遗传 ›› 2021, Vol. 43 ›› Issue (4): 362-374.doi: 10.16288/j.yczz.21-016

• 技术与方法 • 上一篇    下一篇

CUT&Tag产物回收和建库方法的优化

韦晔1,2, 李科2, 卢大儒1(), 朱化星2,*()   

  1. 1. 复旦大学生命科学学院遗传工程国家重点实验室,上海 1200438
    2. 吴江近岸蛋白质科技有限公司,上海 215200
  • 收稿日期:2021-01-15 修回日期:2021-03-04 出版日期:2021-04-16 发布日期:2021-03-11
  • 通讯作者: 卢大儒,朱化星 E-mail:drlu@fudan.edu.cn;zhuhuaxing@novoprotein.com.cn
  • 作者简介:韦晔,在读硕士研究生;专业方向:生物工程。E-mail: 17210700130@fudan.edu.cn
  • 基金资助:
    国家自然科学基金面上项目编号(81372706);上海市科技创新行动计划项目资助编号(17JC1400902)

Optimization of CUT&Tag product recovery and library construction method

Wei Ye1,2, Li Ke2, Lu Daru1(), Zhu Huaxing2,*()   

  1. 1. Statde Key Laboratory of Genetic Engineering School of Life Science, Fudan University, Shanghai 200438, China
    2. Novoprotein Scientific Inc., Wujiang 215200, China
  • Received:2021-01-15 Revised:2021-03-04 Online:2021-04-16 Published:2021-03-11
  • Contact: Lu Daru,Zhu Huaxing E-mail:drlu@fudan.edu.cn;zhuhuaxing@novoprotein.com.cn
  • Supported by:
    Supported by the National Natural Science Foundation of China No(81372706);Shanghai Science and Technology Innovation Action Plan No(17JC1400902)

摘要:

新兴的染色质靶向切割和标签化(clevage under target and tagment, CUT&Tag)技术利用转座酶在目标蛋白结合的DNA附近进行切割并对切割下的DNA片段进行标签化,通过后续的二代测序可以快速鉴定蛋白质- DNA相互作用,极大的简化了染色质免疫共沉淀测序(chromatin immunoprecipitation sequencing, ChIP-seq)的实验过程。CUT&Tag中转座酶完成标签化后需要DNA回收或其他后处理才能进行建库PCR,不同的回收方法对CUT&Tag结果有着显著的影响。通过建立生物素化转座体-链霉亲和素磁珠体系(streptavidin beads recovery CUT&Tag, srCUT&Tag),可以快速便捷地完成CUT&Tag的产物回收。本文在K562细胞中展开H3K4me3、RNA聚合酶II (RNA polymerase II, RNAPII)、转录因子CTCF和HMGA1的CUT&Tag实验,并利用现有的乙醇沉淀、片段分选(solid-phase reversible immobilization, SPRI)磁珠回收和直接PCR法,以及本研究建立的srCUT&Tag方法对产物进行回收。结果表明,从整体上看,SPRI磁珠回收和srCUT&Tag方法着较高的回收效率,而乙醇沉淀法则回收效率低下。在全部4种CUT&Tag产物回收过程中,SPRI磁珠回收均会损失大部分小于150 bp的产物片段。在CTCF和HMGA1 CUT&Tag产物的回收中,直接PCR法则损失了大部分大于300 bp的片段并与其他回收方法的结果有较大的差别。因此,srCUT&Tag能够比其他三种回收方法提供更多更完整的测序信息。综上所述,新建立srCUT&Tag回收方法相比现有的CUT&Tag产物回收方法能提高建库效率并得到更好的数据质量,为表观遗传学研究提供了更好的技术选择。

关键词: CUT&Tag;, DNA回收方法, H3K4me3, RNAPII, CTCF, HMGA1

Abstract:

The emerging cleavage under target and tagment (CUT&Tag) technology uses Tn5 transposase to cleavage near the DNA binding site of target protein and study the generated DNA fragments by the next-generation sequencing. It can quickly identify protein-DNA interactions, which greatly simplifies the experimental process of ChIP-Seq. After CUT&Tag tagment reaction, DNA recovery or other post-processing is required to perform library construction PCR. Different recovery methods have significant impact respectively. By establishing Streptavidin beads recovery CUT&Tag(srCUT&Tag), we can quickly and conveniently complete the product recovery of CUT&Tag. We carried out CUT&Tag assay of H3K4me3, RNA Polymerase II (RNA polymerase II, RNAPII), transcription factor CTCF and HMGA1 in K562 cells with different recovery methods, including ethanol precipitation, fragment separation magnetic beads (SPRI) Magnetic bead recovery, direct PCR method, as well as our srCUT&Tag recovery method. The results show that among the CUT&Tag results of four different targets, the SPRI magnetic bead recovery and our srCUT&Tag methods have higher recovery efficiency than the direct PCR method and ethanol precipitation method. All CUT&Tag results showed that the recovery of SPRI magnetic beads would lose most of the product fragments less than 150 bp. In the recovery of CTCF and HMGA1, direct PCR lost most of the fragments larger than 300 bp and has significant difference from result of other recovery method. This enables srCUT&Tag to provide more real and higher-resolution information than other recovery method. In summary, the newly established srCUT&Tag recovery method can improve the efficiency of CUT&Tag library construction and obtain better data quality compared with the existing CUT&Tag product recovery method, providing a better technical choice for epigenetics research.

Key words: CUT&Tag;, DNA recovery method, H3K4me3, RNAPII, CTCF, HMGA1