Robert A. Beagrie

This study shows FACT maintains promoter topology by preserving nucleosomes and preventing chromatin factor spreading into gene bodies.

The paper compares super-enhancer networks in embryonic stem cells and dopaminergic neurons, revealing their structural differences and functional roles in transcriptional regulation.

The paper identifies a de novo enhancer mutation in KCNB1 causing ST Depression Syndrome, a cardiac arrhythmia, and shows it can be predicted by a deep neural network.

This study identifies Nprl3 as a key regulator of erythroid metabolism, showing its role in coupling metabolic and developmental processes during erythropoiesis.

The paper investigates the role of cohesin-mediated loop extrusion in enhancer-promoter proximity and gene expression during mouse erythropoiesis, finding that it is important but not exclusive for gene activation.

The paper introduces multiplex-GAM, a ligation-free method for genome-wide chromatin contact mapping, showing it detects different strong contacts compared to Hi-C, particularly involving active genomic regions.

This paper establishes a scalable protocol to isolate primitive-like erythroid cells from in vitro differentiated mESCs, showing they recapitulate normal erythropoiesis and mutation effects seen in primary cells.

The paper studies chromatin architecture changes during mouse erythroid differentiation using Tiled-C and shows enhancer-promoter interactions form during differentiation, not before gene expression.

This study shows that enhancers primarily regulate gene expression by promoting transcription initiation rather than by affecting RNA polymerase II pausing.

This study models erythropoiesis in CDA-I by analyzing patient-derived erythroblasts, identifying abnormalities in DNA accessibility, proliferation, and enucleation, with genotype-phenotype correlations.

GAMtools is a pipeline for analysing Genome Architecture Mapping data, providing automated mapping, quality control, proximity matrices, and feature enrichment detection.