Identification of Transcription Factor Binding Sites by Cleavage Under Target and Release Using Nuclease in Zebrafish

IF 1.4 4区生物学 Q4 DEVELOPMENTAL BIOLOGY

Zebrafish Pub Date : 2022-06-01 DOI:10.1089/zeb.2021.0082

Radwa A. Barakat, C. Campbell, Raquel Espín-Palazón

引用次数: 2

Abstract

Cleavage Under Targets and Release Using Nuclease (CUT&RUN) has emerged as a chromatin profiling strategy that excels traditional methods. Although CUT&RUN has been widely utilized in mammalian cells, its use in the zebrafish is at its early stages. In this study, we have developed a protocol to successfully perform CUT&RUN to map transcription factor (TF) binding sites in embryonic, adult tissues, and FACS-sorted zebrafish cells. We also provide a detailed workflow for the identification of predicted TF binding sites that can be utilized in any animal species. Altogether, our strategy will expand this invaluable tool to the zebrafish community, improving the epigenetic resolution that can be achieved in this model organism.

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斑马鱼靶下裂解和核酸酶释放鉴定转录因子结合位点

利用核酸酶在靶下切割和释放(CUT&RUN)已经成为一种超越传统方法的染色质分析策略。尽管CUT&RUN已经在哺乳动物细胞中得到了广泛的应用，但它在斑马鱼中的应用还处于早期阶段。在这项研究中，我们开发了一种方案，成功地执行CUT&RUN来绘制胚胎、成年组织和facs分类的斑马鱼细胞中的转录因子(TF)结合位点。我们还提供了一个详细的工作流程，用于识别可用于任何动物物种的预测TF结合位点。总之，我们的策略将把这个宝贵的工具扩展到斑马鱼群落，提高这种模式生物的表观遗传分辨率。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Zebrafish DEVELOPMENTAL BIOLOGY-ZOOLOGY

CiteScore

3.60

自引率

5.00%

发文量

审稿时长

3 months

期刊介绍： Zebrafish is the only peer-reviewed journal dedicated to the central role of zebrafish and other aquarium species as models for the study of vertebrate development, evolution, toxicology, and human disease. Due to its prolific reproduction and the external development of the transparent embryo, the zebrafish is a prime model for genetic and developmental studies. While genetically more distant from humans, the vertebrate zebrafish nevertheless has comparable organs and tissues, such as heart, kidney, pancreas, bones, and cartilage. Zebrafish introduced the new section TechnoFish, which highlights these innovations for the general zebrafish community. TechnoFish features two types of articles: TechnoFish Previews: Important, generally useful technical advances or valuable transgenic lines TechnoFish Methods: Brief descriptions of new methods, reagents, or transgenic lines that will be of widespread use in the zebrafish community Zebrafish coverage includes: Comparative genomics and evolution Molecular/cellular mechanisms of cell growth Genetic analysis of embryogenesis and disease Toxicological and infectious disease models Models for neurological disorders and aging New methods, tools, and experimental approaches Zebrafish also includes research with other aquarium species such as medaka, Fugu, and Xiphophorus.