Biology subjects

Merrill, C. B.

Publications and source records attributed to Merrill, C. B..

7 recordsLinked to original sources

bioRxiv2023

Large genetic analysis of alcohol resistance and tolerance reveals an inverse correlation and suggests "true" tolerance mutants.

Tolerance occurs when, following an initial experience with a substance, more of the substance is required subsequently to induce the same behavioral effects. Tolerance is historically not well-understood, and numerous researchers have turned to model organisms, particularly Drosophila melanogaster, to unravel its mechanisms. Flies have high translational relevance for human alcohol responses, and there is substantial overlap in disease-causing genes between flies and humans, including those associated with Alcohol Use Disorder. Numerous Drosophila tolerance mutants have been described; however, approaches used to identify and characterize these mutants have varied across time and between labs and have mostly disregarded any impact of initial resistance/sensitivity to ethanol on subsequent tolerance development. Here, we have analyzed a large amount of data - our own published and unpublished data and data published by other labs - to uncover an inverse correlation between initial ethanol resistance and tolerance phenotypes. This inverse correlation suggests that initial resistance phenotypes can explain many perceived tolerance phenotypes. Additionally, we show that tolerance should be measured as a relative increase in time to sedation between an initial and second exposure rather than an absolute change in time to sedation. Finally, based on our analysis, we provide a method for using a linear regression equation to assess the residuals of potential tolerance mutants. We show that these residuals provide predictive insight into the likelihood of a mutant being a true tolerance mutant, and we offer a framework for understanding the relationship between initial resistance and tolerance.

neuroscience↗

bioRxiv2023

Iterative assay for transposase-accessible chromatin by sequencing to isolate functionally relevant neuronal subtypes

The Drosophila brain contains tens of thousands of distinct cell types. Thousands of different transgenic lines reproducibly target specific neuron subsets, yet most still express in several cell types. Furthermore, most lines were developed without a priori knowledge of where the transgenes would be expressed. To aid in the development of cell type-specific tools for neuronal identification and manipulation, we developed an iterative assay for transposase-accessible chromatin (ATAC) approach. Open chromatin regions (OCRs) enriched in neurons, compared to whole bodies, drove transgene expression preferentially in subsets of neurons. A second round of ATAC-seq from these specific neuron subsets revealed additional enriched OCR2s that further restricted transgene expression within the chosen neuron subset. This approach allows for continued refinement of transgene expression, and we used it to identify neurons relevant for sleep behavior. Furthermore, this approach is widely applicable to other cell types and to other organisms.

neuroscience↗

bioRxiv2022

One-carbon Pathways and Methylation Potential in Glutamatergic Neurons Regulate Behavioral Alcohol Responses

Despite the enormous harms of alcohol use disorders (AUDs), many mechanisms, as well as effective prevention or treatment strategies remain elusive. Genetic factors dictate a majority of AUD risk. These risk factors can manifest as reduced naive sensitivity to alcohols intoxicating effects and increased functional tolerance, i.e., brain-mediated decreases in sensitivity upon repeat exposure. The underlying neurobiology of how AUD-associated genes alter these endophenotypes remains poorly understood. Genes implicated in AUDs include epigenetic modifiers, such as histone demethylases, including Kdm3. We previously showed that whole-body and neuronal Kdm3 strongly affect ethanol sensitivity and tolerance in Drosophila. Here, we investigate the mechanisms of these effects, and, by extension, mechanisms of sensitivity and tolerance. RNA-seq and pathway analysis on Kdm3KO flies revealed disproportionate upregulation of genes involved in amino acid metabolism, including 1-carbon pathways. We show that acute amino acid feeding modulates sensitivity and tolerance in a Kdm3-dependent manner. Global manipulation of 1-carbon genes, especially glycine N-methyltransferase (Gnmt), glycine decarboxylase (Gldc), and sarcosine dehydrogenase (Sardh), alters alcohol sensitivity and tolerance. These changes in alcohol responses are likely mediated by global glycine levels (a substrate of these enzymes) rather than by 1-carbon input. Conversely, neuronal manipulations of 1-carbon pathways change alcohol sensitivity and tolerance in a pattern that suggests a mechanism through S-adenosyl methionine (SAM), a 1-carbon metabolite that is the universal methyl donor required for epigenetic methylation. Increasing SAM production specifically in glutamatergic neurons increases sensitivity and tolerance. Together, these findings reveal distinct mechanisms affecting alcohol sensitivity and tolerance globally (via glycine) and neuronally (via SAM), thus revealing an important and complex role of 1-carbon metabolism in mediating AUD phenotypes.

neuroscience↗

bioRxiv2021

Integrating RNA-seq and assay for transposase-accessible chromatin by sequencing (ATAC-seq) predicts functionally-relevant chromatin regions

