Rozemarijn Kleinendorst

The paper introduces SMFNet and PRISM to analyze how transcription factor assemblies influence chromatin accessibility and identifies sequence-encoded principles of combinatorial TF assembly.

The paper quantifies enhancer activation frequency in response to TF perturbations and identifies H3K27Ac as a chromatin mark required for enhancer activation.

The paper measures RNA Polymerase II occupancy at promoters in mouse and Drosophila, finding lower occupancy and higher turnover in mammals.

The paper uses single molecule multi-omics to show DNA methylation can block transcription factor binding at cell-type-specific enhancers, but not all enhancers.

The paper uses single molecule footprinting to study transcription factor co-occupancy and cooperativity in mouse cis-regulatory elements, finding that high DNA co-occupancy can occur without direct physical interaction.

This study identifies vault RNA1-1 as a riboregulator of autophagy by interacting with p62, showing that it modulates autophagic flux.