Craig D. Kaplan

Nanopore tweezers enable monitoring of RNA polymerase II translocation relative to DNA during transcription elongation with single-nucleotide spatial resolution and millisecond-scale temporal resolution at biologically relevant, saturating substrate concentrations.

The paper identifies mutants affecting transcription start site selection in yeast by analyzing promoter scanning mechanisms and their genetic reporters.

The paper investigates how the TFIIH-Pol II-TFIIE interface influences promoter scanning and TSS selection in yeast by analyzing genetic mutants and TSS sequencing data.

The paper identifies Hrp1 as an RNAP II anti-termination factor and shows specific substitutions in Hrp1 and Rpb3 affect termination by altering protein interactions.

The paper uses deep mutational scanning in yeast to analyze residue interactions in the RNA Polymerase II trigger loop, revealing its functional and evolutionary constraints.

The paper investigates higher-order epistasis within Pol II trigger loop haplotypes, identifying complex genetic interactions that influence Pol II function and evolution.

The paper quantitatively analyzes TSS selection in yeast using a new assay, showing sequence, Pol II activity, and NTP levels influence initiation efficiency.

This study investigates thiolutin's mode of action, showing it directly inhibits RNA Polymerase II in vitro but has complex in vivo effects involving oxidative stress and metal interactions.

The paper reanalyzes data from Shen et al. to argue that most synonymous mutations in yeast genes are not deleterious, challenging their original conclusions about fitness effects.

This study investigates how Ssl2/TFIIH influences transcription start site scanning by RNA Polymerase II in yeast, identifying alleles that alter TSS selection and scanning processivity.

The paper investigates promoter scanning by Pol II in yeast, showing that it occurs across all promoters and is influenced by Pol II activity and promoter architecture.

The paper shows that gene expression and transcription-related processes influence cell size distribution in yeast by analyzing single-gene deletion strains.

The paper investigates the effects of altered Pol II catalytic activity on gene expression in yeast, finding unexpected results regarding elongation rates and mRNA stability.

The paper quantitatively phenotypes nearly all single-residue variants of the RNA Polymerase II trigger loop in Saccharomyces cerevisiae to uncover functional classes and their roles in transcription.