Epigenetic rewriting at centromeric DNA repeats leads to increased chromatin accessibility and chromosomal instability

Background Centromeric regions of human chromosomes contain large numbers of tandemly repeated alpha-satellite sequences. These sequences are covered with constitutive heterochromatin which is enriched in trimethylation of histone H3 on lysine 9 (H3K9me3). Although well studied using artificial chromosomes and global perturbations, the contribution of this epigenetic mark to chromatin structure and genome stability remains poorly known in a more natural context. Results Using transcriptional activator-like effectors (TALEs) fused to a histone lysine demethylase (KDM4B), we were able to reduce the level of H3K9me3 on the alpha-satellites repeats of human chromosome 7. We show that the removal of H3K9me3 affects chromatin structure by increasing the accessibility of DNA repeats to the TALE protein. Tethering TALE-demethylase to centromeric repeats impairs the recruitment of HP1 alpha and proteins of Chromosomal Passenger Complex (CPC) on this specific centromere without affecting CENP-A loading. Finally, the epigenetic re-writing by the TALE-KDM4B affects specifically the stability of chromosome 7 upon mitosis, highlighting the importance of H3K9me3 in centromere integrity and chromosome stability, mediated by the recruitment of HP1 alpha and the CPC. Conclusion Our cellular model allows to demonstrate the direct role of pericentromeric H3K9me3 epigenetic mark on centromere integrity and function in a natural context and opens interesting possibilities for further studies regarding the role of the H3K9me3 mark.

Automated summary

The centromeres of human chromosomes are rich in tandemly repeated alpha-satellite sequences covered with constitutive heterochromatin marked by trimethylation of histone H3 on lysine 9 (H3K9me3). By using TALEs fused to a histone lysine demethylase (KDM4B), researchers were able to decrease the level of H3K9me3 on alpha-satellite repeats of chromosome 7, affecting chromatin structure, recruitment of HP1 alpha and CPC proteins, and the stability of chromosome 7 during mitosis. This study highlights the importance of H3K9me3 in centromere integrity and chromosome stability in a natural context.