A simple method for generating high-resolution maps of genome-wide protein binding.
A simple method for generating high-resolution maps of genome-wide protein binding.
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一种简单的方法，用于生成全基因组蛋白结合的高分辨率图。
DOI：
10.7554/elife.09225
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发表时间：
2015-06-16
期刊：
影响因子：
7.7
通讯作者：
Henikoff S
中科院分区：
文献类型：
--
作者：
Skene PJ;Henikoff S
染色质免疫沉淀(ChIP)及其衍生物是用于确定转录因子结合位点的主要技术。然而，传统的测序芯片(CHIP-SEQ)存在分辨率低的问题，而新的技术需要重大的实验改变和复杂的生物信息学。以前，我们已经使用了一种新的交联片-SEQ协议(X-CHIP-SEQ)来执行RNA聚合酶II的高分辨率作图。在此，我们在此工作的基础上将X-CHIP-SEQ与现有的方法进行比较。通过使用同时具有内核酸酶和外核酸酶活性的微球菌核酸酶来片段染色质，从而产生精确的蛋白质-DNA足迹，高分辨率X-CHIP-SEQ实现了转录因子结合的单碱基对分辨。该协议的一个显著优点是对传统的芯片序列工作流程的最小改变和简单的生物信息处理。DOI：http://dx.doi.org/10.7554/eLife.09225.001
Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution, and newer techniques require significant experimental alterations and complex bioinformatics. Previously, we have used a new crosslinking ChIP-seq protocol (X-ChIP-seq) to perform high-resolution mapping of RNA Polymerase II. Here, we build upon this work and compare X-ChIP-seq to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity, to fragment the chromatin and thereby generate precise protein–DNA footprints, high-resolution X-ChIP-seq achieves single base-pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing. DOI: http://dx.doi.org/10.7554/eLife.09225.001