Michael B. Wolfe

ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition

This study investigates how ppGpp regulates RNA polymerase pausing and nucleotide addition through allosteric effects and GTP competition in E. coli.

RNAP-seq: in vitro genome-scale transcription reveals preferential RNA polymerase pausing on Clostridioides difficile antisense DNA

The paper introduces RNAP-seq, an in vitro method to study transcriptional pausing, and finds that CdfRNAP pauses more frequently at T-rich antisense regions compared to EcoRNAP.

ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactions

ShapeME discovers structural DNA motifs that improve prediction of protein-DNA binding beyond traditional PWMs using ChIP-seq data.

The Genetics of Aerotolerant Growth in a Naturally Reduced Genome Alphaproteobacterium

This study identifies conditionally essential genes in Zymomonas mobilis for aerobic and anaerobic growth using CRISPRi-seq, revealing roles of DNA repair and respiratory complexes in energy coupling and isoprenoid biosynthesis.

Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments

The paper uses TEN-map to show H-NS DBDs contact DNA at the same irregularly spaced sites in both bridged and linear filaments, supporting a hemi-sequestration model.

Principles of mRNA control by human PUM proteins elucidated from multi-modal experiments and integrative data analysis

The paper identifies how human PUM proteins regulate gene expression by RNA stability and develops a rulebook to predict functional PREs using machine learning.