核糖核酸
RNA结合蛋白
内生
原位
HEK 293细胞
生物
计算生物学
细胞生物学
融合蛋白
原位杂交
信使核糖核酸
分子生物学
化学
生物化学
基因
有机化学
重组DNA
作者
Qishan Liang,Tao Yu,Eric Kofman,Pratibha Jagannatha,Kevin Rhine,Brian A. Yee,Kevin D. Corbett,G Yeo
标识
DOI:10.1038/s41467-024-50363-4
摘要
Abstract RNA-binding proteins (RBPs) have pivotal functions in RNA metabolism, but current methods are limited in retrieving RBP-RNA interactions within endogenous biological contexts. Here, we develop INSCRIBE ( IN situ S ensitive C apture of R NA-protein I nteractions in B iological E nvironments), circumventing the challenges through in situ RNA labeling by precisely directing a purified APOBEC1-nanobody fusion to the RBP of interest. This method enables highly specific RNA-binding site identification across a diverse range of fixed biological samples such as HEK293T cells and mouse brain tissue and accurately identifies the canonical binding motifs of RBFOX2 (UGCAUG) and TDP-43 (UGUGUG) in native cellular environments. Applicable to any RBP with available primary antibodies, INSCRIBE enables sensitive capture of RBP-RNA interactions from ultra-low input equivalent to ~5 cells. The robust, versatile, and sensitive INSCRIBE workflow is particularly beneficial for precious tissues such as clinical samples, empowering the exploration of genuine RBP-RNA interactions in RNA-related disease contexts.
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