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通过ChIP-seq和CUT&Tag检查NF-κB基因组相互作用

Allison E Daly^1,2, Allison Schiffman^1,2,3, Alexander Hoffmann^1,2,3

¹Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA.

bioRxiv : the preprint server for biology

|August 26, 2024

概括

优化染色体免疫沉降测序 (ChIP-seq) 条件显著影响转录因子结合位点检测. 实验变量,而不仅仅是像CUT&Tag这样的技术,对转录因子相互作用的全基因组分析产生了重大影响.

科学领域:

分子生物学分子生物学
基因组学就是基因组学.
表观遗传学在表观遗传学中,表观遗传学是指表观遗传学.

背景情况:

了解基因调节的转录因子 (TF) 协调,需要对TF-DNA相互作用进行全基因组的映射.
染色体免疫沉测序 (ChIP-seq) 和CUT&Tag识别了数千种TF相互作用,但缺乏功能上下文.
优化ChIP-seq通常仅限于特定网站,因为成本和时间.

研究的目的:

调查化学交联试剂定位对NF-κB家族成员RelA和c-Rel.全基因组ChIP-seq结果的影响.
为了比较这些转录因子的ChIP-seq和CUT&Tag实验的结果.
评估实验条件如何影响TF基因组相互作用的检测和特征.

主要方法:

进行了全基因组ChIP-seq实验,使用不同度的两个化学交联试剂.
研究了NF-κB家族的转录因子RelA和c-Rel.
将ChIP-seq结果与从CUT&Tag实验中获得的结果进行比较.

主要成果:

ChIP-seq实验条件极大地影响了检测到的相互作用数量和DNA基因丰富.
检测到的相互作用与潜在的目标基因的接近程度根据实验参数而异.
虽然ChIP-seq和CUT&Tag显示一致性,但很大一部分相互作用是每个方法独有的.
交叉连接试剂的定位证明对RelA和c-Rel结合部位的识别产生了重大影响.

结论:

实验条件极大地影响全基因组转录因子结合分析.
在ChIP-seq和CUT&Tag之间检测到的相互作用的差异凸显了需要仔细选择和优化方法的需要.
需要进一步研究以了解TF约束性数据中条件依赖变化的功能意义.

关键词:

在CUT&Tag中使用CUT&Tag.在 ChIP-seqq.炎症炎症是一种炎症.巨细胞是一个巨细胞.这就是NF-κBB.

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