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

Nicoletti, C.; Massenet, J.; Pintado-Urbanc, A. P.; Connor, L. J.; Nicolau, M.; Sundar, S.; Xu, M.; Schmitt, A.; Zhang, W.; Fang, Z.; Chan, T. C. I.; Tapscott, S. J.; Cheung, T. H.; Simon, M. D.; Caputo, L.; Puri, P. L.

doi:10.1101/2024.12.05.627024

bioRxiv · 10.1101/2024.12.05.627024

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

Nicoletti, C.·Massenet, J.·Pintado-Urbanc, A. P.·Connor, L. J.·Nicolau, M.·Sundar, S.·Xu, M.·Schmitt, A.·Zhang, W.·Fang, Z.·Chan, T. C. I.·Tapscott, S. J.·Cheung, T. H.·Simon, M. D.·Caputo, L.·Puri, P. L.

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Abstract

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.

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Nicoletti, C., Massenet, J., Pintado-Urbanc, A. P., Connor, L. J., Nicolau, M., Sundar, S., Xu, M., Schmitt, A., Zhang, W., Fang, Z., Chan, T. C. I., Tapscott, S. J., Cheung, T. H., Simon, M. D., Caputo, L., Puri, P. L.. 2024-12-05. E-box independent chromatin recruitment turns MYOD into a transcriptional repressor. https://doi.org/10.1101/2024.12.05.627024

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