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. 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. A promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription. The only difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides.

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. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand. 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. 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. 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. JTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities.

Sequence of mrna