This study investigates enhancer-promoter contact architecture and communication, finding that RNA polymerase II and PARP1 activity stabilize these contacts.

Nature Genetics · Jul 10, 2023Peer-reviewedGenomics

A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility

Angelo Alberto Ruggieri, Luca Livraghi, James J. Lewis, Elizabeth Evans, Francesco Cicconardi, Laura Hebberecht, Stephen Hugh Montgomery, Alfredo Ghezzi, José A. Rodríguez‐Martínez, Chris D. Jiggins, W. Owen McMillan, Brian A. Counterman, Riccardo Papa, Steven M. Van Belleghem

The paper characterizes structural variation in Heliconius butterfly genomes and links it to chromatin accessibility and cis-regulatory elements.

bioRxiv · Apr 14, 2022 · PreprintGenomics

Multiple stages of evolutionary change in anthrax toxin receptor expression in humans

Lauren A. Choate, Gilad Barshad, Pierce W. McMahon, Iskander Said, Edward J. Rice, Paul R. Munn, James J. Lewis, Charles G. Danko

The paper examines evolutionary changes in ANTXR2 expression in humans, finding regulatory changes and recent positive selection linked to adaptation to anthrax disease.

Nature Communications · Nov 15, 2021Peer-reviewedGenetics

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock

Judhajeet Ray, Paul R. Munn, Anniina Vihervaara, James J. Lewis, Abdullah Ozer, Charles G. Danko, John T. Lis

This study shows that chromatin conformation remains stable during heat shock-induced transcriptional changes in human and Drosophila cells.

Proceedings of the National Academy of Sciences · Sep 10, 2019Peer-reviewedMolecular Biology