Biology subjects

Jones, G. D.

Publications and source records attributed to Jones, G. D..

5 recordsLinked to original sources

bioRxiv2025

Dynamic updating of spatial working memory across eye movements: a computational investigation of transsaccadic integration

The brain continuously integrates rapidly changing visual input across eye movements to maintain stable perception, yet the precise mechanisms underpinning dynamic working memory and how these break down in brain diseases remain unclear. We developed a novel eye-tracking paradigm and computational models to investigate how spatial and colour information are updated across saccades. Our findings reveal that saccades selectively impair spatial but not colour memory. Computational modelling identified that spatial representations are maintained in a dual eye-centred frame of reference which is actively updated by a noisy memory of saccades but is vulnerable to interference. Using this model, we found that specific mechanistic failures in initial encoding and memory decay, rather than the saccadic updating process itself, account for spatial working memory deficits in Alzheimers and Parkinsons disease. These results provide a mechanistic understanding of how dynamic spatial memory operates in health and its disruption in neurodegenerative disorders.

neuroscience↗

bioRxiv2025

Stalled translation on transcripts cleaved by RNase L activates signaling important for innate immunity

RNase L is an endonuclease that responds to infections by cleaving most host- and pathogen-derived single-stranded RNAs. This widespread RNA cleavage can lead to death of the infected cell via the ribotoxic stress response (RSR). An ongoing challenge is to understand how RNase Ls endonuclease activity triggers cell death to benefit the host. To address this question, we used nanopore-based long-read sequencing to show that 3 mRNA fragments in the cell were not fully degraded after RNase L activation and that these fragments were translated by ribosomes. We further asked whether ribosomes on mRNA fragments stall when they reach 3 ends created by RNase L. We used ribosome profiling to capture footprints protected by these ribosomes, which can be identified by their short length (15-18 nt). We found that RNase L activation increased the number of stalled ribosomes at RNase L cleavage sites. Loss of the ribosome rescue factor PELO increased the number of short footprints derived from stalled ribosomes and augmented the RSR. Our work therefore establishes a role for fragmented mRNA in causing ribosome stalling that promotes innate immunity via the RSR. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/658914v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1f08b5forg.highwire.dtl.DTLVardef@14e2cd1org.highwire.dtl.DTLVardef@160814corg.highwire.dtl.DTLVardef@c8ddb4_HPS_FORMAT_FIGEXP M_FIG Stalled translation of mRNAs that are fragmented by RNase L leads to ribosome stalling and potentially collisions. Stalled ribosomes are rescued by PELO or activate innate immune signaling via ZAK. Renderings based on PDB 4o1o and 3jag. C_FIG HighlightsO_LIActivation of RNase L leads to accumulation and translation of mRNA fragments C_LIO_LIRibosomes stall at the 3 end of the RNase L cleaved mRNA fragments C_LIO_LIPELO rescues ribosomes stalled due to RNase L activation C_LI

molecular biology↗

bioRxiv2024

Regulated mRNA recruitment in dinoflagellates is reflected in hyper-variable mRNA spliced leaders and novel eIF4Es

Dinoflagellates are eukaryotic algae with large genomes that rely heavily on post-transcriptional control for the regulation of gene expression. Dinoflagellate mRNAs are trans-spliced with a conserved 22 base spliced leader sequence (SL) that includes the 5-cap to which the translation initiation factor 4E (eIF4E) binds to facilitate ribosomal recruitment. The binding of an eIF4E to a specific mRNA SL is a potential regulatory point in controlling dinoflagellate gene expression. Here we show that m7G is the 5-cap base of the 65 bp SL RNA with additional methylations throughout the SL to give a mixture of novel multi-methylated sequences in Amphidinium carterae (CCMP1314). There is also sequence variability in all four bases seen at the first position followed by a variety of polymorphisms. Three novel clades of eIF4E have been shown in dinoflagellates that are distinct from the three metazoan classes of eIF4E. Members of each clade differ significantly from each other, but all bear the distinctive features of a cap-binding protein. Here we show large differences in expression and activity in six of the eight eIF4E family members from A. carterae. Transcripts of each are expressed throughout the diel cycle, but only eIF4E-1 family members and eIF4E-2a show discernable expression at the level of protein. Recombinant eIF4E-1 family members and eIF4E-3a, but not eIF4E-2a, are able to bind to m7GTP substrates in vitro. Overall, eIF4E-1a emerges with characteristics consistent with the role of a prototypical initiation factor; eIF4E-1a is the most conserved and highly expressed eIF4E family member, has the highest affinity for m7GpppG and m7GpppC by surface plasmon resonance, and is able to complement a yeast strain conditionally deficient in eIF4E. The large number of eIF4E family members along with the sequence and methylation state variability in the mRNA SLs underscore the unique nature of the translational machinery in the dinoflagellate lineage and suggest a wide range of possibilities for differential recruitment of mRNAs to the translation machinery. Impact StatementIn the dinoflagellate, A. carterae, hyper-variable mRNA spliced leaders and novel eIF4Es reflect the reliance of dinoflagellates on variable mRNA recruitment for the regulation of gene expression.

molecular biology↗

bioRxiv2023

Syncytiotrophoblast 5'-tRNA fragments are placental endocrine signals contributing to sterile inflammation in preeclampsia

BackgroundThe relationship between placental pathology and the maternal syndrome of preeclampsia is incompletely characterised. Mismatch between placental nutrient supply and fetal demands induces stress in the syncytiotrophoblast, the layer of placenta in direct contact with maternal blood. Such stress alters the content and increases the release of extracellular vesicles (STB-EVs) into the maternal circulation. We have previously shown 5-tRNA fragments (5-tRFs) constitute the majority of small RNA in STB-EVs in healthy pregnancy. 5-tRFs are produced in response to stress. We hypothesised STB-EV 5-tRF release might change in preeclampsia. MethodsWe perfused placentas from eight women with early-onset preeclampsia and six controls, comparing small RNA expression in STB-EVs. We used membrane-affinity columns to isolate maternal plasma vesicles and investigate placental 5-tRFs in-vivo. We quantified 5-tRFs from circulating STB-EVs using a placental alkaline phosphatase immunoassay. 5-tRFs and scrambled RNA controls were added to monocyte, macrophage and endothelial cells in culture to investigate transcriptional responses. Results5-tRFs constitute the majority of small RNA in STB-EVs from both preeclampsia and normal pregnancies. >900 small RNA fragments are differentially expressed in preeclampsia STB-EVs. Preeclampsia-dysregulated 5-tRFs are detectable in maternal plasma, where we identified a placentally-derived load. 5-tRF-Glu-CTC, the most abundant preeclampsia-upregulated 5-tRF in perfusion STB-EVs, is also increased in preeclampsia STB-EVs from maternal plasma. 5-tRF-Glu-CTC induced inflammation in macrophages but not monocytes. The conditioned media from 5-tRF-Glu-CTC-activated macrophages reduced eNOS expression in endothelial cells. ConclusionsIncreased release of syncytiotrophoblast-derived vesicle-bound 5-tRF-Glu-CTC contributes to preeclampsia pathophysiology.

molecular biology↗

bioRxiv2020

Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences

Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5 and 3 UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase Ls cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity.

molecular biology↗