK2011321）.
文摘The newly developed next-generation sequencing platforms, in combination with gcnome-scale amplification methods, provide a powerful tool to study genomics from a single cell. This mini-review summarizes the technologies of single cell genomics and their applications in several areas of biomedical research including stem cells, cancer biology and reproductive medicine. Particularly, it highlights recent advances in single cell exome sequencing, RNA-seq, and genome sequencing. The application of these powerful techniques will shed new light on the fundamental principles of gene transcription and genome organization at single-cell level and improve our understanding of cellular heterogeneity and diversity in multicellular organisms
