DNA G-Quadruplex Is a Transcriptional Control Device That Regulates Memory.

The conformational state of DNA fine-tunes the transcriptional rate and abundance of RNA. Here, we report that G-quadruplex DNA (G4-DNA) accumulates in neurons, in an experience-dependent manner, and that this is required for the transient silencing and activation of genes that are critically involved in learning and memory in male C57/BL6 mice. In addition, site-specific resolution of G4-DNA by dCas9-mediated deposition of the helicase DHX36 impairs fear extinction memory. Dynamic DNA structure states therefore represent a key molecular mechanism underlying memory consolidation.One-Sentence Summary: G4-DNA is a molecular switch that enables the temporal regulation of the gene expression underlying the formation of fear extinction memory.

Fear extinction is regulated by the activity of long noncoding RNAs at the synapse.

Long noncoding RNAs (lncRNAs) represent a multidimensional class of regulatory molecules that are involved in many aspects of brain function. Emerging evidence indicates that lncRNAs are localized to the synapse; however, a direct role for their activity in this subcellular compartment in memory formation has yet to be demonstrated. Using lncRNA capture-seq, we identified a specific set of lncRNAs that accumulate in the synaptic compartment within the infralimbic prefrontal cortex of adult male C57/Bl6 mice. Among these was a splice variant related to the stress-associated lncRNA, Gas5. RNA immunoprecipitation followed by mass spectrometry and single-molecule imaging revealed that this Gas5 isoform, in association with the RNA binding proteins G3BP2 and CAPRIN1, regulates the activity-dependent trafficking and clustering of RNA granules. In addition, we found that cell-type-specific, activity-dependent, and synapse-specific knockdown of the Gas5 variant led to impaired fear extinction memory. These findings identify a new mechanism of fear extinction that involves the dynamic interaction between local lncRNA activity and RNA condensates in the synaptic compartment.

Genome-Wide 5-Formylcytosine Redistribution in KCl-Stimulated Mouse Primary Cortical Neurons is Associated with Neuronal Activity.

An abundant accumulation of DNA demethylation intermediates has been identified in mammalian neurons. While the roles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in neuronal function have been extensively studied, little is known about 5-formylcytosine (5fC) in neurons. Therefore, this study was to investigate the genome-wide distribution and potential functions of 5fC in neurons. In an in vitro culture model of mouse primary cortical neurons, we observed a dynamic increase in the total 5fC level in the neuronal genome after potassium chloride (KCl) stimulation. Subsequently, we employed chemical-labeling-enabled C-to-T conversion sequencing (CLEVER-seq) to examine the 5fC distribution at a single-base resolution. Bioinformatic analysis revealed that 5fC was enriched in promoter regions, and gene ontology (GO) analysis indicated that the differential formylation positions (DFP) were correlated with neuronal activities. Additionally, integration with previously published nascent RNA-seq data revealed a positive correlation between gene formylation and mRNA expression levels. As well, 6 neuro-activity-related genes with a positive correlation were validated. Furthermore, we observed higher chromatin accessibility and RNA pol II binding signals near the 5fC sites through multiomics analysis. Motif analysis identified potential reader proteins for 5fC. In conclusion, our work provides a valuable resource for studying the dynamic changes and functional roles of 5fC in activated mammalian neurons.

Synapse-Enriched m6A-Modified Malat1 Interacts with the Novel m6A Reader, DPYSL2, and Is Required for Fear-Extinction Memory.

The RNA modification N6-methyladenosine (m6A) regulates the interaction between RNA and various RNA binding proteins within the nucleus and other subcellular compartments and has recently been shown to be involved in experience-dependent plasticity, learning, and memory. Using m6A RNA-sequencing, we have discovered a distinct population of learning-related m6A- modified RNAs at the synapse, which includes the long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 (Malat1). RNA immunoprecipitation and mass spectrometry revealed 12 new synapse-specific learning-induced m6A readers in the mPFC of male C57/BL6 mice, with m6A-modified Malat1 binding to a subset of these, including CYFIP2 and DPYSL2. In addition, a cell type- and synapse-specific, and state-dependent, reduction of m6A on Malat1 impairs fear-extinction memory; an effect that likely occurs through a disruption in the interaction between Malat1 and DPYSL2 and an associated decrease in dendritic spine formation. These findings highlight the critical role of m6A in regulating the functional state of RNA during the consolidation of fear-extinction memory, and expand the repertoire of experience-dependent m6A readers in the synaptic compartment.SIGNIFICANCE STATEMENT We have discovered that learning-induced m6A-modified RNA (including the long noncoding RNA, Malat1) accumulates in the synaptic compartment. We have identified several new m6A readers that are associated with fear extinction learning and demonstrate a causal relationship between m6A-modified Malat1 and the formation of fear-extinction memory. These findings highlight the role of m6A in regulating the functional state of an RNA during memory formation and expand the repertoire of experience-dependent m6A readers in the synaptic compartment.

