Biology subjects

Marshall, P.

Publications and source records attributed to Marshall, P..

6 recordsLinked to original sources

bioRxiv2026

Light-inducible proximity labelling in vivo captures sex-specific RNA at excitatory synapses

Local RNA regulation is essential for synaptic plasticity, yet the full repertoire of RNA species and associated isoforms within specific synaptic compartments in vivo has yet to be determined. Existing RNA profiling approaches lack the spatial and temporal precision needed to resolve RNA repertoires restricted to cell-type specific synaptic compartments. To overcome this challenge, we developed PSD-95-Halo-seq, a light-induced proximity labelling technique that, when combined with long-read sequencing, selectively captures all post-synaptic full length RNA species in the excitatory post-synaptic compartment. Here, we applied this approach to investigate sex differences in RNA expression within excitatory synapses following exposure to an associative fear learning task in C57/Bl6 mice. We found dramatic sex differences in pseudogene and protein coding RNA expression, which are most abundant in females, with males exhibiting multiple noncoding RNA classes, including lncRNA, snoRNA, and rRNA. Females generally showed more 3' UTR expression, and there was widespread differential exon usage following fear conditioning, including 179 isoforms in males, 69 in females, with no significant gene-level differential expression, indicating that behavioural state modifies sex-specific isoform usage rather than overall transcript abundance. Our discovery that synaptic RNA composition is dynamic, sexually dimorphic, and profoundly shaped by experience, offers new insight into previously inaccessible mechanisms underlying sex differences in fear-related learning and memory. PSD-95-Halo-seq is therefore a powerful method for the precise spatiotemporal identification of compartment-and cell-type-specific RNA. One sentence take-awaySynapse-targeted proximity labelling and Long-Read sequencing demonstrate that excitatory post-synapses encode experience through sex-specific, isoform-level RNA remodeling.

neuroscience↗

bioRxiv2025

A mobile circular DNA element drives memory-related processes in mice

Extrachromosomal circular DNAs (ecDNAs) are double stranded, closed loop DNA molecules that act independently of the genome. Here we report the discovery of a brain-enriched ecDNA, ecCldn34d, that regulates the transcriptional state of plasticity-related genes and is temporally associated with the stability of fear memories. ecDNA therefore represents a novel class of mobile DNA elements that are involved in experience-dependent neuroadaptation.

neuroscience↗

bioRxiv2022

Inhibiting circRNA Cdr1as expression in the ILPFC of adult male C57BL/6J mice impairs fear extinction memory

Circular RNAs (circRNAs) comprise a novel class of regulatory RNAs that are abundant in the brain, particularly within synapses. They are highly stable, dynamically regulated, and display a range of functional roles, including as decoys for miRNAs and proteins and, in some cases, translation. Early work in animal models revealed an association between circRNAs and neurodegenerative and neuropsychiatric disorders; however, relatively few studies have shown a causal link between circRNA function and memory. To address this knowledge gap, we sequenced circRNAs in the synaptosome compartment of the medial prefrontal cortex of fear extinction trained male C57BL/6J mice and found 12837 circRNAs enriched at the synapse, including Cdr1as. Targeted knockdown of Cdr1as in the neural processes of the infralimbic prefrontal cortex of male C57BL/6J mice led to impaired fear extinction memory. Altogether, our findings highlight the importance of localised circRNA activity at the synapse for memory formation and suggest that circRNAs may have a more widespread effect on brain function than previously thought.

neuroscience↗

bioRxiv2021

On the discovery of ADRAM, an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3

