Tools for DNA adenine methyltransferase identification analysis of nuclear organization during C. elegans development
Tools for DNA adenine methyltransferase identification analysis of nuclear organization during C. elegans development
复制标题
线虫发育过程中核组织 DNA 腺嘌呤甲基转移酶鉴定分析工具
作者：
Rahul Sharma;Dominic Ritler;P. Meister
C.最近，通过将显微镜方法、全基因组作图技术与先进的遗传学相结合，秀丽线虫成为了解核组织与细胞命运之间联系的有价值的模型。这些分析的关键是确定蛋白质与DNA的全基因组相互作用模式的技术。染色质免疫沉淀已被证明是有价值的，但它需要大量的起始材料。这有时很难实现，特别是对于特定基因型（平衡菌株、不同性别、严重表型.）。作为ChIP的替代方案，DNA腺嘌呤甲基转移酶测序鉴定（DamID‐seq）最近被证明能够表征单个哺乳动物细胞中的结合位点。此外，可以通过在组织特异性启动子下以受控方式表达Dam融合蛋白来实现DamID用于细胞类型特异性分析。在这份报告中，我们提出了一个用户友好的管道来分析C中的DamID-seq数据。优美的基于这个管道，我们提供了一个比较分析的图书馆产生不同的起始材料，并讨论了重要的图书馆功能。此外，我们引入了一种基于成像的工具来在体内可视化任何感兴趣蛋白质的细胞特异性三维结合模式。创世纪54：151-159，2016。© 2016 Wiley Periodicals，Inc.
C. elegans has recently emerged as a valuable model to understand the link between nuclear organization and cell fate, by combining microscopy approaches, genome‐wide mapping techniques with advanced genetics. Crucial to these analyses are techniques to determine the genome‐wide interaction pattern of proteins with DNA. Chromatin immunoprecipitation has proven valuable but it requires considerable amounts of starting material. This is sometimes difficult to achieve, in particular for specific genotypes (balanced strains, different sexes, severe phenotypes…). As an alternative to ChIP, DNA adenine methyltransferase identification by sequencing (DamID‐seq) was recently shown to be able to characterize binding sites in single mammalian cells. Additionally, DamID can be achieved for cell‐type specific analysis by expressing Dam fusion proteins under tissue specific promoters in a controlled manner. In this report, we present a user‐friendly pipeline to analyse DamID‐seq data in C. elegans. Based upon this pipeline, we provide a comparative analysis of libraries generated with different starting material and discuss important library features. Moreover, we introduce an adaptation of an imaging based tool to visualize in vivo the cell‐specific tridimensional binding pattern of any protein of interest. genesis 54:151–159, 2016. © 2016 Wiley Periodicals, Inc.
DOI：
10.1895/wormbook.1.169.1
发表时间：
2014-04-02
期刊：
WormBook : the online review of C. elegans biology
影响因子：
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作者：
Askjaer, Peter;Ercan, Sevinc;Meister, Peter
通讯作者：
Meister, Peter