Studying Stimulus‐Induced Changes in RNA Dynamics by Mutational Mapping through TimeLapse‐seq

Abstract

The eukaryotic transcriptome is dynamically regulated through RNA transcription and decay allowing cells to respond to environmental stimuli in a rapid and specific manner. The bromodomain inhibitor JQ1, has been extensively studied in the context of cancer cells, as it blocks the activation of specific sets of oncogenes perturbing RNA population dynamics.1 Recently, JQ1 has additionally been found to repress pathogenic response genes in models of heart failure, however the mechanism of this action remains unclear.2 JQ1 is known to block the BET bromodomain reader proteins involved in chromatin remodeling, affecting the transcription of the target genes. We, therefore, aim to study the effect of JQ1 in heart failure on the transcriptional level. While RNA‐sequencing (RNA‐seq) provides a snapshot of the cellular transcriptome, temporal information is lost as rapid changes in the RNA population remain undetected among the excess of preexisting RNA. To gain insight into the role of JQ1‐induced pathways in cardiomyocytes, we are studying changes in RNA dynamics using TimeLapse‐seq3, recently developed nucleotide recoding chemistry that utilizes metabolic labeling in an enrichment‐free RNA‐seq approach. Through recoding of the hydrogen bonding pattern of the metabolic label, TimeLapse‐seq identifies new transcripts through apparent mutations in the RNA‐seq reads. We will describe progress using TimeLapse‐seq as a strategy to study differently regulated transcripts in disease and to deduce the mechanism of JQ1 in heart failure.Support or Funding InformationThis work was supported by the NIH NIGMS T32GM007223 (J.A.S. and E.E.D); NSF Graduate Research Fellowship (E.E.D); NIH New Innovator Award DP2 HD083992‐01 (M.D.S.), and a Searle scholarship (M.D.S.).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.