Biology subjects

Soles, L. V.

Publications and source records attributed to Soles, L. V..

4 recordsLinked to original sources

bioRxiv2025

The competition between splicing and 3' processing shapes the human transcriptome

Eukaryotic pre-mRNA processing steps, including splicing and 3' processing, are tightly coordinated, yet the underlying mechanisms remain incompletely understood. U1 snRNP has been proposed to inhibit 3' processing at intronic polyadenylation (IPA) sites through a splicing-independent mechanism termed telescripting. In contrast, we discovered that disrupting splicing--by targeting various key components such as U1 snRNP, U2 snRNP, U2AF, and SF3b--activates 3' processing at thousands of IPA sites. Notably, splicing inhibition, especially of U1 snRNP, induced widespread premature transcription termination within gene bodies through both IPA-coupled and -independent mechanisms. Different splicing factors activated overlapping and distinct sets of IPA sites, reflecting their specific contributions to transcription and spliceosome function. Conversely, inhibition of 3' processing enhanced splicing globally. These findings support a model in which splicing and 3' processing are competing processes that intersect with transcription to shape the transcriptome landscape.

molecular biology↗

bioRxiv2025

LENG8 mediates RNA nuclear retention and degradation in eukaryotes

In eukaryotes, incompletely processed and misprocessed mRNAs as well as numerous noncoding RNAs are retained in the nucleus and often degraded. However, the mechanisms for this critical quality control pathway remain poorly understood. Here we identify LENG8 as a conserved RNA nuclear retention factor. We showed that LENG8 is recruited to pre-mRNAs by splicing factors, including the U1 snRNP. LENG8 binds to PCID2 and SEM1 to form the REX (Repressor of EXport) complex, which is conserved from yeast to human, and causes RNA nuclear retention by acting as a dominant negative factor for the essential mRNA export factor TREX-2. LENG8 depletion leads to the leakage of misprocessed mRNAs, including intronically polyadenylated and intron-retained mRNAs, as well as noncoding RNAs into the cytoplasm. Finally, LENG8 promotes RNA degradation by recruiting PAXT and the RNA exosome. Thus our study revealed a conserved quality control mechanism for eukaryotic gene expression that ensures only fully and correctly processed RNAs are exported from the nucleus.

molecular biology↗

bioRxiv2024

A nuclear RNA degradation code for eukaryotic transcriptome surveillance

The RNA exosome plays critical roles in eukaryotic RNA degradation, but it remains unclear how the exosome specifically recognizes its targets. The PAXT connection is an adaptor that recruits the exosome to polyadenylated RNAs in the nucleus, especially transcripts polyadenylated at intronic poly(A) sites. Here we show that PAXT-mediated RNA degradation is induced by the combination of a 5' splice site and a poly(A) junction, but not by either sequence alone. These sequences are bound by U1 snRNP and cleavage/polyadenylation factors, which in turn cooperatively recruit PAXT. As the 5' splice site-poly(A) junction combination is typically not found on correctly processed full-length RNAs, we propose that it functions as a "nuclear RNA degradation code" (NRDC). Importantly, disease-associated single nucleotide polymorphisms that create novel 5' splice sites in 3' untranslated regions can induce aberrant mRNA degradation via the NRDC mechanism. Together our study identified the first NRDC, revealed its recognition mechanism, and characterized its role in human diseases.

molecular biology↗

bioRxiv2023

The anti-cancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery

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.

molecular biology↗