BackgroundGene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. Studies investigating the epigenome have begun to uncover the complex mechanisms regulating transcription. Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is quickly becoming the assay of choice for many epigenomic investigations. However, whether intervention-mediated changes in accessible chromatin determined by ATAC-seq can be harnessed to generate intervention-inducible reporter constructs has not been systematically assayed. ResultsWe used the insulin signaling pathway as a model to investigate chromatin regions and gene expression changes using ATAC- and RNA-seq in insulin-treated Drosophila S2 cells. We found correlations between ATAC- and RNA-seq data, especially when stratifying differentially-accessible chromatin regions by annotated feature type. In particular, our data demonstrated a strong correlation between chromatin regions annotated to distal promoters (1-2 kb from the transcription start site) and downstream gene expression. We cloned candidate distal promoter regions upstream of luciferase and demonstrate insulin-inducibility of several of these reporters. ConclusionsInsulin-induced chromatin accessibility determined by ATAC-seq reveals enhancer regions that drive insulin-inducible reporter gene expression.

cell biology↗

bioRxiv2021

An optimized protocol for neuronal assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation using Drosophila melanogaster

Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is rapidly becoming the assay of choice to investigate chromatin-mediated gene regulation, largely because of low input requirements, a fast workflow, and the ability to interrogate the entire genome in an unbiased manner. Many studies using ATAC-seq use mammalian or human-derived tissues, and established protocols work well in these systems. However, ATAC-seq is not yet widely used in Drosophila. Vinegar flies present several advantages over mammalian systems that make them an excellent model for ATAC-seq studies, including abundant genetic tools that allow straightforward targeting, transgene expression, and genetic manipulation, and are not available in mammalian models. Because current ATAC-seq protocols are not optimized to use flies, we developed an optimized workflow that accounts for several complicating factors present in Drosophila. We examined parameters affecting nuclei isolation, including input size, freezing time, washing, and possible confounds from retinal pigments. Then, we optimized the enzymatic steps of library construction to account for the smaller Drosophila genome size. Finally, we used our optimized protocol to generate ATAC-seq libraries that meet ENCODE quality metrics. Our optimized protocol enables extensive ATAC-seq experiments in Drosophila, thereby leveraging the advantages of this powerful model system to understand chromatin-mediated gene regulation.

neuroscience↗

bioRxiv2019

Dopaminergic learning and arousal circuits mediate opposing effects on alcohol consumption in Drosophila

The response to drugs of abuse is a combination of aversive and reinforcing reactions. While much is known about the role of dopamine in mammalian drug reinforcement, we know little about the brain circuits mediating drug aversion. Here we show that two distinct dopaminergic circuits mediate reinforcing and acute aversive responses to alcohol consumption in Drosophila. Protocerebral anterior medial dopamine neurons projecting to the mushroom bodies are required for flies to acquire alcohol preference. Conversely, a bilateral pair of dopamine neurons projecting to the dorsal fan-shaped body (dFSB) mediates acute alcohol avoidance. Alcohol consumption can be reduced by decreasing the activity of the appetitive reinforcement-circuit to the mushroom bodies, or by increasing activity in the dopamine neurons projecting to the dFSB. Thus, distinct dopaminergic pathways can be targeted to reduce the intake of harmful drugs.

neuroscience↗

bioRxiv2019

Altered actin filament dynamics in the Drosophila mushroom bodies lead to fast acquisition of alcohol consumption preference.

Alcohol use is highly prevalent in the United States and across the world, and every year millions of people suffer from alcohol use disorders (AUDs). While the genetic contribution to developing AUDs is estimated to be 50-60%, many of the underlying molecular mechanisms remain unclear. Previous studies from our lab revealed that Drosophila lacking RhoGAP18B and Ras Suppressor 1 (Rsu1) display reduced sensitivity to ethanol-induced sedation. Both Rsu1 and RhoGAP18B are negative regulators of the small Rho-family GTPase, Rac1, a modulator of actin dynamics. Here we investigate the role of Rac1 and its downstream target, the actin-severing protein cofilin, in alcohol consumption preference. We show that these two regulators of actin dynamics can alter experience-dependent alcohol preference in a bidirectional manner: expressing either activated Rac1 or dominant-negative cofilin in the mushroom bodies (MB) abolishes experience-dependent alcohol preference. Conversely, dominant-negative Rac1 or activated cofilin MB expression lead to faster acquisition of alcohol preference. Our data show that Rac1 and cofilin activity are key to determining the rate of acquisition of alcohol preference, revealing a critical role of actin dynamics regulation in the development of voluntary self-administration in Drosophila.\n\nSignificance StatementThe risks for developing an alcohol use disorder (AUD) are strongly determined by genetic factors. Understanding the genes and molecular mechanisms that contribute to that risk is therefore a necessary first step for the development of targeted therapeutic intervention. Here we show that regulators of actin cytoskeleton dynamics can bidirectionally determine the acquisition rate of alcohol self-administration, highlighting this process as a key mechanism contributing to the risk of AUD development.

neuroscience↗