Combinatorial regulation of shared target genes by LMD and MEF2
The development of any multicellular organism involves the coordinated expression of different genes in complex spatio-temporal patterns. These complex patterns of gene expression result from the interplay between multiple transcription factors (TFs) and their co-factors, acting on specific cis-regu...
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|The development of any multicellular organism involves the coordinated expression of different genes in complex spatio-temporal patterns. These complex patterns of gene expression result from the interplay between multiple transcription factors (TFs) and their co-factors, acting on specific cis-regulatory modules to activate or repress the affected locus. This study investigates the interaction between two essential regulators of myogenesis: the transcription factors Myocyte enhancing factor 2 (Mef2) and lame duck (lmd). Mutations in either of these transcription factors results in a similar block of fusion phenotype, but the molecular basis for this similar phenotype is not yet understood.
The analysis started with ChIP-on-chip to identify the genomic location where each TF binds in vivo. Microarrays were used again to conduct expression profiling of loss-of-function mutants, and the combination of these two approaches yielded a list of direct target genes of the two TFs. Interestingly, the majority of enhancers bound by Lmd are also bound by Mef2 at the same developmental timepoint. Likewise, almost 80% of the lmd direct target genes are also direct targets of Mef2, revealing an extensive co-regulation between the two TFs. A group of shared direct targets was then selected for further study; Lmd and Mef2, alone or in combination, were used to drive ectopic expression of these genes, resulting in both synergistic and antagonistic interactions.
The affected enhancer for each target was identified using a variety of predictions, and transgenic fly lines were created to demonstrate the capacity of the enhancers for correct expression in vivo. These enhancers were also analyzed in the mutant background of loss-of-function mutations and revealed specific requirements for each transcription factor. Lmd and Mef2 were also tested in vitro for their effect on transcription from these enhancers, revealing additive, cooperative, and repressive interactions.
These results indicate that lmd is a temporal and tissue-specific modulator of Mef2 activity, acting both as a transcriptional activator and repressor on a sub- set of the catalog of target genes of Mef2. More generally, it demonstrates a scenario of flexibility in the regulatory output of two transcription factors, leading to additive, cooperative and repressive interactions.