Localised Cdr1as activity is required for 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 functions, including serving as decoys for microRNAs and proteins and, in some cases, circRNAs also undergo translation. Early work in animal models revealed an association between circRNAs and neurodegenerative and neuropsychiatric disorders; however, little is known about the link between circRNA function and memory. To address this, we examined circRNA in synaptosomes derived from the medial prefrontal cortex of fear extinction-trained male C57BL/6J mice and found 12,837 circRNAs that were enriched at the synapse, including cerebellar degeneration-related protein 1 antisense RNA (Cdr1as). Targeted knockdown of Cdr1as in the neural processes of the infralimbic cortex led to impaired fear extinction memory. These findings highlight the involvement of localised circRNA activity at the synapse in memory formation.

ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3.

Here, we used RNA capture-seq to identify a large population of lncRNAs that are expressed in the infralimbic prefrontal cortex of adult male mice in response to fear-related learning. Combining these data with cell-type-specific ATAC-seq on neurons that had been selectively activated by fear extinction learning, we find inducible 434 lncRNAs that are derived from enhancer regions in the vicinity of protein-coding genes. In particular, we discover an experience-induced lncRNA we call ADRAM (activity-dependent lncRNA associated with memory) 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 and is required fear extinction memory. This study expands the lexicon of experience-dependent lncRNA activity in the brain and highlights enhancer-derived RNAs (eRNAs) as key players in the epigenomic regulation of gene expression associated with the formation of fear extinction memory.

Evaluation of Bone Wax Coated Bipolar Coagulation Forceps: Performance and Safety Assessment.

BACKGROUND: Improving the performance of bipolar coagulation forceps is crucial for safer and more accurate neurosurgery. In our department, we found that bone wax (BW) melted by thermal effect of bipolar electrocoagulation can achieve more efficient hemostasis and reduce the amount of BW in neurosurgical procedures associated with bleeding from emissary and diploic veins. Nevertheless, relevant studies are still lacking to verify our finding. OBJECTIVE: The study objectives were to evaluate the performance and safety in electrocoagulation: (1) compare the performance of BW coated bipolar coagulation forceps and the conventional anti-stick forceps in vivo, and (2) assess the safety of electrocoagulation with BW coated bipolar coagulation forceps in rat primary motor cortex. METHODS: Tissue adhesion was evaluated by comparing the wetting tension and the amount of protein adhered to the forceps tips after electrocoagulation. Thermal damage was assessed by analyzing the thermography and H&E staining of coagulated rat brain tissues. The hemostatic efficiency was reflected by the number of electrocoagulation until complete hemostasis and the condition of damaged common carotid arteries. The safety of BW coated forceps in electrocoagulation was assessed by evaluating the inflammation of coagulated rat primary motor cortex and the motor functions at the 7th day postoperatively. RESULTS: Bone wax coated forceps had a significantly higher contact angle and adhered less coagulum. Thermography was acquired at 3 s, 6 W units in rat primary motor cortex in vivo. The highest temperature recorded during BW coated tips application was significantly lower than the uncoated. In addition, there was a relatively smaller tissue injury area produced by the BW coated forceps. Additionally, BW coated forceps improved the hemostatic efficiency and caused fewer injuries on the damaged arteries (3 s, 10 W units). More importantly, electrocoagulation with BW coated forceps led to no significant motor function impairments and less glial and microglia responses. CONCLUSION: This study reveals that BW coated bipolar coagulation forceps can provide a convenient, cost-efficient, safer, and more efficient way for hemostasis. More research is needed to evaluate the electrocoagulation with BW in the long term and verify our finding in human beings.

Stable isotope analyses reveal anthropogenically driven spatial and trophic changes to Indo-Pacific humpback dolphins in the Pearl River Estuary, China.

As long-lived apex predators in the Pearl River Estuary (PRE) of China, Indo-Pacific humpback dolphins (Sousa chinensis) are particularly vulnerable to anthropogenic impact and may undergo considerable ecological trait changes. The variability of traits, however, is often difficult to trace back in nature. Here, we analyzed stable isotope ratios of carbon and nitrogen in muscle samples of 88 S. chinensis stranded in the PRE from 2004 to 2016 to investigate the ecological changes occurring in the dolphins. Stable isotope analysis revealed the existence of two sub-aggregations of S. chinensis in the PRE. Generalized additive models showed significant decreasing trends in both carbon and nitrogen isotopic signatures over time, indicating the habitat changes and dietary shifts, possibly due to the influence of increased coastal developments and fishing activities in the PRE. Diet modeling suggests that the proportional contribution of higher trophic-level prey decreased in the S. chinensis diet over time, while increased consumption of lower trophic-level prey was observed. This shift was related to depletion of higher trophic-level prey caused by overfishing. Although S. chinensis could temporarily compensate for the lost energy supply through feeding plasticity (revealed by the negligible differences of isotope niche width among different stranding periods), long-term depletion in prey availability may cause long-lasting negative effects on this dolphin population. This study highlights the crucial relationships between fishery management and dolphin conservation, providing scientific evidence for the long-term protection of this threatened species in the PRE region.