Biology subjects

Day, E.

Publications and source records attributed to Day, E..

3 recordsLinked to original sources

bioRxiv2025

FUS post-transcriptional splicing is autoregulated via RNA condensation with therapeutic potential for ALS-FUS

Mutations in the FUS gene cause aggressive and often juvenile forms of amyotrophic lateral sclerosis (ALS-FUS). In addition to mRNA, the FUS gene gives rise to a partially processed RNA with retained introns 6 and 7. We demonstrate that these FUSint6&7-RNAs form nuclear condensates scaffolded by the highly structured intron 7 and associated with nuclear speckles. Using hybridization-proximity labelling proteomics, we show that the FUSint6&7-RNA condensates are enriched in splicing factors and the m6A reader YTHDC1. These ribonucleoprotein structures facilitate post-transcriptional FUS splicing and depend on m6A/YTHDC1 for their maintenance. FUSint6&7-RNAs become hypermethylated in cells expressing mutant FUS, leading to their enhanced condensation and consequently, splicing. We further demonstrate that FUS protein is repelled by m6A. Thus, ALS-FUS mutations may cause an abnormal activation of FUS post-transcriptional splicing via altered RNA methylation. Strikingly, ectopic expression of FUS intron 6&7 sequences dissolves the endogenous FUSint6&7-RNA condensates, downregulating FUS mRNA and protein. Overall, we describe an RNA condensation-dependent mechanism regulating FUS splicing that can be harnessed for developing new therapies.

cell biology↗

bioRxiv2024

Deep-Learning Structure Elucidation from Single-Mutant Deep Mutational Scanning

Deep learning has revolutionized the field of protein structure prediction. AlphaFold2, a deep neural network, vastly outperformed previous algorithms to provide near atomic-level accuracy when predicting protein structures. Despite its success, there still are limitations which prevent accurate predictions for numerous protein systems. Here we show that sparse residue burial restraints from deep mutational scanning (DMS) can refine AlphaFold2 to significantly enhance results. Burial information extracted from DMS is used to explicitly guide residue placement during structure generation. DMS-Fold was validated on both simulated and experimental single-mutant DMS, with DMS-Fold outperforming AlphaFold2 for 89% of protein targets and with 253 proteins having an improvement greater than 0.1 in TM-score. DMS-Fold is free and publicly available: https://github.com/LindertLab/DMS-Fold.

biochemistry↗

bioRxiv2024

A prion-like protein regulates the 2-dimensional to 3-dimensional growth transition in the moss Physcomitrium patens

The colonization of the land by plants coincided with the evolution of 3-dimensional (3D) growth; the acquisition of apical cells with the capacity to rotate the plane of cell division. The moss Physcomitrium patens has recently been developed as a model to dissect the genetic basis of 3D growth, an invariable and unifying feature of all land plants. The cytokinin-unresponsive Ppnog1-R mutant incorrectly orients division planes in developing buds and thus fails to make the transition to 3D growth. To reveal the genetic interactors of the PpNOG1 gene, which encodes a protein with a C-terminal UBA domain, we performed a screen and identified the suppressor of nog1a (snog1a) mutant. We have mapped the causative mutation to a gene that encodes a prion-like protein related to FLOE2/3 and demonstrated that the mutant phenotypes observed in both a nog1 disruptant mutant (nog1dis) and snog1a can be attributed to changes in cytokinin perception. We present a revised model for 3D growth and suggest that the 2D-to-3D growth transition is regulated, at least in part, by liquid-liquid phase separation (LLPS). SUMMARY STATEMENTThe transition to 3D growth is negatively regulated by a prion-like protein that both alters cytokinin signaling and has been implicated in liquid-liquid phase separation (LLPS).

plant biology↗