Abstract Genome graphs, including the recently released draft human pangenome graph, can represent breadth of genetic diversity and thus transcend limits traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored accurate DNA methylation analysis by mapping WGBS data to graph. Notably, methylGrapher reconstruct patterns along haplotype...

Allele-specific expression (ASE) is a phenomenon in which one allele preferentially expressed over the other. Genetic and epigenetic factors cause ASE by altering final composition of gene's product, leading to imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific expression, but how they contribute this cross talk remains understudied. Here, we explored genotype, parent-of-origin, tissue, sex, dietary fat simultaneously influence...

The relationship between TP53 and transposable elements (TEs) has been obscure. Given the important role of TEs in oncogenesis, a comprehensive profiling TE expression dynamics under regulation provides valuable resources for more clarity TP53's roles cancer. In this study, we characterized transcriptomic landscape using long-read RNA-seq short-read three cancer cell lines varying only genetic status. To identify transcripts that use as potential promoters, developed computational pipeline,...

Parent-of-origin effects are unexpectedly common in complex traits, including metabolic and neurological traits. can be modified by the environment, but architecture of these gene-by-environmental on phenotypes remains to unraveled. Previously, quantitative trait loci (QTL) showing context-specific parent-of-origin traits were mapped F 16 generation an advanced intercross between LG/J SM/J inbred mice. However, QTL not enriched for known imprinted genes, suggesting another mechanism is...

The potato psyllid, Bactericera cockerelli (Sulc), is a native of North America and occurs from Central to Canada. A newly emerging plant pathogen, Candidatus Liberibacter solanacearum, associated with psyllids in New Zealand, has become major concern many solanaceous crops worldwide. In potato, Solanum tuberosum L., the resulting disease called zebra chip, but similar foliar vascular symptoms have been reported tomato, lycopersicum peppers, Capsicum annuum L. To date, it known that transmit...

We leverage the SM/J mouse to understand glycemic control in obesity. High-fat-fed mice initially develop poor glucose homeostasis relative controls. Strikingly, their dysfunction resolves by 30 weeks of age despite persistent The dramatically expand brown adipose depots as they resolve dysfunction. This occurs naturally and spontaneously on a high-fat diet, with no temperature or genetic manipulation. Removal depot impairs insulin sensitivity, indicating that expanded tissue is functioning...

Maintenance of functional β-cell mass is critical to preventing diabetes, but the physiological mechanisms that cause populations thrive or fail in context obesity are unknown. High fat-fed SM/J mice spontaneously transition from hyperglycemic-obese normoglycemic-obese with age, providing a unique opportunity study adaptation. Here, we characterize insulin homeostasis, islet morphology, and function during SM/J's diabetic remission. As they resolve hyperglycemia, obese dramatically increase...

Iron is a critical component of metabolic homeostasis, but consumption dietary iron has increased dramatically in the last 30 years, corresponding with rise disease. While link between metabolism and health well established, extent to which contributes disease risk unexplored. Further, it unknown how interacts genetic background modify risk.

Zebra chip of potato, Solanum tuberosum L., is caused by the phytopathogen Candidatus Liberibacter solanacearum (Lso) transmitted potato psyllid, Bactericera cockerelli Sulc. While psyllid native to United States and northern Mexico, Lso range has expanded north south during past 10 years. Historically, population-level studies have used mitochondrial gene Cytochrome Oxidase I (COI) applied molecular biology techniques understand population genetics species. Unfortunately, most published...

Abstract Disruption of glucose homeostasis increases the risk type II diabetes, cardiovascular disease, stroke, and cancer. We leverage a novel rodent model, SM/J mouse, to understand glycemic control in obesity. On high fat diet, obese mice initially develop impaired tolerance elevated fasting glucose. Strikingly, their dysfunction resolves by 30 weeks age despite persistence A prominent phenotype is that they dramatically expand brown adipose depots as resolve dysfunction. This occurs...

Abstract Background Understanding how heterogeneous β-cell function impacts diabetes is imperative for therapy development. Standard single-cell RNA sequencing analysis illuminates some factors driving heterogeneity, but new strategies are required to enhance information capture. Results We integrate pancreatic islet and bulk data identify subpopulations based on gene expression characterize genetic networks associated with in obese SM/J mice. basal insulin secretion, hypoxia response, cell...

ABSTRACT Parent-of-origin effects are unexpectedly common in complex traits, including metabolic and neurological diseases. can be modified by the environment, but architecture of these gene-by-environmental on phenotypes remains to unraveled. Previously, quantitative trait loci (QTL) showing context-specific parent-of-origin traits were mapped F 16 generation an advanced intercross between LG/J SM/J inbred mice. However, QTL not enriched for known imprinted genes, suggesting another...

ABSTRACT Parent-of-origin effects (POE) are unexpectedly common in complex traits, including metabolic and neurological diseases. POE can also be modified by the environment, but architecture of these gene-by-environmental on phenotypes remains to unraveled. Previously, quantitative trait loci (QTL) showing context-specific traits were mapped F 16 generation an advanced intercross between LG/J SM/J inbred mice. However, QTL not enriched for known imprinted genes, suggesting another mechanism...

Abstract Maintenance of functional β-cell mass is critical to preventing diabetes, but the physiological mechanisms that cause populations thrive or fail in context obesity are unknown. High fat-fed SM/J mice spontaneously transition from hyperglycemic-obese normoglycemic-obese with age, providing a unique opportunity study adaptation. Here, we characterize insulin homeostasis, islet morphology, and function during SM/J’s diabetic remission. As they resolve hyperglycemia, obese dramatically...

Abstract The alteration of gene expression due to variations in the sequences transcriptional regulatory elements has been a focus substantial inquiry humans and model organisms. However, less is known about extent which natural variation contributes post-transcriptional regulation. Allelic Expression Imbalance (AEI) classical approach for studying association specific haplotypes with relative changes transcript abundance. Here, we piloted new TRAP based associate genetic occupancy on...

ABSTRACT Allele-specific expression ( ASE ) is a phenomenon where one allele preferentially expressed over the other. Genetic and epigenetic factors cause by altering final allelic composition of gene’s product, leading to imbalances that can have functional consequences on phenotypes. Environmental signals also impact allele-specific gene regulation, but how they contribute this crosstalk remains understudied. Here, we explored genotype, parent-of-origin, tissue type, sex, dietary fat...