Project description:The genome of the white-throated sparrow (Zonotrichia albicollis) contains an inversion polymorphism on chromosome 2 that is linked to predictable variation in a suite of phenotypic traits including plumage color, aggression, and parental behavior. Differences in gene expression between the two color morphs, which represent the two common inversion genotypes (ZAL2/ZAL2 and ZAL2/ZAL2m), are therefore of potential interest toward understanding the molecular underpinnings of these phenotypes. To identify genes that are differentially expressed between the two morphs and correlated with behavior, we quantified both behavior and gene expression in a population of free-living white-throated sparrows. We quantified behavioral responses to simulated territorial intrusions (STIs) early during the breeding season. In the same birds, we then performed a transcriptomewide analysis of gene expression in two behaviorally relevant brain regions, the medial amygdala and hypothalamus. Using network analyses, we identified modules of genes that were correlated with both morph and STI-induced singing behavior. The majority of these genes were located within the inversion, demonstrating the profound effect the inversion has on the expression of genes captured by the rearrangement. Gene pathway analyses revealed that in the medial amygdala, the most prominent pathways were those related to steroid hormone receptor activity. Within these pathways, the only gene encoding such a receptor was ESR1 (estrogen receptor alpha). Our results thus suggest that ESR1 and related genes are important for behavioral differences between the morphs.
Project description:Epigenomics is developing a colon cancer screening assay based on differential methylation of specific CpG sites for the detection of early stage disease. A genome-wide methylation analysis and oligonucleotide array study using DNA from various stages of colon cancer and normal tissue have been completed to obtain candidate CpG markers. Based on results obtained in the above studies, Epigenomics has moved to the final stages of feasibility with a specific, highly sensitive real-time marker assay that is able to detect colon cancer DNA in blood plasma.
Project description:We compared genome-wide DNA methylation profiles between chronically demyelinated MS lesions and matched normal-appearing white matter (NAWM).
2023-06-29 | GSE224455 | GEO
Project description:Captive White Crowned Sparrows
Project description:We depicted a genome-wide integrative view of DNA methylome by reduced representation bisulfite sequencing (RRBS) and transcriptome by RNA-seq during brown and white adipocyte differentiation. Our analysis demonstrated that DNA methylation is a stable epigenetic signature for brown and white cell lineage before, during and after differentiation. When comparing white to brown adipocytes at all three time points of differentiation, we identified five members of the Hox family whose expression levels were anti-correlated with promoter methylation, suggesting a regulatory role of DNA methylation in transcription.
Project description:We depicted a genome-wide integrative view of DNA methylome by reduced representation bisulfite sequencing (RRBS) and transcriptome by RNA-seq during brown and white adipocyte differentiation. Our analysis demonstrated that DNA methylation is a stable epigenetic signature for brown and white cell lineage before, during and after differentiation. When comparing white to brown adipocytes at all three time points of differentiation, we identified five members of the Hox family whose expression levels were anti-correlated with promoter methylation, suggesting a regulatory role of DNA methylation in transcription.
Project description:We examined genome-wide patterns of DNA methylation from whole genome DNA methylation maps of five tissues (brain, kidney, lung, skeletal muscle, and pancreas) from one male koala and one female koala (Phascolarctos cinereus), and present the first whole genome, multi-tissue “methylome atlas” with information on tissue- and sex-specific variation of DNA methylation for a marsupial.
