Decoding chromatin states by proteomic profiling of nucleosome readers
Nature article from the Bartke lab
06.03.2024
Saulius Lukauskas, Andrey Tvardovskiy, Nhuong V. Nguyen, Mara Stadler, Peter Faull, Tina Ravnsborg, Bihter Özdemir Aygenli, Scarlett Dornauer, Helen Flynn, Rik G. H. Lindeboom, Teresa K. Barth, Kevin Brockers, Stefanie M. Hauck,
Michiel Vermeulen, Ambrosius P. Snijders, Christian L. Müller, Peter A. DiMaggio, Ole N. Jensen, Robert Schneider & Till Bartke. Decoding chromatin states by proteomic profiling of nucleosome readers. Nature (2024). https://doi.org/10.1038/s41586-024-07141-5
Abstract cited directly from the article:
DNA and histone modifications combine into characteristic patterns that demarcate functional regions of the genome. While many ‘readers’ of individual modifications have been described, how chromatin states comprising composite modification signatures, histone variants and internucleosomal linker DNA are interpreted is a major open question. Here we use a multidimensional proteomics strategy to systematically examine the interaction of around 2,000 nuclear proteins with over 80 modified dinucleosomes representing promoter, enhancer and heterochromatin states. By deconvoluting complex nucleosome-binding profiles into networks of co-regulated proteins and distinct nucleosomal features driving protein recruitment or exclusion, we show comprehensively how chromatin states are decoded by chromatin readers. We find highly distinctive binding responses to different features, many factors that recognize multiple features, and that nucleosomal modifications and linker DNA operate largely independently in regulating protein binding to chromatin. Our online
resource, the Modification Atlas of Regulation by Chromatin States (MARCS), provides in-depth analysis tools to engage with our results and advance the discovery of fundamental principles of genome regulation by chromatin states.