Biology subjects

Philpott, A.

Publications and source records attributed to Philpott, A..

6 recordsLinked to original sources

bioRxiv2026

Tissue-specific chromatin accessibility and co-factor availability together define ASCL1-dependent neural reprogrammability across germ layers during embryogenesis

The proneural transcription factor ASCL1 is well established as a pioneering neuronal reprogramming factor in several contexts. However, the extent to which distinct tissue types adopt a similar or divergent response to the same ASCL1 fate challenge is unclear. By expressing ASCL1 across germ layers and tissues of the developing Xenopus neurula embryo, we reveal widespread but largely distinct transcriptomic and chromatin responses to ASCL1. Ectopic ASCL1 can access partially open chromatin sites across all tissues, but it is able to further open those sites specifically in neuroectoderm. Using motif enrichment and accessibility analyses we identify Sox transcription factor motifs as enriched and preferentially accessible at ASCL1-bound regions in neuroectoderm. We show that co-expression of Sox3 and ASCL1 can enable the activation of otherwise refractory ASCL1 target genes in mesoderm and epidermal skin. Our findings reveal how the chromatin landscape and co-factor availability work together to modulate the response to transcription factor-driven fate challenge during development. Summary statementSingle-cell multi-omics reveals how chromatin accessibility and cofactor availability constrains ASCL1-driven neuronal reprogramming across tissues in the developing Xenopus embryo.

developmental biology↗

bioRxiv2026

Chromatin priming and co-factor availability shape lineage response to the neuronal pioneer factor ASCL1 in pluripotency

Transcription factors act within defined developmental windows, yet how naive pluripotent cells acquire competence to execute specific transcription factor-driven fate programmes remains unclear. Pioneer transcription factors that engage target sites in closed chromatin to initiate gene expression programmes often act at the top of hierarchies in cell identity transitions. However, we show that the ability of ASCL1 to induce a coherent neuronal programme emerges only after exit from pluripotency, coincident with progressive chromatin remodelling and accumulation of permissive histone marks at neuronal ASCL1 target sites. Binding analysis reveals that although ASCL1 can access a subset of neuronal loci in mESCs and EpiLCs, ASCL1 is preferentially diverted to non-neuronal sites, resulting in divergent transcriptional responses. Increasing global histone acetylation enhances activation of individual neuronal genes but is insufficient to drive full neuronal differentiation. In contrast, co-expression of the homeodomain transcription factor PHOX2B redirects ASCL1 towards neuronal targets while suppressing inappropriate programmes in mESCs. These findings demonstrate that ASCL1 pioneer activity is highly context-dependent and that developmental priming of chromatin is essential for appropriate lineage specification. HIGHLIGHTSO_LIEctopic ASCL1 drives non-neuronal transcriptional responses in naive and formative pluripotent cells C_LIO_LIASCL1 occupies distinct, predominantly non-neuronal genomic targets in pluripotent cells due to differential chromatin accessibility C_LIO_LIASCL1 pioneer activity is locus- and cell type-specific and predicted by histone acetylation status C_LIO_LICo-expression of ASCL1 with Phox2 homeodomain cofactors potentiates neuronal lineage acquisition in pluripotent cells C_LI

developmental biology↗

bioRxiv2026

Hierarchical TBX6-FOXC Regulatory Logic Controls Human Trunk Mesoderm Diversification

Mesoderm forms during gastrulation and diversifies to generate many embryonic tissues, yet the regulatory logic governing early human mesodermal lineage decisions remains poorly defined. We use human iPSC-derived 3D trunk-like structures (hTLS) to model lineage specification during early post-gastrulation development, a stage experimentally inaccessible in humans. Developing hTLS generate neural and mesodermal lineages and recapitulate progressive mesodermal diversification into paraxial (somitic) and intermediate (renal) identities. Using genetic perturbations and temporally controlled transcription factor activation, we identify duration-dependent TBX6 activity as a critical determinant of mesodermal diversification. Downstream, the forkhead box transcription factors FOXC1 and FOXC2 stabilise somitic identity and are required for sclerotome differentiation. These findings reveal a duration-dependent hierarchical regulatory logic in early human mesoderm, in which competence for diversification is established before downstream lineage identities are stabilised, positioning hTLS as a powerful platform to experimentally dissect human developmental programs. HighlightsO_LIHuman trunk-like structures model mesodermal diversification during early post-gastrulation human trunk development C_LIO_LITBX6 duration acts as a temporal gate controlling mesodermal fate potential C_LIO_LIFOXC1/2 function downstream of TBX6 to lock in somitic identity and restrict alternative fates C_LIO_LIDegTrace enables lineage tracing following transient transcription factor activation C_LI

