Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs.
journal contributionposted on 2022-01-11, 13:48 authored by Mahmoud-Reza Rafiee, Julian A Zagalak, Sviatoslav Sidorov, Sebastian Steinhauser, Karen Davey, Jernej Ule, Nicholas M Luscombe
RNA-binding proteins (RBPs) play diverse roles in regulating co-transcriptional RNA-processing and chromatin functions, but our knowledge of the repertoire of chromatin-associated RBPs (caRBPs) and their interactions with chromatin remains limited. Here, we developed SPACE (Silica Particle Assisted Chromatin Enrichment) to isolate global and regional chromatin components with high specificity and sensitivity, and SPACEmap to identify the chromatin-contact regions in proteins. Applied to mouse embryonic stem cells, SPACE identified 1459 chromatin-associated proteins, ∼48% of which are annotated as RBPs, indicating their dual roles in chromatin and RNA-binding. Additionally, SPACEmap stringently verified chromatin-binding of 403 RBPs and identified their chromatin-contact regions. Notably, SPACEmap showed that about 40% of the caRBPs bind chromatin by intrinsically disordered regions (IDRs). Studying SPACE and total proteome dynamics from mES cells grown in 2iL and serum medium indicates significant correlation (R = 0.62). One of the most dynamic caRBPs is Dazl, which we find co-localized with PRC2 at transcription start sites of genes that are distinct from Dazl mRNA binding. Dazl and other PRC2-colocalised caRBPs are rich in intrinsically disordered regions (IDRs), which could contribute to the formation and regulation of phase-separated PRC condensates. Together, our approach provides an unprecedented insight into IDR-mediated interactions and caRBPs with moonlighting functions in native chromatin.
Crick (Grant ID: 10110, Grant title: Luscombe FC001110) European Commission (Grant ID: 799948 - NeuroRBP, Grant title: EC 799948 - NeuroRBP)
AnimalsBinding SitesCells, CulturedChromatinIntrinsically Disordered ProteinsMass SpectrometryMiceMouse Embryonic Stem CellsProtein BindingProtein Interaction MapsProteomeProteomicsRNA-Binding ProteinsReproducibility of ResultsLuscombe FC001110Ule - sec05 Environmental Sciences06 Biological Sciences08 Information and Computing SciencesDevelopmental Biology