Chromatin Domain Reorganization During the Epithelial-to-Mesenchymal Transition
DOI:
https://doi.org/10.5281/zenodo.22757845Keywords:
epithelial-mesenchymal transition, A/B compartment, Hi-C, ZEB1, TAD reorganization, TGF-beta, chromatin accessibilityAbstract
The epithelial-to-mesenchymal transition (EMT) involves a coordinated switch in gene expression from an epithelial
to a mesenchymal transcriptional programme, but how this switch relates to larger-scale three-dimensional
chromatin organisation, including A/B compartment identity and topologically associating domain (TAD) structure,
has not been comprehensively resolved across a time-resolved EMT induction. Here we combined in situ Hi-C,
ATAC-seq, ChIP-seq for the EMT transcription factor ZEB1 and CTCF, and RNA-sequencing across a 7-day
TGF-beta-induced EMT time course in MCF10A mammary epithelial cells to define the chromatin domain
reorganisation accompanying EMT. Hi-C showed that 8.2% of the genome switched A/B compartment status
between day 0 and day 7, with genes switching from B (repressed) to A (active) compartment significantly enriched
for mesenchymal identity genes and genes switching from A to B enriched for epithelial junction and polarity genes,
and compartment switching direction closely matched the direction of gene expression change at the same loci.
TAD boundary strength was largely stable genome-wide, but a defined subset of boundaries flanking mesenchymal
genes showed significant weakening by day 7, coinciding with increased ATAC-seq accessibility and new ZEB1
occupancy at the affected boundary and enhancer elements. ZEB1 ChIP-seq peaks gained during EMT were
significantly enriched at the boundaries and internal elements of domains undergoing A/B compartment switching,
and ZEB1 depletion by short hairpin RNA blunted both the compartment switch and the transcriptional induction of
mesenchymal genes without preventing the initial accessibility gain at their promoters. These results show that EMT
is accompanied by coordinated, gene-expression-matched A/B compartment switching and selective TAD boundary
weakening at mesenchymal loci, and that ZEB1 is required for this chromatin domain reorganisation to proceed to
completion rather than solely for downstream transcriptional activation.
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