Differential regulation of histone H1 subtypes by N6-methyladenosine RNA methylation

Histone H1 is involved in the regulation of chromatin structure and gene expression. Up to seven H1 subtypes or variants are expressed in human somatic cells. The H1 complement, defined as the subtype composition and proportions in a given cell, is highly variable depending on the cell type, cell cycle, developmental stage, and several diseases such as cancer. It is the result of the combined action of the different regulatory processes. Epitranscriptome modifications have emerged as a new regulatory mechanism able to control all aspects of mRNA metabolism. In this work, we have examined the role of the most prevalent mRNA modification, N6-methyladenosine RNA methylation (m6A), in the regulation of H1 subtypes. MeRIP-seq showed that H1.0 and H1.4 are enriched in m6A, while H1.2 has medium levels of this mark. We found that m6A inhibition altered transcript and protein levels, de novo transcription, and ribosome occupancy at the translation start site of specific H1 subtypes. Pull-down experiments using biotinylated-specific probes followed by mass spectrometry or RNA-immunoprecipitation coupled with RT-qPCR, allowed the identification of IGF2BP1, hnRNPD, and YTHDF2 as m6A readers of H1 subtypes. Integration of the functional studies, with m6A inhibition and partial depletion of the m6A readers led us to propose the first model of the differential regulation of H1 subtypes by m6A. In this model, m6A promotes the degradation of H1.0 mRNA mediated by YTHDF2, the stabilization of H1.2 mRNA by IGF2BP1 binding, and the H1.4 mRNA translation mediated by hnRNPD. These findings suggest that m6A is involved in the subtype-specific regulation of H1 subtypes, adding another layer to their complex regulation and contributing to the variability of the H1 complement in cancer.