Julie Donaghey

TL;DR: Although in theory every CpG can change its methylation state, the results suggest that only a fraction does so as part of coordinated regulatory programs, which highlights the general inefficiency of whole-genome bisulphite sequencing.

TL;DR: Comprehensive transcriptional and epigenetic profiling of populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers reveals unique events associated with specification toward each lineage.

TL;DR: This data provides a comprehensive characterization of DNMT-mutant ESCs, including single-base genome-wide maps of the targets of these enzymes, and inactivated all three catalytically active DNA methyltransferases using CRISPR/Cas9 genome editing.

TL;DR: This work reports the integrative analysis of genome-wide binding data for 38 transcription factors with extensive epigenome and transcriptional data across the differentiation of human embryonic stem cells to the three germ layers, and describes core regulatory dynamics and shows the lineage-specific behaviour of selected factors.

TL;DR: In this paper, a clonal, inducible human reprogramming system that provides a reliable source of cells at any stage of the process was constructed and characterized, which enabled integrative transcriptional and epigenomic analysis across the human reprogrogramming timeline at high resolution.