New ‘PLAMseq’ method revolutionizes the study of genome proteins

A team from the Andalusian Centre for Molecular Biology and Regenerative Medicine (CABIMER) has developed an innovative technique called PLAMseq (proximity-labelled affinity-purified mass spectrometry plus sequencing) that, for the first time, allows simultaneous analysis of chromatin-associated proteins and their location in the genome in a single experiment.

Until now, researchers have had to combine several complex and costly techniques, such as chromatin immunoprecipitation (ChIP-seq) or mass spectrometry analysis, and rely on highly specific antibodies, which has greatly limited the study of many proteins involved in DNA regulation. PLAMseq overcomes this limitation by using a rapid biotinylation enzyme called TurboID, which tags nearby proteins and enables their isolation together with the DNA fragments to which they are bound.

The power of this new technology, developed entirely in Seville using the state-of-the-art genomics and proteomics facilities at CABIMER and the Institute of Biomedicine of Seville (IBiS), is shown by its application to essential genome proteins such as CTCF and RNA polymerase II, as well as SUMO-modified H1 histones, key molecules in chromatin organisation. The results reveal new molecular interactions, including the binding of the SETDB1 enzyme to modified histones, which could help in understanding how DNA compaction and gene activation or silencing are regulated.

Beyond its technical value, PLAMseq opens up new perspectives for biomedical research. Its ability to simultaneously identify which proteins interact and where they act in the genome will enable precise exploration of the epigenetic mechanisms underlying diseases such as cancer, and neurological and developmental disorders. This comprehensive proteogenomic vision could also accelerate the discovery of new therapeutic targets and biomarkers.

‘With PLAMseq, we can observe, in a single experiment, the dual dimension of genome biology: the proteins that shape it and the regions where they act,’ explains Román González-Prieto, principal investigator with the University of Seville Department of Cell Biology in CABIMER. ‘This opens up a whole new horizon for understanding how deregulation of these interactions contributes to human diseases.’

The breakthrough, published in Science Advances, consolidates the Andalusian groups as international leaders in the development of cutting-edge technologies for the study of epigenetics and chromatin biology. Laboratories around the world have already expressed interest in applying PLAMseq to their research.