Vrinda Venu

Abstract Dysregulation of epigenetic processes leads to a plethora of abnormalities including disease states such as cancer. Therapies focused on epigenetic modulation alter gene expression to correct dysfunction, though the mechanisms and perpetuation of these states is unknown. Here, we use integrated epigenomics and three-dimensional chromatin structure-function analyses after acute histone deacetylase inhibitor cancer drug treatment (suberoylanilide hydroxamic acid in lung cancer cells).

Abstract There is increasing demand to quickly process multiple types of sequencing-based data to completely capture epigenetic alterations and associated changes in chromatin structure underlying cellular responses. Furthermore, the need for a set of bioinformatic tools that leverage high performance computing and parallelization for processing omics data from many experiments has become apparent.

Abstract The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection.