Applying Peptide and Protein Synthesis to Study Post-translational Modifications in Epigenetics and Beyond.

Beat Fierz

doi:10.2533/chimia.2021.484

Abstract

Epigenetics research focuses on the study of heritable gene regulatory mechanisms that do not involve changes of the DNA sequence. Such mechanisms include post-translational modifications of histone proteins that organize the genome in the nucleus into a nucleoprotein complex called chromatin, and which are of key importance in development and disease. Chemical biology tools as developed by my group, in particular synthetic peptide and protein chemistry, have been critical to elucidate epigenetic signaling mechanisms. As outlined below, they allow the reconstitution of chromatin carrying defined modifications and thus the elucidation of detailed molecular mechanisms.

Highlights

Epigenetics research focuses on the study of heritable gene regulatory mechanisms that do not involve changes of the DNA sequence
Nature has solved these challenges by organizing the genomic DNA into an intricate nucleoprotein complex called chromatin (Fig. 1a): short stretches of DNA are wrapped around spindles made of histone proteins
Posttranslational modifications (PTMs) of histone proteins play a key role, as they serve as a chemical address system to mark genomic regions that are actively expressed or temporarily, as well as permanently, shut down.[4]

Summary

NH O RS

Establishment of Facultative Heterochromatin In contrast, gene silencing in facultative HC involves PcG proteins, in particular the two complexes polycomb repressive complex 1 (PRC1) and PRC2. We developed a general method to assemble nucleosomes containing an asymmetric distribution of PTMs[21] (Fig. 3a) In this approach, the differently modified histones, one containing H3K27me and the other H3K4me (or any other combination of modified or unmodified histones) are synthesized via EPL. The lnc-tag is removed using TEV protease, leaving no trace of the whole procedure Using this approach[21] (and variants thereof targeting H4,[22] Fig. 3c) we synthesized the whole ensemble of nucleosomes carrying asymmetric modifications on H3 and H4 which were found in stem cells.[20] Using this library we could show that PRC2 methyltransferase activity is activated by pre-existing H3K27me in asymmetric nucleosomes across the nucleosome surface, allowing the enzyme to propagate this PTM along the chromatin fiber. SMLM experiments further demonstrated that H3K27me (and surprisingly H3K36me3)

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Conclusions and Outlook