ArticleNucleic acids research2021
Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 20 citations in OpenAlex.
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- Neuronal protein Sex-lethal modulates tRNA synthesis via the polymerase III subunit Polr3E in male Drosophila neurons.PLoS biology · 2026Article
- Native chromatome profiling reveals hundreds of metabolic enzymes in the nucleus across tissues.Nature communications · 2026Article
- Proteomic Screening Identifies HNRNPA2B1 as an Epigenetic Repressor of Epstein-Barr Virus Reactivation.bioRxiv : the preprint server for biology · 2026Article
- caRBP-Pred: Leveraging Protein Language Models for the Prediction of Chromatin-Associated RNA-Binding Proteins.Computational and structural biotechnology journal · 2026Article
- Article
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- RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis.Brain : a journal of neurology · 2023Article
- Dimensional Reduction for Single-Molecule Imaging of DNA and Nucleosome Condensation by Polyamines, HP1α and Ki-67.The journal of physical chemistry. B · 2023Article
- Intrinsically Disordered Proteins: An Overview.International journal of molecular sciences · 2022Review
- TRIM28-dependent SUMOylation protects the adult ovary from activation of the testicular pathway.Nature communications · 2022Article
- Nuclear RNA binding regulates TDP-43 nuclear localization and passive nuclear export.Cell reports · 2022Article
- Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus.Cells · 2021Review
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Authors and funding
7 authors at 2 institutions in 3 countries.
Funding
Abstract
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.
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