Sites of Developmental & Tissue-specific DNA Methylation

发育部位

• 批准号: 7225212
• 负责人: WILLIAM A HELD
• 金额: $ 29.54万
• 依托单位: ROSWELL PARK CANCER INSTITUTE CORP
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-05-01 至 2009-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7225212
• 关键词: Sites; Developmental; Tissue; specific; DNA

DNA methylation is intrinsically linked to chromatin structure and gene expression. Changes in DNA methylation during development suggest that it may play a role in development and in tissue-specific differentiation. Restriction Landmark Genomic Scanning (RLGS) will be used to identify sites of developmental and tissue specific differences in DNA methylation. RLGS is a method for the two dimensional display of end-labeled DNA restriction fragments. Using Notl as the restriction landmark, RLGS targets gene rich CpG island regions and detects differences in DNA methylation since cleavage by Notl is methylation sensitive. RLGS will be performed on a collection of different tissues from C57BL6/J mice of different ages. Green Fluorescent Protein (GFP) transgenic mice in conjunction with fluorescence activated cell sorting will be used to mark and purify selected populations of cells within a tissue for RLGS analysis. Magnetic Cell Sorting and Centrifugal Elutriation methods will be used to purify "differentiating" cell populations within adult mice for RLGS analysis. New advances in development of "virtual" RLGS software provide unique opportunities to rapidly clone "in silico" the genomic regions with tissue specific differences in DNA methylation/chromatin structure. Quantitative and semi-quantitative methylation sensitive PCR, along with bisulfite sequencing, will be used to delineate the boundaries and density of methylation in the regions. The tissue expression patterns of genes associated with the region will be accessed using available microarray data to evaluate possible "long distance effects" of chromatin structure on gene expression. Quantitative RTPCR methods will be used to evaluate expression of genes with apparent CpG island promoter DNA methylation. It is becoming increasing clear that epigenetic alterations have a major role in aging and the development of Cancer and some other diseases. Yet our understanding of the role of epigenetic alterations during normal development is poorly understood. Recent advances in completing the sequence of the mouse genome and the vast array of bioinformatics tools that are now available makes this an opportune time to undertake a systematic, genome-wide investigation of developmental and tissue-specific differences in genome methylation and assess its impact on gene expression and differentiation.

DNA甲基化与染色质结构和基因表达有内在联系。DNA甲基化在发育过程中的变化表明，它可能在发育和组织特异性分化中发挥作用。限制性标志基因组扫描（RLGS）将用于鉴定DNA甲基化中发育和组织特异性差异的位点。RLGS是一种用于末端标记的DNA限制性片段的二维展示的方法。使用NotI作为限制性标志，RLGS靶向富含基因的CpG岛区域并检测DNA甲基化的差异，因为NotI的切割是甲基化敏感的。将对不同年龄C57 BL 6/J小鼠的不同组织进行RLGS。将使用绿色荧光蛋白（GFP）转基因小鼠结合荧光激活细胞分选来标记和纯化组织内的选定细胞群，以进行RLGS分析。将使用磁性细胞分选和离心洗脱方法纯化成年小鼠内的“分化”细胞群，用于RLGS分析。“虚拟”RLGS软件开发的新进展 提供了独特的机会，以快速克隆“在计算机模拟”的基因组区域与组织特异性差异的DNA甲基化/染色质结构。将使用定量和半定量甲基化敏感性PCR沿着亚硫酸氢盐测序来描绘区域中甲基化的边界和密度。与该区域相关的基因的组织表达模式将使用可用的微阵列数据来评估染色质结构对基因表达的可能的“长距离效应”。将使用定量RTPCR方法评价具有明显CpG岛启动子DNA甲基化的基因的表达。越来越清楚的是，表观遗传学改变在遗传学中起着重要作用。 衰老和癌症以及其他一些疾病的发展。然而，我们对表观遗传改变在正常发育过程中的作用的理解却知之甚少。最近在完成小鼠基因组序列和大量的生物信息学工具，现在可用的进展，使这是一个合适的时间进行系统的，全基因组的发育和组织特异性差异的基因组甲基化的调查，并评估其对基因表达和分化的影响。

项目成果

Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development.

• DOI: 10.1016/j.ygeno.2008.09.003
• 发表时间: 2009-02
• 期刊: GENOMICS
• 影响因子: 4.4
• 作者: Song, Fei;Mahmood, Saleh;Ghosh, Srimoyee;Liang, Ping;Smiraglia, Domminic J.;Nagase, Hiroki;Held, William A.
• 通讯作者: Held, William A.

Identification of aberrant methylation regions in neuroblastoma by screening of tissue-specific differentially methylated regions.

通过筛选组织特异性差异甲基化区域来鉴定神经母细胞瘤中的异常甲基化区域。

• DOI: 10.1002/pbc.24282
• 发表时间: 2013
• 期刊: Pediatric blood & cancer
• 影响因子: 3.2
• 作者: Sugito,Kiminobu;Kawashima,Hiroyuki;Uekusa,Shota;Yoshizawa,Shinsuke;Hoshi,Reina;Furuya,Takeshi;Kaneda,Hide;Hosoda,Toshifumi;Masuko,Takayuki;Ohashi,Kensuke;Ikeda,Taro;Koshinaga,Tsugumichi;Fujiwara,Kyoko;Igarashi,Jun;Ghosh,Srimoy
• 通讯作者: Ghosh,Srimoy

Non-promoter DNA hypermethylation of Zygote Arrest 1 (ZAR1) in neuroblastomas.

神经母细胞瘤中 Zygote Arrest 1 (ZAR1) 的非启动子 DNA 高甲基化。

• DOI: 10.1016/j.jpedsurg.2012.08.008
• 发表时间: 2013
• 期刊: Journal of pediatric surgery
• 影响因子: 2.4
• 作者: Sugito,Kiminobu;Kawashima,Hiroyuki;Yoshizawa,Shinsuke;Uekusa,Shota;Hoshi,Reina;Furuya,Takeshi;Kaneda,Hide;Hosoda,Toshifumi;Konuma,Noriyoshi;Masuko,Takayuki;Ohashi,Kensuke;Ikeda,Taro;Koshinaga,Tsugumichi;Tomita,Ryouichi;Shinojim
• 通讯作者: Shinojim

Nr4a3, a possibile oncogenic factor for neuroblastoma associated with CpGi methylation within the third exon.

• DOI: 10.3892/ijo.2014.2340
• 发表时间: 2014-05
• 期刊: International journal of oncology
• 影响因子: 5.2
• 作者: Uekusa S;Kawashima H;Sugito K;Yoshizawa S;Shinojima Y;Igarashi J;Ghosh S;Wang X;Fujiwara K;Ikeda T;Koshinaga T;Soma M;Nagase H
• 通讯作者: Nagase H