Liu Zhengzhi, Naler Lynette B, Zhu Yan, Deng Chengyu, Zhang Qiang, Zhu Bohan, Zhou Zirui, Sarma Mimosa, Murray Alexander, Xie Hehuang, Lu Chang
Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA.
Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA.
NAR Genom Bioinform. 2022 Apr 7;4(2):lqac030. doi: 10.1093/nargab/lqac030. eCollection 2022 Jun.
Genome-wide profiling of interactions between genome and various functional proteins is critical for understanding regulatory processes involved in development and diseases. Conventional assays require a large number of cells and high-quality data on tissue samples are scarce. Here we optimized a low-input chromatin immunoprecipitation followed by sequencing (ChIP-seq) technology for profiling RNA polymerase II (Pol II), transcription factor (TF), and enzyme binding at the genome scale. The new approach produces high-quality binding profiles using 1,000-50,000 cells. We used the approach to examine the binding of Pol II and two TFs (EGR1 and MEF2C) in cerebellum and prefrontal cortex of mouse brain and found that their binding profiles are highly reflective of the functional differences between the two brain regions. Our analysis reveals the potential for linking genome-wide TF or Pol II profiles with neuroanatomical origins of brain cells.
全基因组范围内对基因组与各种功能蛋白之间相互作用的分析，对于理解发育和疾病所涉及的调控过程至关重要。传统检测方法需要大量细胞，且关于组织样本的高质量数据稀缺。在此，我们优化了一种低输入量的染色质免疫沉淀测序（ChIP-seq）技术，用于在基因组规模上分析RNA聚合酶II（Pol II）、转录因子（TF）和酶的结合情况。这种新方法使用1000 - 50000个细胞就能产生高质量的结合图谱。我们用该方法检测了小鼠大脑小脑和前额叶皮质中Pol II和两种转录因子（EGR1和MEF2C）的结合情况，发现它们的结合图谱高度反映了这两个脑区之间的功能差异。我们的分析揭示了将全基因组转录因子或Pol II图谱与脑细胞的神经解剖学起源相联系的潜力。
