Investigating molecular mechanisms and cellular functions of genomic imprinting

PROJECT SUMMARY Individuals inherit one copy of each chromosome from each parent. However, the parental genomes within offspring are not functionally equivalent due to genomic imprinting, an epigenetic phenomenon in which certain genes are expressed from only one parental copy. Imprinted genes are widely expressed during development and play important roles in growth and neurodevelopment. Genomic imprinting increases disease susceptibility: genetic disruptions in the only expressed parental copy can result in imprinted disorders with frequent metabolic and neurodevelopmental symptoms. The Whipple lab seeks to determine (i) the molecular mechanisms regulating imprinted gene expression, including cell type-specific imprinted expression, and (ii) the cellular and physiological functions of imprinted genes, with a focus on imprinted non-coding RNAs. Fundamental discoveries related to genomic imprinting is expected to inform better treatments for imprinted disorders, as previously experienced in Angelman syndrome. (i) Using neuron differentiation as a model system to understand cell type-specific imprinted expression, the Whipple lab has recently identified parent-specific chromatin structure in the Kcnk9 imprinted domain that is strengthened during differentiation. This work will be extended to comprehensively quantify differences in the 3D folding of maternal and paternal alleles across imprinted domains. Future experiments will then probe the functional relationships between epigenetic modifications, chromatin structure, and gene expression in different tissues and cell types. (ii) Regarding the function of imprinted non-coding RNAs, the lab will primarily focus the next five years on discovering the targets and functions of imprinted small nucleolar RNAs (snoRNAs). snoRNAs typically guide chemical modifications on complementary RNA targets, but the targets of imprinted snoRNAs have largely evaded scientists for the past twenty years. Moreover, loss of paternally expressed snoRNAs are a major cause of Prader-Willi syndrome. The lab is developing new transcriptomic tools to discover snoRNA:target interactions, including an optimized snoRNA-RNA chimeric ligation approach for directly sequencing snoRNA targets. These findings will then be used to better understand the cellular and physiological effects of imprinted snoRNA activity and the pathways under parental influence in offspring. Through these efforts, the Whipple lab expects to uncover principles regarding epigenetic control of gene regulation and chromatin organization that broadly apply across diverse cell types, tissues, and organisms. The lab also expects to find new non-coding RNA functions with direct implications for understanding the biological processes dysregulated in imprinted disorders.