PT  - JOURNAL ARTICLE
AU  - Rafiee, Mahmoud-Reza
AU  - Zagalak, Julian A
AU  - Sidorov, Sviatoslav
AU  - Steinhauser, Sebastian
AU  - Davey, Karen
AU  - Ule, Jernej
AU  - Luscombe, Nicholas M
TI  - Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs
AID  - 10.1101/2020.07.13.200212
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2020.07.13.200212
4099  - http://biorxiv.org/content/early/2021/09/16/2020.07.13.200212.short
4100  - http://biorxiv.org/content/early/2021/09/16/2020.07.13.200212.full
AB  - 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 1,459 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 404 RBPs and identified their chromatin-contact regions. Notably, SPACEmap showed that about half of the caRBPs bind to 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.Competing Interest StatementThe authors have declared no competing interest.