ePRINT: exonuclease assisted mapping of protein-RNA interactions.

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-05-28 DOI:10.1186/s13059-024-03271-1

Sophie Hawkins, Alexandre Mondaini, Seema C Namboori, Grady G Nguyen, Gene W Yeo, Asif Javed, Akshay Bhinge

引用次数: 0

Abstract

RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new method, ePRINT, maps RBP-RNA interaction networks on a global scale without purifying individual RBPs. ePRINT uses exoribonuclease XRN1 to precisely map the 5' end of the RBP binding site and uncovers direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, including neural progenitor differentiation into neurons.

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ePRINT：外切酶辅助绘制蛋白质-RNA相互作用图。

RNA 结合蛋白（RBPs）通过物理结合 RNA 分子来调节 RNA 处理的关键环节，包括替代剪接、mRNA 降解和定位。目前绘制这些相互作用图的方法（如 CLIP）依赖于一次纯化单个蛋白质。我们的新方法 ePRINT 无需纯化单个 RBP 即可绘制全球范围的 RBP-RNA 相互作用网络图。ePRINT 利用外核酸酶 XRN1 精确绘制 RBP 结合位点的 5' 端，并发现感兴趣的 RBP 的直接和间接靶标。重要的是，ePRINT 还能发现在细胞命运转换（包括神经祖细胞向神经元的分化）过程中被不同程度激活的 RBPs。

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

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.

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