Epigenetic landscape of intestinal cell line HT29 cocultured with <i>Lacticaseibacillus</i>

<b>Aim:</b> To investigate the changes in epigenetic landscape of HT29 cells upon coculture with the <i>Lacticaseibacillus.</i> <b>Materials &amp; methods:</b> Histone and m6A mRNA modifications were examined by biochemical and NGS-based methods including western blotting, colorimetric assays, ChIP-Seq and direct mRNA sequencing. LC-MS was performed to identify <i>Lacticaseibacillus</i> secretome. <b>Results:</b> In cocultured HT29 cells global enrichment of H3K9ac and H3K4me3 and depletion of H3K9me3 mark was observed; mean genic positional signals showed depletion of H3K9ac and H3K4me3 at the TSS but enrichment in the upstream region; m6A methylation was altered in mRNAs corresponding to specific gene pathways; <i>Lacticaseibacillus</i> HU protein interacts with histone H3. <b>Conclusion: </b><i>Lacticaseibacillus</i> can epigenetically alter specific genetic pathways in human intestinal cells. <i>Lactocaseibacillus</i>, considered as a good bacterium, is present in human gut and helps in maintaining good health of an individual. In this study, we have examined how this bacterium influences the regulation of gene expression in the intestinal cells. We observed that <i>L. rhamnosus</i> alters the packaging of DNA into chromatin by altering histone modifications and methylation of adenine residues in the mRNA molecules. This was found to be correlated with interaction of <i>Lactocaseibacillus</i> histone-like protein, HU, with histone H3 in the intestinal cell nucleus. Global and local distribution of activating and repressive histone modifications in HT29 cells are altered upon coculture with <i>L. rhamnosus</i>. mRNAs in control and cocultured HT29 cells are differentially methylated for m6A. Histone modifications and m6A mRNA methylation acts in conjunction to differentially regulate gene expression in cocultured HT29 cells. Epigenetic effector proteins like histone-like protein, HU, are components of <i>L. rhamnosus</i> secretome. <i>L. rhamnosus</i> histone-like protein, HU, has the capability of interacting with histone H3 inside HT29 cell nucleus.