PO.MCB06.01 · 分子与细胞生物学
TIP-ChIP：转座标记、加索引并混合的 ChIP-seq，为低起始量样本生成高通量、多样本结果
TIP-ChIP: Tagmented, indexed and pooled ChIP-seq to generate high-throughput, multi-sample results for low input samples
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
表观遗传分析方法极大地扩展了我们对基因调控和疾病潜在机制的理解。组蛋白修饰和转录因子在染色质组织和转录控制中起关键作用，其失调常与各种病理状态相关。染色质免疫沉淀后测序（ChIP-seq）仍是全基因组组蛋白修饰图谱绘制的金标准；然而，其高起始量要求、易受批次效应影响以及劳动密集的工作流程限制了其可扩展性和效率。在此，我们提出了转座标记、加索引并混合的 ChIP（TIP-ChIP），这是一种高通量替代方法，能够在单次反应中同时分析多达 96 个样本的组蛋白修饰和转录因子。与传统 ChIP-seq 相比，该方法大幅降低批次效应，提高重现性，并且所需起始材料显著更低。此外，简化的工作流程最快可在 3 天内完成，最大限度减少手工操作时间并降低总体成本，同时保持高灵敏度和高分辨率。通过利用优化的平板化工作流程和可实现混合的转座标记条形码策略，我们的方法能够高效地进行样本多重复用而不影响数据质量。为验证其性能，我们在多种细胞类型（包括人原代细胞）中应用了该方法，并证明其在组蛋白修饰和转录因子靶标方面与传统 ChIP-seq 高度一致。此外，TIP-ChIP 捕获了 LPS 刺激的 THP-1 细胞中动态的染色质和转录反应，揭示了 H3K27ac、H3K4me3、RNA 聚合酶 II Ser2P 和 NF-κB（p50）的时间分辨变化。这一进展使大规模表观基因组和 TF 分析研究更易开展且更具成本效益，能够以前所未有的效率研究多样生物学背景下的调控动态。
查看英文原文 English abstract
Epigenetic profiling approaches have greatly expanded our understanding of the mechanisms underlying gene regulation and disease. Histone modifications and transcription factors play a crucial role in chromatin organization and transcriptional control, with dysregulation often linked to various pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains the gold standard for genome-wide mapping of histone modifications; however, its high input requirements, susceptibility to batch effects, and labor-intensive workflow limit its scalability and efficiency. Here we present Tagmented, Indexed and Pooled ChIP (TIP-ChIP), a high-throughput alternative that enables the simultaneous profiling of histone modifications and transcription factors across up to 96 samples in a single reaction. This method substantially reduces batch effects, enhances reproducibility, and requires significantly lower input material compared to conventional ChIP-seq. Furthermore, the streamlined workflow can be completed in as little as 3 days, minimizing hands-on time and reducing overall costs while maintaining high sensitivity and resolution. By leveraging an optimized plate-based workflow and a tagmentation barcoding strategy that enables pooling, our method allows for efficient sample multiplexing without compromising data quality. To validate its performance, we apply this approach across multiple cell types, including human primary cells, and demonstrate strong concordance with conventional ChIP-seq for both histone modifications and transcription-factor targets. Further, TIP-ChIP captured dynamic chromatin and transcriptional responses in LPS-stimulated THP-1 cells, revealing time-resolved changes in H3K27ac, H3K4me3, RNA polymerase II Ser2P, and NF-κB (p50). This advancement makes large-scale epigenomic and TF-profiling studies more accessible and cost-effective, enabling the investigation of regulatory dynamics across diverse biological contexts with unprecedented efficiency
利益披露 Disclosure
S. Traynor, None..
S. Wang, None..
S. Mahmoudi, None..
S. Gonuguntla, None..
J. Cayford, None..
B. Egan, None.