Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.10.25.761723

Multivalent Scaffolding by XIST E-Repeats Tunes RNA Binding Protein Cooperativity and Lowers the Phase Separation Threshold

Eusse, B.·Vidal-Ceballos, A.·Meyer, A. K.·Bose, E.·Martino, R. A.·Haynes, K.·Jones, A.
View original source ↗Export metadata ↓

Abstract

The long-noncoding RNA XIST coordinates the random silencing of one X-chromosome in female placental mammals as a class of chromosomal dosage compensation across sexes. Critical to this process is the diffusion of XIST foci across the 155 Mb of the X-chromosome to achieve 96% repression. The E-Repeat domain on XIST primarily drives this process through the recruitment of several RNA-binding proteins, which seed condensate formation for controlled distal spreading. To date, there is a lack of biophysical characterization of interactions between the E-Repeats and its protein binding partners. Herein, we define the interaction, in vitro, between E-Repeat RNA and proteins PTBP1, ELAVL1, TDP43, and hnRNPU by applying a combination of bioinformatics, in silico characterization, and biochemical assays. We designed minimal E-Repeat RNA constructs to study the molecular mechanisms of RBP recognition and the E-Repeat ensemble. We find that all proteins sustain nanomolar interactions with single E-Repeat RNA. Through a systematic domain study, we deduce protein domain-specific RNA binding affinities, providing insight into mechanisms of E-Repeat binding. With four E-Repeats, we find that PTBP1 and ELAVL1 form higher-order assemblies and demonstrate protein competition and co-occupancy, reflecting previous in cellulo CLIP experiments. Finally, we find that PTBP1 and ELAVL1 phase separate with the four-repeat minimal constructs under minimal in vitro conditions, recapitulating the cellular behavior crucial to XIST function. All together, our findings provide mechanistic insight into the amplified impact of XIST, which at approximately 1 molecule per megabase can modulate long-range chromatin organization, illuminating another aspect of lncRNA potency, and potentially informing engineered derivatives of XIST and other lncRNAs as genetic therapeutics.

Explore related subjects

biophysicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Eusse, B., Vidal-Ceballos, A., Meyer, A. K., Bose, E., Martino, R. A., Haynes, K., Jones, A.. 2026-10-27. Multivalent Scaffolding by XIST E-Repeats Tunes RNA Binding Protein Cooperativity and Lowers the Phase Separation Threshold. https://doi.org/10.64898/2026.10.25.761723

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Cancers relax selection on charge at the mitochondrial complex I quinone cavity

Mitochondrial complex I translocates protons through hydrated channels whose connectivity and electrostatics are both defined by structure, but whether they are distinctly constrained is unknown. From a 2.39 cryo-EM structure modelling 2,945 ordered waters, we built the proton wire of the seven mtDNA-encoded ND subunits and scored all 40,166 missense substitutions on two near-orthogonal axes (r = 0.17): electrostatic shift at proton-loading sites, and topological disruption of the wire. Across 858 germline variant sites, loading sites (0.51) and cut vertices (0.67) are both depleted. In tumours only loading sites are enriched (1.42 TCGA, 1.67 PCAWG, 1.29 MSK-IMPACT), a 3.06-fold difference tested as a wire class tissue-type interaction (P = 3.6 10-). It survives adjustment for conservation, burial and coverage, and is concentrated in ND1 within 15 of the quinone cavity, not spread along the proton path. Selection separates charge from connectivity, without establishing a fitness benefit.

biophysics↗
bioRxiv2026

Rugnux: from diffraction images to structure at synchrotrons and XFELs in one program

Rising data rates in macromolecular crystallography outpace multi-program pipelines on computing clusters. Rugnux, a single GPU-accelerated program, turns rotation or serial still diffraction images into merged data and an initial structure. At synchrotrons, results arrive seconds after the last image; on one workstation, 207 public datasets from 36 sources took a median of 15 s each, with deposition-quality. Serial XFEL data were processed faster than the collection rate, enabling real-time structure determination.

biophysics↗
bioRxiv2026

Phase Separation of Intracellular Proteins Influences Synaptic Bistability

Synaptic bistability at the post synaptic density has been proposed to be the result of the nucleation and evaporation of receptor clusters. The exact biophysical mechanism underlying these inter-receptor attractions that can trigger nucleation remains to be elucidated. Emerging evidence demonstrates that numerous postsynaptic density submembrane proteins, that interact with various membrane receptors, can undergo phase separation, necessitating a revised conceptual model. By employing Langevin dynamics simulations of coarse-grained scaffold proteins and interacting membrane receptors, we study how phase transitions of scaffold proteins alter receptor clustering at the membrane. In our model, scaffold macromolecules can undergo phase separation and interact with receptor molecules at the model membranes. We observed that the presence of scaffold polymers across the membrane creates an attractive interaction between otherwise purely repulsive receptors. By systematically varying the number of receptors at the membrane, we dissected the coupling between receptor clustering and the phase behavior of scaffold macromolecules. We show that the propensity for receptor clustering is enhanced by the condensation of scaffold proteins. We then used two different scaffolds and systematically varied the interaction between them, to change the spatial organization of two condensed phases w.r.t. one another. Interestingly, we observed that receptor clustering can be reduced by co-phase separation of scaffold macromolecules, indicating the role of competing interactions in receptor clustering. Our work advances understanding of receptor-mediated signaling and phase separation, providing insights into cellular compartmentalization and biochemical regulation at the synapse.

biophysics↗