David L. Bentley

The paper uses AI to discover sequence rules for RNA polymerase II pausing, challenging the pause-release model of gene activation by showing pausing is not required for certain activation responses.

The paper shows that U1-70K promotes exon definition by destabilizing U1-5' SS interactions, leading to exon skipping when depleted.

The paper identifies a direct interaction between Integrator and NELF that regulates transcriptional pausing and premature termination.

The paper presents a new phased assembly of the Antarctic spiny plunderfish and identifies genomic features linked to cold adaptation in notothenioids.

The paper shows that Maf1 and PR work together to reduce tRNA transcription in breast cancer cells under progestin treatment.

CAR-SPLASH identifies RNA kinetic switches that regulate alternative splicing based on transcription speed, with potential therapeutic applications using antisense oligonucleotides.

This study shows that inhibiting Mediator kinases CDK8/CDK19 suppresses hyperactive IFN signaling in Down syndrome by affecting transcription, splicing, and lipid metabolism.

The paper identifies PP1 phosphatase activity in the PPWZ complex as essential for antisense transcription termination by dephosphorylating RNA pol II CTD Ser5.

The paper shows that Pol II elongation speed affects poly(A) site clustering and that poly(A) site clusters are linked to local elongation rates and DNA sequence elements.

LABRAT quantifies alternative polyadenylation (APA) and identifies its associations with RNA localization, transcription speed, cancer survival, and RNA-binding protein regulation.