Biology subjects

Bonitto, K.

Publications and source records attributed to Bonitto, K..

2 recordsLinked to original sources

bioRxiv2026

H4K20me3 and CTCF act reciprocally at TAD boundaries to regulate cell state transitions

Reversible transitions between proliferative and quiescent cell states involve widespread gene expression changes despite stable topologically associating domain (TAD) boundaries. We report a reciprocal antagonism between TAD boundary element CTCF and histone modification H4K20me3 as a central mechanism governing the proliferation-quiescence transition. Genome-wide studies and functional perturbations reveal that elevated H4K20me3 in quiescent fibroblasts displaces CTCF at specific TAD boundaries while CTCF binding predominates in proliferating cells. Increased H4K20me3 reversibly induces a compact chromatin state, elliptical nuclear morphology, and transcriptional programs associated with quiescence. Conversely, elevated CTCF binding drives open chromatin, proliferative gene expression, and cell division despite quiescence signals. Fibroblasts lacking H4K20me3 methyltransferase KMT5C/Suv4-20h2 are hyper-proliferative and KMT5C-deficient mice are larger. Our findings provide a mechanistic framework for how architectural and epigenetic regulators exchange at TAD boundaries to coordinate reversible cell state transitions, a finding with implications for organismal development and diseases of dysregulated proliferation.

cell biology↗

bioRxiv2024

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

Enhancers are critical genetic elements controlling transcription from promoters, but the mechanisms by which they convey regulatory information across large genomic distances remain elusive. Here, we engineered pluripotent stem cells in which cohesin loop extrusion can be inducibly disrupted without causing confounding cell cycle defects. While evident, transcriptional dysregulation was cell-type specific, and not all loci with distal enhancers depend equally on cohesin extrusion. Using comparative genome editing, we demonstrate that enhancer-promoter communication across as little as 20 kilobases can rely on cohesin. However, promoter-proximal regulatory elements can support long-range, cohesin-independent enhancer action - either upon disabling extrusion or across strong CTCF insulators. Finally, transcriptional dynamics and the emergence of new embryonic cell types in response to differentiation cues remained largely robust to disrupting cohesin extrusion. Beyond establishing novel experimental strategies to study cohesin functions in enhancer biology, our work provides mechanistic insight accounting for both cell type- and genomic context-specificity.

molecular biology↗