Transcription factor redundancy and tissue specific regulation: evidence from functional and physical network connectivity

Abstract

Two major transcriptional regulators of Caenorhabditis elegans bodywall muscle (BWM) differentiation, hlh-1 and unc-120, are expressed in muscle where they are known to bind and regulate several well-studied muscle-specific genes. Simultaneously mutating both factors profoundly inhibits formation of contractile BWM consistent with a simple network structure in which the regulatory factors drive tissue-specific transcription by binding selectively near muscle-specific targets to activate them. However, the number, identity, and tissue specificity of functional regulatory targets for these factors were unknown, as was the extent of joint regulation by the two major regulators. Here we construct global functional maps that identify regulatory targets of unc-120 or hlh-1 by RNA-seq, determine HLH-1 occupancy from ChIP-Seq, and create a genetic-interaction map that identifies additional HLH-1 collaborating transcription factors. 760 genes are significant regulatory targets of both hlh-1 and unc-120, but each factor has a larger number of unique targets. As expected, some joint target genes (218) are BWM-specific, but the majority of functional targets, including those with nearby HLH-1 occupancy, were not BWM-specific. We conclude that these strongly tissue-specific factors contribute much more broadly to the transcriptional output of muscle tissue than previously thought, offering partial explanation for widespread HLH-1 occupancy. We also identify a novel regulatory connection between the BWM-specific hlh-1 network and the hlh-8/twist non-striated muscle network. Finally, our results suggest a molecular basis for synthetic lethality in which hlh-1 and unc-120 mutant phenotypes are mutually buffered by joint additive regulation of essential target genes, with additional buffering suggested via newly identified hlh-1 interacting factors.