Biology subjects

Pintado-Urbanc, A. P.

Publications and source records attributed to Pintado-Urbanc, A. P..

3 recordsLinked to original sources

bioRxiv2026

Histone H4 acetyl-methyllysine marks accessible chromatin that resists compaction

Certain regulatory DNA regions remain accessible even under conditions of widespread chromatin compaction. These regions are often marked by specific protein factors and histone modifications that help maintain their accessibility. Here, we examine the genomic landscape of acetyl-methyllysine (Kacme), a recently discovered histone post-translational modification. Across multiple systems, Kacme is highly enriched at sites of accessible chromatin, including active promoters, enhancers, silencers, and CTCF-binding sites. We find that Kacme is selectively retained at loci that resist condensation during mitosis, marks XIST and escapee regions on the inactive X chromosome in female cells and demarcates the boundaries of broad heterochromatin domains. Kacme-marked insulator elements block heterochromatin spreading and protect adjacent genes from transcriptional repression, even when H3K27me3 levels are pharmacologically elevated through KDM6A/6B inhibition. Taken together, our findings establish the chromatin features associated with Kacme and support a model in which Kacme helps safeguard chromatin accessibility at loci that resist compaction.

molecular biology↗

bioRxiv2025

RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and WNT pathway activation

Acute megakaryoblastic leukemia driven by the RBM15-MKL1 fusion protein (RM-AMKL) is the only known recurrent mutation involving the N6-methyladenosine (m6A) writer complex. Dysregulation of m6A modification affects RNA fate and is linked to oncogenesis. Inhibition of m6A deposition via inhibition of the METTL3 writer protein has anti-tumour activity, but the mechanism underlying its efficacy and cancer specificity remains unclear. We treated murine RM-AMKL cells with a novel METTL3 inhibitor, STM3675, and showed apoptosis in vitro and prolonged survival of mice transplanted with RM-AMKL, implicating m6A as an essential component of AMKL and identifying Wnt signalling as a key driver of leukemogenesis. To elucidate the mechanism by which m6A contributes to leukemogenesis we employed a multi-omic approach, combining transcriptome-wide assessment of RNA binding, methylation and turnover. We show for the first time that RM retains the RNA-binding and m6A-modifiying functions of its RBM15 component, while also selectively regulating distinct mRNA targets, particularly genes involved in Wnt signalling including Frizzled. Frizzled genes are upregulated by RM and downregulated in RM-AMKL cells in response to METTL3 inhibition, providing an m6A-dependent explanation for their upregulation. Direct Frizzled knockdown reduced RM-AMKL growth, which was partially rescued by treatment with a {beta}-catenin agonist, underscoring a functional role of Wnt signalling in RM-AMKL. Human AMKLs show elevated Wnt pathway and Frizzled gene expression, highlighting the relevance of our work. Together, our findings reveal that RM-specific m6A modifications and activation of Wnt signalling are critical drivers of RM-AMKL, highlighting these pathways as potential therapeutic targets. Key PointsO_LIRM retains functional abilities of RBM15 and additionally interacts with Wnt-related transcripts to increase expression of Fzd proteins. C_LIO_LIThe METTL3 writer complex and WNT signalling pathways are essential for RM-driven leukemia. C_LI

cancer biology↗

bioRxiv2024

E-box independent chromatin recruitment turns MYOD into a transcriptional repressor

MYOD is an E-box sequence-specific basic Helix-Loop-Helix (bHLH) transcriptional activator that, when expressed in non-muscle cells, induces nuclear reprogramming toward skeletal myogenesis by promoting chromatin accessibility at previously silent loci. Here, we report on the identification of a previously unrecognized property of MYOD as repressor of gene expression, via E-box-independent chromatin binding within accessible genomic elements, which invariably leads to reduced chromatin accessibility. MYOD-mediated repression requires the integrity of functional domains previously implicated in MYOD-mediated activation of gene expression. Repression of mitogen-and growth factor-responsive genes occurs through promoter binding and requires a highly conserved domain within the first helix. Repression of cell-of-origin/alternative lineage genes occurs via binding and decommissioning of distal regulatory elements, such as super-enhancers (SE), which requires the N-terminal activation domain as well as two chromatin-remodeling domains and leads to reduced strength of CTCF-mediated chromatin interactions. Surprisingly, MYOD-mediated chromatin compaction and repression of transcription do not associate with reduction of H3K27ac, the conventional histone mark of enhancer or promoter activation, but with reduced levels of the recently discovered histone H4 acetyl-methyl lysine modification (Kacme). These results extend MYOD biological properties beyond the current dogma that restricts MYOD function to a monotone transcriptional activator and reveal a previously unrecognized functional versatility arising from an alternative chromatin recruitment through E-box or non-E-box sequences. The E-box independent repression of gene expression by MYOD might provide a promiscuous mechanism to reduce chromatin accessibility and repress cell-of-origin/alternative lineage and growth factor/mitogen-responsive genes to safeguard the integrity of cell identity during muscle progenitor commitment toward the myogenic lineage.

molecular biology↗