developmental biology↗

bioRxiv2025

Comparative ASCL1 interactome analysis reveals CDK2-Cyclin A2 as suppressors of differentiation in MYCN-amplified neuroblastoma

Neuroblastoma is a heterogeneous paediatric cancer arising from developmentally arrested neuronal precursors, where restoring differentiation offers therapeutic promise. ASCL1, a pro-neural transcription factor, is widely expressed in neuroblastoma and can drive either proliferation or differentiation depending on the cellular context. Here, we show that distinct MYCN-amplified neuroblastoma cell lines exhibit differing cell cycle and differentiation responses to ASCL1 overexpression. By comparing genome-wide ASCL1 chromatin binding, transcriptional changes, and protein-protein interactions, we found that ASCL1 binds more extensively to neuronal proteins in a cell line that is more susceptible to ASCL1-driven differentiation, but associates with cell cycle regulators in less responsive cells. We show that CDK2-Cyclin A2 bind ASCL1 in less responsive cells, with CDK-mediated phosphorylation of ASCL1 limiting the ability of ASCL1 to drive differentiation. Our study reveals that context-dependent interactions of ASCL1 with protein partners on the chromatin control its ability to re-engage a differentiation program in neuroblastoma.

cancer biology↗

bioRxiv2024

Distinct proliferative and neuronal programmes of chromatin binding and gene activation by ASCL1 are cell cycle stage-specific

ASCL1 is a potent proneural factor with paradoxical functions during development, promoting both progenitor pool expansion and neuronal differentiation. How a single factor executes and switches between these potentially opposing functions remain to be understood. Using neuroblastoma cells as a model system, we show that ASCL1 exhibits cell cycle phase-dependent chromatin binding patterns. In cycling cells, S/G2/M phase-enriched binding occurs at promoters of transcribed pro-mitotic genes, while G1 phase-enriched binding of ASCL1 is associated with the priming of pro-neuronal enhancer loci. Prolonged G1 arrest is further required to activate these ASCL1-bound and primed neuronal enhancers to drive neuronal differentiation. Thus, we reveal that the same transcription factor can control distinct transcriptional programmes at different cell cycle stages, and demonstrate how lengthening of G1 allows engagement of a differentiation programme by turning unproductive factor binding into productive interactions.

developmental biology↗

bioRxiv2018

Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration

The intestinal epithelium is maintained by a small number of self-renewing stem cells in homeostasis. In addition committed progenitors can contribute to the functional stem cell compartment at a low level during homeostasis and substantially during regeneration following tissue damage. However the mechanism of, and requirement for, progenitor plasticity in mediating pathological response has not been demonstrated. Here we show that multisite phosphorylation of the transcription factor Atoh1 is required both for the contribution of secretory progenitors to the intestinal stem cell pool and for a robust regenerative response following damage. In lineage tracing experiments Atoh1+ cells (Atoh1(WT)CreERT2 mice) show stem cell activity by giving rise to multilineage intestinal clones both in the steady state and after tissue damage. Notably in the colonic epithelium a single generation of Atoh1+ progenitors sustains 1 in 15 stem cells. In an activating Atoh1(9S/T-A)CreERT2 line, the loss of phosphorylation sites on the Atoh1 protein promotes secretory differentiation and inhibits the contribution of these cells to self-renewal. Finally, in a chemical colitis model the Atoh1+ cells of Atoh1(9S/T-A)CreERT2 mice have reduced clonogenic capacity that impacts overall regenerative response of the epithelium. Thus progenitor plasticity plays an integral part in maintaining robust self-renewal in the intestinal epithelium and the balance between stem and progenitor fate behaviour is directly co-ordinated by Atoh1 multi-site phosphorylation.

cell biology↗