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Transcriptome-wide identification of single-stranded RNA binding proteins.


ABSTRACT: RNA-protein interactions are precisely regulated by RNA secondary structures in various biological processes. Large-scale identification of proteins that interact with particular RNA structure is important to the RBPome. Herein, a kethoxal assisted single-stranded RNA interactome capture (KASRIC) strategy was developed to globally identify single-stranded RNA binding proteins (ssRBPs). This approach combines RNA secondary structure probing technology with the conventional method of RNA-binding proteins profiling, realizing the transcriptome-wide identification of ssRBPs. Applying KASRIC, we identified 3180 candidate RBPs and 244 candidate ssRBPs in HeLa cells. Importantly, the 244 candidate ssRBPs contained 55 previously reported ssRBPs and 189 novel ssRBPs. Function analysis of the candidate ssRBPs exhibited enrichment in cellular processes related to RNA splicing and RNA degradation. The KASRIC strategy will facilitate the investigation of RNA-protein interactions.

SUBMITTER: Zhao R 

PROVIDER: S-EPMC10094363 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature

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Transcriptome-wide identification of single-stranded RNA binding proteins.

Zhao Ruiqi R   Fang Xin X   Mai Zhibiao Z   Chen Xi X   Mo Jing J   Lin Yingying Y   Xiao Rui R   Bao Xichen X   Weng Xiaocheng X   Zhou Xiang X  

Chemical science 20230324 15


RNA-protein interactions are precisely regulated by RNA secondary structures in various biological processes. Large-scale identification of proteins that interact with particular RNA structure is important to the RBPome. Herein, a kethoxal assisted single-stranded RNA interactome capture (KASRIC) strategy was developed to globally identify single-stranded RNA binding proteins (ssRBPs). This approach combines RNA secondary structure probing technology with the conventional method of RNA-binding p  ...[more]

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