Maksimov Daniil A, Laktionov Petr P, Belyakin Stepan N
Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.
Novosibirsk State University, Novosibirsk, Russia.
Chromosome Res. 2016 Dec;24(4):481-494. doi: 10.1007/s10577-016-9538-4. Epub 2016 Oct 21.
Analysis of gene expression regulation typically requires identification of genomic sites bound by regulatory proteins. For this purpose, chromatin immunoprecipitation (ChIP) and Dam identification (DamID) methods can be applied to cell lines, whole organisms, or enriched cell populations. In this work, we present modifications to the experimental DamID protocol, as well as a custom data processing algorithm, that allow to confidently identify genomic sites enriched with the proteins of interest. This algorithm is implemented in Perl and is also available as executable files, thereby making DamID analysis relatively straightforward. Finally, we demonstrate how this pipeline performs when fed with real experimental data.
基因表达调控分析通常需要鉴定与调控蛋白结合的基因组位点。为此，染色质免疫沉淀（ChIP）和Dam识别（DamID）方法可应用于细胞系、整个生物体或富集的细胞群体。在这项工作中，我们对实验性DamID方案以及自定义数据处理算法进行了改进，从而能够可靠地鉴定富含目标蛋白的基因组位点。该算法用Perl语言实现，也可作为可执行文件获取，从而使DamID分析相对简便。最后，我们展示了将真实实验数据输入该流程时的运行情况。
