Spt5 (also known as DSIF-P160, Tat-CT, and Foggy) is an evolutionarily conserved essential protein that represses as well as stimulates transcription elongation in vitro. Although less than a handful of genes are shown to be under direct regulation by Spt5, the prevalence and identity of its target genes is poorly defined in vivo.
Through expression profiling studies on ~10,000 protein-coding genes, a surprisingly small fraction (less than 5%) was differentially expressed between fogsk8 mutants and their wild-type (WT) siblings while less than 1.5% was differentially expressed between foggy m806 and their WT siblings. Further classification analyses revealed that these differentially expressed genes are involved in diverse biological pathways ranging from pattern specification to stress response. Many previously uncharacterized, novel genes were also differentially expressed in these mutants.
A permutation based analysis revealed that genes upregulated in fogsk8 and foggym806 embryos have significantly shorter gene length compared to the average gene length in zebrafish, suggesting an additional repressive level of regulation of shorter genes by Foggy/Spt5. In vivo chromatin immunoprecipitation further uncovered genes that are directly bound and regulated by Foggy/Spt5 at the level of transcription elongation. Furthermore, Foggy and RNAPII occupancies suggest the poised transcriptional status of many upregulated genes, and active transcription of many downregulated genes in WT embryos.
Our comparison of RNAPII occupancy between WT and sk8 embryos identified Growth Arrest and DNA-damage inducible gene (gadd45b) to be a novel target for repression by Foggy. Transcription elongation control of such inducible genes might be crucial to integrate signals from multiple pathways to coordinate regulation of important signaling pathways that ultimately determine cell fate and survival. In conclusion, our results identify a small but functionally diverse set of genes that are regulated by Foggy/Spt5 and provides interesting insights into the identities and characteristics of target genes of Foggy/Spt5 in vertebrate development.