The Energy Landscape of the Mouse Cargome: A Mechanically Sensitive Family of Genes

Abstract

Myocardin related transcription factor (MRTF) and serum response factor (SRF) co-regulate hundreds of genes across thousands of sites in the genome through the CArG box cis element (canonically CC-W6-GG). Their signaling can be pathological in pulmonary fibrosis where increased extracellular matrix stiffness drives nuclear translocation of MRTF - but how this increase in transcription factor concentration acts across the “CArGome” is not understood. We are using a high-throughput ‘seq’ based approach to identify the in vitro binding affinity of the various CArG permutations for SRF and for SRF-MRTF complexes. The power of this approach allows us to investigate all possible consensus (64 possible sequences) and single mutant (768 possible sequences) using traditional EMSA-based approaches. Additionally we aim to identify cooperativity effects between MRTF and SRF in a sequence dependent fashion. These sequence sets (consensus and single mutants) account for up to 70% of all naturally occurring murine CArG boxes and understanding this energy landscape will facilitate the development of thermodynamic models for understanding the gene specific, mechanically driven behavior of MRTF/SRF across the genome. These models may be useful in understanding a variety of soft-tissue fibrotic conditions and other pathological processes, like metastasis, that appear MRTF/SRF responsive.