Affinity purification-mass spectrometry to identify nuclear protein interactions of N-terminal acetyltransferase...

Histone proteins are subjected to numerous modifications that are being catalysed by enzymes known as 'writers', and this phenomenon constitutes one of the main epigenetic mechanisms through which the cell regulates DNA-based processes, ultimately impacting cellular phenotypes. One such writer is N-terminal acetyltransferase 40 (NAA40) which mediates the N-terminal acetylation (Nt-Ac) of histones H4 and H2A. This epigenetic modifier belongs in the N-terminal acetyltransferase (NAT) family of enzymes, which altogether target approximately 80 % of all eukaryotic proteins. NAA40 is thought to mediate this histone modification co-translationally when associated with the ribosomes, but recent work has also suggested that NAA40 acts within the nucleus. Hence in this study, we performed affinity purification coupled to mass spectrometry (AP-MS), aiming to identify nuclear protein interactions of NAA40 in an attempt to further characterise its function within the nuclear compartment. The AP-MS described here can be applied to other NAT enzymes to enhance the understanding on their molecular functions and that of their corresponding protein N-terminal acetylation.