RT Journal Article
SR Electronic
T1 The anti-cancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3′ processing machinery
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.04.11.536453
DO 10.1101/2023.04.11.536453
A1 Liang Liu
A1 Angela M Yu
A1 Xiuye Wang
A1 Lindsey V. Soles
A1 Yiling Chen
A1 Yoseop Yoon
A1 Kristianna S.K. Sarkan
A1 Marielle Cárdenas Valdez
A1 Johannes Linder
A1 Ivan Marazzi
A1 Zhaoxia Yu
A1 Feng Qiao
A1 Wei Li
A1 Georg Seelig
A1 Yongsheng Shi
YR 2023
UL http://biorxiv.org/content/early/2023/04/11/2023.04.11.536453.abstract
AB JTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities. Upon entering the cell, it is hydrolyzed to Compound 2, which directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-mRNA 3′ processing. Although CPSF73 is universally required for mRNA 3′ end formation, we have unexpectedly found that Compound 2- mediated inhibition of pre-mRNA 3′ processing is sequence-specific and that the sequences flanking the cleavage site (CS) are a major determinant for drug sensitivity. By using massively parallel in vitro assays, we have measured the Compound 2 sensitivities of over 260,000 sequence variants and identified key sequence features that determine drug sensitivity. A machine learning model trained on these data can predict the impact of JTE-607 on poly(A) site (PAS) selection and transcription termination genome-wide. We propose a biochemical model in which CPSF73 and other mRNA 3′ processing factors bind to RNA of the CS region in a sequence-specific manner and the affinity of such interaction determines the Compound 2 sensitivity of a PAS. As the Compound 2-resistant CS sequences, characterized by U/A-rich motifs, are prevalent in PASs from yeast to human, the CS region sequence may have more fundamental functions beyond determining drug resistance. Together, our study not only characterized the mechanism of action of a compound with clinical implications, but also revealed a previously unknown and evolutionarily conserved sequence-specificity of the mRNA 3′ processing machinery.Competing Interest StatementThe authors have declared no competing interest.