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使用seq-DAP-seqq识别植物转录因子DNA结合部位

Stephanie Hutin¹, Romain Blanc-Mathieu¹, Philippe Rieu¹

¹Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, Université Grenoble Alpes, INRAE, IRIG, CEA Grenoble, Grenoble, France.

Methods in molecular biology (Clifton, N.J.)

|September 8, 2023

概括

DNA亲和力净化测序 (DAP-seq) 和其修改,测序 DAP-seq (seq-DAP-seq),绘制全基因组转录因子结合位 (TFBS). 这些强大的 in vitro 方法可以识别用于破译监管网络的 TF 结合位点.

科学领域:

分子生物学分子生物学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

识别全基因组转录因子结合位 (TFBS) 对于理解基因调节至关重要.
目前用于映射TFBS的方法,特别是对于TF复合体,面临技术挑战.

研究的目的:

介绍一个详细的协议序列DNA亲和力净化测序 (seq-DAP-seq) 对异构聚合物TF复合体.
描述下游生物信息管道,用于从DAP-seq数据开发TFBS模型.

主要方法:

DNA亲和力净化测序 (DAP-seq) 和测序 DAP-seq (seq-DAP-seq) 是使用碎片化基因组DNA库的体外方法.
图书馆以亲和标记的TF或TF复合体进行化,随后进行化,PCR放大和下一代测序.
生物信息学管道分析序列阅读以识别TFBS并生成预测模型.

主要成果:

该研究概述了seq-DAP-seq的综合性协议,适用于各种生物体.
描述的生物信息学管道使得TFBS能够从DAP-seq实验数据中进行可靠的建模.
这种方法可以确定TF结合裸体或内生修饰的DNA.

结论:

Seq-DAP-seq为TF和TF复杂结合点的全基因组映射提供了一个强大的方法.
协议和相关的生物信息管道有助于解读转录性监管网络.
这项工作提升了在全基因组范围内研究基因调节的技术能力.

关键词:

DNA亲和力净化测序 (DAP-seq) 是一种测序方法.通过DNA甲基化.再组合蛋白质的表达方式序列DNA亲和力净化测序 (seq-DAP-seq) 是一个测序.连续的拉下拉下方式.转录因子结合位点 (TFBS)转录因子 (TF) 是一种转录因子.

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相关概念视频

Chromatin Immunoprecipitation- ChIP

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...