Phase Separation Potential of Marsupial RSX RNA Reveals Convergent Evolution of X-Chromosome Inactivation Mechanisms
- 1Unit of Cell and Developmental Biology, Department of Biology, University of Pisa, Strada Statale dell Abetone Brennero 4, 56123, Pisa, Italy
Abstract
Background: X-chromosome inactivation (XCI) evolved independently in eutherian and marsupial mammals, where it is orchestrated by the unrelated long non-coding RNAs Xist and RSX, respectively. Xist organizes a repressive nuclear compartment through multivalent RNA-protein interactions, but whether RSX exploits similar biophysical principles remains unknown. A recent paper has identified bona fide RSX interacting proteins. Results: We integrated proteome-scale RNA-protein interaction prediction, experimental validation, phase-separation propensity analysis, functional annotation and comparative RNA-structure modelling to characterize the RSX interaction landscape. Using catRAPID, we ranked 1,168 RNA-binding proteins from the native Monodelphis domestica proteome. Predictions were significantly enriched for experimentally identified RSX interactors, with 4.85-fold enrichment among the top 50 candidates (P approximately 1.6 x 10-5), increasing to approximately eightfold for proteins shared by the experimental RSX and Xist interactomes (P approximately 2 x 10-6). Among 30 high-confidence RSX interactors, 13 were experimentally supported, 17 were previously unrecognized candidates and 17 exhibited high phase-separation propensity. The network was enriched in ribonucleoprotein granules and nuclear bodies and converged on m6A regulators and SR-family splicing factors. Comparative modelling detected no conserved secondary or tertiary architecture between RSX and Xist. Conclusions: RSX and Xist appear to have converged not through RNA sequence or global structure, but through recruitment of related, condensation-prone protein networks. These findings identify interaction-network and biophysical convergence as a potential principle of lncRNA-mediated chromosome regulation and provide testable candidates for determining whether RSX establishes a condensate-like compartment on the marsupial inactive X.
Related
- XIST drives X-chromosome inactivation and safeguards female extraembryonic cells in humans
- A three-factor model can explain symmetry breaking and the n-1 rule during X-chromosome inactivation
- A Novel NKAP Gene Frameshift Mutation in a Sardinian Family Causes Early Cell Death and Secondary Skewed X-Chromosome Inactivation and Associates with Multiple Male Miscarriages
- Lineage-specific X chromosome inactivation escape and skew underlie sex-biased immune gene dosage and deleterious variant exposure
- STAG2-truncating variants reveal a mosaic STAG2 inactivation pattern and compensatory mechanisms involving cohesin complex remodeling
BibTeX
@misc{danga2026phase,
title = {{Phase Separation Potential of Marsupial RSX RNA Reveals Convergent Evolution of X-Chromosome Inactivation Mechanisms}},
author = {A. K. Danga and C. Canale and R. D. Ponti and G. G. Tartaglia and A. Cerase},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.18.752704},
url = {https://www.biorxiv.org/content/10.64898/2026.09.18.752704v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Phase Separation Potential of Marsupial RSX RNA Reveals Convergent Evolution of X-Chromosome Inactivation Mechanisms
AU - A. K. Danga
AU - C. Canale
AU - R. D. Ponti
AU - G. G. Tartaglia
AU - A. Cerase
PY - 2026
DA - 2026/09/18
PB - bioRxiv
DO - 10.64898/2026.09.18.752704
UR - https://www.biorxiv.org/content/10.64898/2026.09.18.752704v1
AB - Background: X-chromosome inactivation (XCI) evolved independently in eutherian and marsupial mammals, where it is orchestrated by the unrelated long non-coding RNAs Xist and RSX, respectively. Xist organizes a repressive nuclear compartment through multivalent RNA-protein interactions, but whether RSX exploits similar biophysical principles remains unknown. A recent paper has identified bona fide RSX interacting proteins. Results: We integrated proteome-scale RNA-protein interaction prediction, experimental validation, phase-separation propensity analysis, functional annotation and comparative RNA-structure modelling to characterize the RSX interaction landscape. Using catRAPID, we ranked 1,168 RNA-binding proteins from the native Monodelphis domestica proteome. Predictions were significantly enriched for experimentally identified RSX interactors, with 4.85-fold enrichment among the top 50 candidates (P approximately 1.6 x 10-5), increasing to approximately eightfold for proteins shared by the experimental RSX and Xist interactomes (P approximately 2 x 10-6). Among 30 high-confidence RSX interactors, 13 were experimentally supported, 17 were previously unrecognized candidates and 17 exhibited high phase-separation propensity. The network was enriched in ribonucleoprotein granules and nuclear bodies and converged on m6A regulators and SR-family splicing factors. Comparative modelling detected no conserved secondary or tertiary architecture between RSX and Xist. Conclusions: RSX and Xist appear to have converged not through RNA sequence or global structure, but through recruitment of related, condensation-prone protein networks. These findings identify interaction-network and biophysical convergence as a potential principle of lncRNA-mediated chromosome regulation and provide testable candidates for determining whether RSX establishes a condensate-like compartment on the marsupial inactive X.
ER -