2cChIP-seq and 2cMeDIP-seq: The Carrier-Assisted Methods for Epigenomic Profiling of Small Cell Numbers or Single Cells

作者：Hu, Congxia; Wu, Jun; Li, Pengxiao; Zhang, Yabin; Peng, Yonglin; Liu, Ruiqi; Du, Wenfei; Kang, Yani; Sun, Jielin; Wu, Ji; Shao, Zhifeng^*; Zhao, Xiaodong^*

来源：INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2022, 23(22): 13984.

DOI：10.3390/ijms232213984

• low-input ChIP-seq
• low-input MeDIP-seq
• single-cell ChIP-seq
• female germline stem cells

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) can profile genome-wide epigenetic marks associated with regulatory genomic elements. However, conventional ChIP-seq is challenging when examining limited numbers of cells. Here, we developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during conventional ChIP procedures (hereafter referred to as 2cChIP-seq), thus dramatically improving immunoprecipitation efficiency and reducing DNA loss of low-input ChIP-seq samples. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10-1000 cells. By introducing Tn5 transposase-assisted fragmentation, 2cChIP-seq reliably captured genomic regions with histone modification at the single-cell level in about 100 cells. Moreover, we characterized the methylome of 100 differentiated female germline stem cells (FGSCs) and observed a particular DNA methylation signature potentially involved in the differentiation of mouse germline stem cells. Hence, we provided a reliable and robust epigenomic profiling approach for small cell numbers and single cells.

• 单位
  上海交通大学