Proximity proteomics using AMPL-MS

Eukaryotic chromatin is organised in individual domains, which are defined by their location within the nuclear space and their distinct proteomic compositions. In contrast to cellular organelles surrounded by lipid membranes, the composition of distinct chromatin domains is rather ill described and considered to be highly dynamic. To identify proteins associated with a specific chromatin domain and to better understand how those domains are established and maintained, we established AMPL-MS (Antibody mediated proximity labelling mass spectrometry). As this method is based on antibodies and does not require the expression of fusion proteins, it constitutes a versatile and very sensitive method to characterize chromatin domains containing specific signature proteins or histone modifications. We used AMPL-MS to characterize the chromocenter as well as the chromosome territory containing the hyperactive X-chromosome in Drosophila. Our data revealed the presence of many RNA binding proteins in these domains thereby underscoring the importance of nuclear RNA in the organisation of the genome.