Genetics Department, Stanford University, Stanford, CA 94305, USA.
Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA.
Cells. 2023 Jul 14;12(14):1860. doi: 10.3390/cells12141860.
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
癌症的表型特征之一是转录调控异常。转录调控受一系列复杂的分子因素控制，包括转录因子的存在、组蛋白翻译后修饰的沉积以及长距离 DNA 相互作用。确定这些不同因素的分子特征和功能对于理解癌症生物学的特定方面和揭示潜在的治疗靶点是必要的。通过使用特定因子的抗体，通过染色质免疫沉淀（ChIP）测序（ChIP-Seq）可以确定全基因组的结合相互作用，从而研究特定因子对基因组的调控。许多实验室的一个长期目标是开发一种“反向 ChIP”方法，以鉴定感兴趣基因座上未知的结合伙伴。已经采用了多种策略来实现对序列定义的染色质区域的选择性生化纯化，包括单拷贝基因座，以及随后对相关蛋白的分析检测。本综述涵盖了在提供用于开发作为“反向 ChIP”技术的序列特异性染色质纯化策略的方法概述之前，实现定量蛋白质组学的质谱技术。完全实现的反向 ChIP 技术具有识别癌症特异性靶标和开发个性化治疗方案的巨大潜力。
