40S hnRNP particles are a novel class of nuclear biomolecular condensates

Abstract

Heterogenous nuclear ribonucleoproteins (hnRNPs) are abundant proteins implicated in various steps of RNA processing that assemble on nuclear RNA into larger complexes termed 40S hnRNP particles. Despite their initial discovery 55 years ago, our understanding of these intriguing macromolecular assemblies remains limited. Here, we report the biochemical purification of native 40S hnRNP particles and the determination of their complete protein composition by label-free quantitative mass spectrometry, identifying A-group and C-group hnRNPs as the major protein constituents. Isolated 40S hnRNP particles dissociate upon RNA digestion and can be reconstituted in vitro on defined RNAs in the presence of the individual protein components, demonstrating a scaffolding role for RNA in nucleating particle formation. Finally, we revealed their nanometer scale, condensate-like nature, promoted by intrinsically disordered regions of A-group hnRNPs. Collectively, we identify nuclear 40S hnRNP particles as novel dynamic biomolecular condensates.

ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins

“…One intriguing possibility that is consistent with our data is that the ASAR RNAs serve as scaffolds for the assembly of extensive RNA-protein and protein-protein complexes that form a chromosome-tethered liquid-liquid phase that facilitates the recruitment of the requisite chromatin modifiers and DNA replication machinery. In support of this notion, HNRNPA1 and HNRNPC are components of the 40S hnRNP particle, which forms a nuclear biomolecular condensate 23 . In addition, HNRNPU and HNRNPUL1 interact with each of the 40S hnRNP particle subunits 35 , suggesting the possibility of extensive protein-protein interactions.…”

“…It is likely that additional insights into the network of RBP/ASAR interactions could be gained by extending our replication timing analyses to knockdowns of additional RBPs. Another limitation of these studies is that all of the RBPs implicated in control of replication timing are known to play various roles in essential nucleic acid metabolic pathways, including DNA replication, transcription, splicing, mRNA export, and RNA degradation 22,23 . It is possible that knocking down these RBPs has an indirect effect on replication related to these other functions of the RBPs, rather than a direct effect on ASAR function.…”

“…The functions of hnRNPs vary according to their subcellular localization. Most of the hnRNPs possess conventional nuclear localization signals and are predominantly present in the nucleus during steady state, where they function in various RNA metabolic processes including transcription, splicing, nuclear export, and 3’ end processing 22,23 , and more recently have been implicated in DNA replication 24 . A direct connection between chromosome territory associated C0T-1 RNA and hnRNPs was established by the observation that siRNA mediated depletion, or forced expression of dominant interfering mutants, of HNRNPU results in dissociation of C0T-1 RNA from chromosome territories 13,20,21 .…”

Phase Separation in Mixtures of Prion-Like Low Complexity Domains is Driven by the Interplay of Homotypic and Heterotypic Interactions

“…Here, we explored how the interplay between homotypic versus heterotypic interactions of PLCDs with at least cursorily similar compositional biases can influence the driving forces for phase separation. Our results set the stage for understanding how dynamical control over compositions in complex mixtures might be achieved and how this can influence condensate formation of bodies such as 40S hnRNP particles (84) or stress granules. There is also growing interest in understanding how the interplay of homotypic and heterotypic interactions impact the dynamically controlled (85) or purely thermodynamically influenced miscibility of condensates formed in multicomponent systems (71, 86–88).…”

Roles of RNA Methylations in Cancer Progression, Autophagy, and Anticancer Drug Resistance

“…IGF2BP2 enhances renal cell carcinoma tumorigenesis by stabilizing sphingosine-1-phosphate receptor 3 (S1PR3) mRNA [ 60 ]. HNRNPs mainly regulate alternative splicing or the processing of transcripts [ 61 , 62 ].…”