Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation
Rong Ye, Naijing Hu, Changchang Cao, Ruibao Su, Shihan Xu, Chen Yang, Xiangtian Zhou, Yuanchao Xue
Abstract
RNA-binding proteins (RBPs) bind at different positions of the pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a capture RIC-seq (CRIC-seq) method to enrich specific RBP-associated in situ proximal RNA-RNA fragments for deep sequencing. We determine hnRNPA1-, SRSF1-, and PTBP1-associated proximal RNA-RNA contacts and regulatory mechanisms in HeLa cells. Unexpectedly, the 3D RNA map analysis shows that PTBP1-associated loops in individual introns preferentially promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. These “positional rules” can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-associated RNA-RNA proximal contacts in gene regulation and disease.
附件下载：
Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation, Mol Cell, 23 Mar 2023
Molecular Cell, 23 March, 2023, DOI：https://doi.org/10.1016/j.molcel.2023.03.001
Capture RIC-seq reveals positional rules of PTBP1-associated RNA loops in splicing regulation
Rong Ye, Naijing Hu, Changchang Cao, Ruibao Su, Shihan Xu, Chen Yang, Xiangtian Zhou, Yuanchao Xue
Abstract
RNA-binding proteins (RBPs) bind at different positions of the pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a capture RIC-seq (CRIC-seq) method to enrich specific RBP-associated in situ proximal RNA-RNA fragments for deep sequencing. We determine hnRNPA1-, SRSF1-, and PTBP1-associated proximal RNA-RNA contacts and regulatory mechanisms in HeLa cells. Unexpectedly, the 3D RNA map analysis shows that PTBP1-associated loops in individual introns preferentially promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. These “positional rules” can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-associated RNA-RNA proximal contacts in gene regulation and disease.
文章链接：https://www.sciencedirect.com/science/article/pii/S1097276523001582?via%3Dihub
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