Long-noncoding RNA (lncRNA) comprise a new class of genes that have been assigned key roles in development and disease. Many lncRNAs are specifically transcribed in the brain where they regulate the expression of protein-coding genes that underpin neuronal function; however, their role in learning and memory remains largely unexplored. We used RNA Capture-Seq to identify a large population of lncRNAs that are expressed in the infralimbic cortex of adult male mice in response to fear-related learning, with 14.5% of these annotated in the GENCODE database as lncRNAs with no known function. We combined these data with cell-type-specific ATAC-seq on neurons that had been selectively activated by fear-extinction learning, and revealed 434 lncRNAs derived from enhancer regions in the vicinity of protein-coding genes. In particular, we discovered an experience-induced lncRNA called ADRAM that acts as both a scaffold and a combinatorial guide to recruit the brain-enriched chaperone protein 14-3-3 to the promoter of the memory-associated immediate early gene Nr4a2. This leads to the expulsion of histone deactylases 3 and 4, and the recruitment of the histone acetyltransferase creb binding protein, which drives learning-induced Nr4a2 expression. Knockdown of ADRAM disrupts this interaction, blocks the expression of Nr4a2, and ultimately impairs the formation of fear-extinction memory. This study expands the lexicon of experience-dependent lncRNA activity in the brain, highlights enhancer-derived RNAs (eRNAs) as key players in the epigenetic regulation of gene expression associated with fear extinction, and suggests eRNAs, such as ADRAM, may constitute viable targets in developing novel treatments for fear-related anxiety disorders.

neuroscience↗

bioRxiv2019

Dynamic DNA structure states interact with the RNA editing enzyme ADAR1 to modulate fear extinction memory

RNA modification has recently emerged as an important mechanism underlying gene diversity linked to behavioral regulation. The conversion of adenosine to inosine by the ADAR family of enzymes is a particularly important RNA modification as it impacts the physiological readout of protein-coding genes. However, not all variants of ADAR appear to act solely on RNA. ADAR1 binds directly to DNA when it is in a non-canonical, left handed, \"Z\" conformation, but little is known about the functional relevance of this interaction. Here we report that ADAR1 binds to Z-DNA in an activity-dependent manner and that fear extinction learning leads to increased ADAR1 occupancy at DNA repetitive elements, with targets adopting a Z-DNA structure at sites of ADAR1 recruitment. Knockdown of ADAR1 leads to an inability to modify a previously acquired memory trace and this is associated with a concomitant change in DNA structure and a decrease in RNA editing. These findings suggest a novel mechanism of learning-induced gene regulation whereby ADAR1 physically interacts with Z-DNA in order to mediate its effect on RNA, and both are required for memory flexibility following fear extinction learning.

neuroscience↗

bioRxiv2018

The DNA repair associated protein Gadd45g regulates the temporal coding of immediate early gene expression and is required for the consolidation of associative fear memory

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC=\"FIGDIR/small/265355_fig6.gif\" ALT=\"Figure 6\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@16a5a7forg.highwire.dtl.DTLVardef@15b53dborg.highwire.dtl.DTLVardef@de7376org.highwire.dtl.DTLVardef@6e6732_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOVisual abstractC_FLOATNO C_FIG We have identified a member of the Growth arrest and DNA damage (Gadd45) family, Gadd45{gamma}, which is known to be involved in the regulation of DNA repair, as a key player in the formation of associative fear memory. Gadd45{gamma} regulates the temporal dynamics of learning-induced immediate early gene (IEG) expression in the prelimbic prefrontal cortex through its interaction with DNA double-strand break (DSB)-mediated changes in DNA methylation. Our findings suggest a two-hit model of experience-dependent IEG activity and learning that comprises 1) a first wave of IEG expression governed by DSBs followed by an increase in DNA methylation, and 2) a second wave of IEG expression associated with Gadd45{gamma} and active DNA demethylation at the same site, which is necessary for memory consolidation.\n\nSignificance statementHow does the pattern of immediate early gene (IEG) transcription in the brain relate to the storage and accession of information, and what controls these patterns? This paper explores how GADD45{gamma}, a gene that is known to be involved with DNA modification and repair, regulates the temporal coding of IEGs underlying associative learning and memory. We reveal that, during fear learning, GADD45{gamma} serves to act as a coordinator of IEG expression and subsequent memory consolidation by directing temporally specific changes in active DNA demethylation at the promoter of plasticity-related IEGs.

neuroscience↗