Biology subjects

Tooley, K. B.

Publications and source records attributed to Tooley, K. B..

3 recordsLinked to original sources

bioRxiv2024

Changes in microglia chromatin accessibility in aged female mice.

Aged female microglia display a more inflammatory and disease-associated phenotype compared to age-matched males. Epigenetic mechanisms, such as chromatin accessibility, are key drivers of microglial plasticity and phenotypes necessary for development, priming, and immune activation. Therefore, alterations in chromatin accessibility patterns can potentially regulate the neuroimmune responses and phenotypes observed in female microglia with aging, but to date have not been assessed. In this study, hippocampal microglia chromatin accessibility in young (4-5 months) and old (23-24 months) female mice was interrogated by Assay for Transposable Accessible Chromatin using Sequencing (ATAC-Seq). Cx3cr1-cre/ERT2+: NuTRAP mice were used to tag microglia and enable INTACT (isolation of nuclei tagged in specific cell types) collection of microglia-specific nuclei. With aging, loci specific gains and losses in chromatin accessibility were observed. Notably, changes in chromatin accessibility were skewed, with aged female microglia having more regions gaining accessibility than loosing accessibility. These changes were under-represented in the proximal promoter region ([≤]1kb) of genes but were enriched in intergenic regions. Regions that gained accessibility were more concentrated around genes responsible for myeloid cell differentiation and the regulation of immune and inflammatory responses. In contrast, regions that became less accessible were closest to genes involved in neuronal and synaptic function. In addition, X Chromosome accessibility changes were less common compared to autosomal changes, which argues against increased X Chromosome escape from inactivation with aging in female microglia. Overall, our data demonstrate age-related chromatin accessibility changes in female microglia, which may be regulated within enhancers and distal regulatory elements, and that these changes have potential downstream implications for the inflammatory phenotype of microglia in aging female mice.

molecular biology↗

bioRxiv2023

Differential usage of DNA modifications in neurons, astrocytes, and microglia

BackgroundCellular identity is determined partly by cell type-specific epigenomic profiles that regulate gene expression. In neuroscience, there is a pressing need to isolate and characterize the epigenomes of specific CNS cell types in health and disease. This is especially true as for DNA modifications where most data are derived from bisulfite sequencing that cannot differentiate between DNA methylation and hydroxymethylation. In this study, we developed an in vivo tagging mouse model (Camk2a-NuTRAP) for paired isolation of neuronal DNA and RNA without cell sorting and then used this model to assess epigenomic regulation of gene expression between neurons and glia. ResultsAfter validating the cell-specificity of the Camk2a-NuTRAP model, we performed TRAP-RNA-Seq and INTACT whole genome oxidative bisulfite sequencing to assess the neuronal translatome and epigenome in the hippocampus of young mice (3 months old). These data were then compared to microglial and astrocytic data from NuTRAP models. When comparing the different cell types, microglia had the highest global mCG levels followed by astrocytes and then neurons, with the opposite pattern observed for hmCG and mCH. Differentially modified regions between cell types were predominantly found within gene bodies and distal intergenic regions, with limited differences occurring within proximal promoters. Across cell types there was a negative correlation between DNA modifications (mCG, mCH, hmCG) and gene expression at proximal promoters. In contrast, a negative correlation of mCG with gene expression within the gene body while a positive relationship between distal promoter and gene body hmCG and gene expression was observed. Furthermore, we identified a neuron-specific inverse relationship between mCH and gene expression across promoter and gene body regions. ConclusionsIn this study, we identified differential usage of DNA modifications across CNS cell types, and assessed the relationship between DNA modifications and gene expression in neurons and glia. Despite having different global levels, the general modification-gene expression relationship was conserved across cell types. The enrichment of differential modifications in gene bodies and distal regulatory elements, but not proximal promoters, across cell types highlights epigenomic patterning in these regions as potentially greater determinants of cell identity.

genomics↗

bioRxiv2021

Differential regulation of mouse hippocampal gene expression sex differences by chromosomal content and gonadal sex

Common neurological disorders, like Alzheimers disease (AD), multiple sclerosis (MS), and autism, display profound sex differences in prevalence and clinical presentation. However, sex differences in the brain with health and disease are often overlooked in experimental models. Sex effects originate, either directly or indirectly, from hormonal or sex chromosomal mechanisms. To delineate the contributions of genetic sex (XX v. XY) versus gonadal sex (ovaries v. testes) to the epigenomic regulation of hippocampal sex differences, we use the Four Core Genotypes (FCG) mouse model to uncouple chromosomal and gonadal sex. Transcriptomic and epigenomic analyses of [~]12-month-old FCG mice hippocampi, revealed genomic context-specific regulatory effects of genotypic and gonadal sex on X- and autosome-encoded gene expression and DNA modification patterns. X-chromosomal epigenomic patterns, classically associated with X-inactivation, were established almost entirely by genotypic sex, independent of gonadal sex. Differences in X-chromosome methylation were primarily localized to gene regulatory regions including promoters, CpG islands, CTCF binding sites, and active/poised chromatin, with an inverse relationship between methylation and gene expression. Whereas, autosomal gene expression demonstrated regulation by both genotypic and gonadal sex, particularly in immune processes. These data demonstrate an important regulatory role of sex chromosomes, independent of gonadal sex, on sex-biased hippocampal transcriptomic and epigenomic profiles. Future studies will need to further interrogate specific CNS cell types, identify the mechanisms by which sex chromosomes regulate autosomes, and differentiate organizational from activational hormonal effects.

genomics↗