Biology subjects

MacDonald, C. C.

Publications and source records attributed to MacDonald, C. C..

4 recordsLinked to original sources

bioRxiv2026

Alternative polyadenylation in the brain is altered by chronic ethanol exposure in a sex- and cell type-specific manner

Alternative polyadenylation (APA) is a common posttranscriptional mechanism to regulate gene expression. APA generates mRNAs with varying lengths of 3' UTRs or transcripts that encode distinct protein carboxy-terminal ends. APA is especially important in neurons, where different mRNA variants are often asymmetrically localized to dendrites and axons, and can be locally translated into proteins. Local protein synthesis is crucial for axon guidance, synaptic plasticity, and learning and memory, key processes associated with the development of alcohol use disorder (AUD). We investigated the role of APA in AUD using a mouse model of alcohol dependence characterized by increased voluntary drinking after chronic intermittent ethanol (CIE) exposure. We examined APA during protracted withdrawal from alcohol in three brain regions of male and female mice. Our analyses revealed hundreds of genes undergoing APA in males, but substantially fewer in females, suggesting sex-specific effects of CIE on APA. Notably, male and female mice displayed distinct APA signatures. APA genes were different from differentially expressed genes (DEGs), suggesting that these molecular processes are regulated independently. We also determined that the expression of APA genes was associated with neurons, while DEGs were associated with non-neuronal cells. Many of the APA genes were involved in synaptic integrity, neuroplasticity, and neuronal maintenance, which was consistent with their enrichment in neurons. Our study suggests that APA is a crucial sex- and cell type-specific mechanism in AUD with the potential to influence localized neuronal protein expression during protracted withdrawal and to modify alcohol consumption behavior. HIGHLIGHTSO_LIChronic ethanol exposure in mice results in profound changes of APA genes in brain. C_LIO_LICommonly regulated cleavage and polyadenylation sites and genes were identified in male but not in female mice. C_LIO_LIThere was a minimal overlap between APA and differentially expressed genes (DEGs). C_LIO_LIAPA genes were primarily associated with neurons, whereas DEGs were associated with non-neuronal cells. C_LI

neuroscience↗

bioRxiv2026

RIC-3 Interacts Directly with the 5-HT3A Receptor to Mediate Trafficking Across Subcellular Compartments

The serotonin type 3A (5-HT3A) receptor is a pentameric ligand-gated ion channel (pLGIC) in central and peripheral neurons that conducts sodium and potassium ions upon serotonin binding. 5-HT3 receptors modulate neurotransmission and synaptic plasticity, influencing mood, sleep, appetite, and addiction. Disruptions in serotonin signaling are linked to central nervous system disorders, including schizophrenia, anxiety and depression. Clinically, these receptors are targeted by antagonists to treat chemotherapy-induced nausea and vomiting. The functional surface expression of these channels is regulated by the chaperone protein Resistant to Inhibitors of Cholinesterase 3 (RIC-3) that promotes plasma-membrane expression, maturation, and trafficking of 5-HT3A and nicotinic acetylcholine receptors. Our previous work identified a duplicated RIC-3 binding motif within the 5-HT3A intracellular domain (ICD). However, it was unclear whether this interaction reflected native conditions. Here, we used a recombinant 5-HT3A ICD peptide in peptide-resin pull-down assays to investigate RIC-3 Interactions in plasma membrane (PM) fractions from Xenopus oocytes, endoplasmic reticulum (ER) fractions from SH-SY5Y cells, and mouse brain tissue. Across all tested systems, the 5-HT3A ICD peptide specifically bound RIC-3. Furthermore, RIC-3 knockdown (RIC-3 KD) SH-SY5Y cells showed a marked reduction in peptide binding and decreased surface levels of nAChR7 and 5-HT3A receptors. These results demonstrate RIC-3-5-HT3A ICD interaction in native cellular contexts and support a role for RIC-3 in regulating receptor surface expression and neuronal signaling.

neuroscience↗

bioRxiv2020

Integrated analysis of a compendium of RNA-Seq datasets for splicing factors

A vast amount of public RNA-sequencing datasets have been generated and used widely to study transcriptome mechanisms. These data offer precious opportunity for advancing biological research in transcriptome studies such as alternative splicing. We report the first large-scale integrated analysis of RNA-Seq data of splicing factors for systematically identifying key factors in diseases and biological processes. We analyzed 1,321 RNA-Seq libraries of various mouse tissues and cell lines, comprising more than 6.6 TB sequences from 75 independent studies that experimentally manipulated 56 splicing factors. Using these data, RNA splicing signatures and gene expression signatures were computed, and signature comparison analysis identified a list of key splicing factors in Rett syndrome and cold-induced thermogenesis. We show that cold-induced RNA-binding proteins rescue the neurite outgrowth defects in Rett syndrome using neuronal morphology analysis, and we also reveal that SRSF1 and PTBP1 are required for energy expenditure in adipocytes using metabolic flux analysis. Our study provides an integrated analysis for identifying key factors in diseases and biological processes and highlights the importance of public data resources for identifying hypotheses for experimental testing.

bioinformatics↗

bioRxiv2020

A Point Mutation in the RNA Recognition Motif of CSTF2 Associated with Intellectual Disability in Humans Causes Defects in 3' End Processing

CSTF2 encodes an RNA-binding protein that is essential for mRNA cleavage and polyadenylation (C/P). No disease-associated mutations have been described for this gene. Here, we report a mutation in the RNA recognition motif (RRM) of CSTF2 that changes an aspartic acid at position 50 to alanine (p.D50A), resulting in intellectual disability in male patients. In mice, this mutation was sufficient to alter polyadenylation sites in over 1,000 genes critical for brain development. Using a reporter gene assay, we demonstrated that C/P efficiency of CSTF2D50A was lower than wild type. To account for this, we determined that p.D50A changed locations of amino acid side chains altering RNA binding sites in the RRM. The changes modified the electrostatic potential of the RRM leading to a greater affinity for RNA. These results highlight the importance of 3' end mRNA processing in correct expression of genes important for brain plasticity and neuronal development.

molecular biology↗