Cell-type and tissue specific patterns of gene expression during development are regulated by transcriptional activation and repression. The acetylation state of chromosomal histones plays an essential role in the developmental regulation of gene expression; while hyperacetylated chromatin is usually associated with active transcription units, hypoacetylated regions of chromatin frequently are transcriptionally silent. This acetylation status is enzymatically regulated by histone acetyltransferases (HATs) and by histone deacetylases (HDACs). 17 HDACs genes have been identified in humans so far, which fall into three categories based on their homology to yeast HDACs. C.elegans has 11 HDACs, and three of them belong to class I. Histone Deacetylase 1 (
hda-1) is a class I C.elegans HDAC gene that shows ubiquitous expression throughout development. The existing
hda-1 genetic mutant (
gon-10, gonadogenesis defective-10)is not useful to analyze the role of
hda-1in early embryogenesis since
gon-10 animals are sterile. However, depletion of both maternal and zygotic
hda-1 by RNAi results in embryonic lethality of variable penetrance. A high proportion of
hda-1 (RNAi) embryos display ectopic
end-1 expression in the early embryo. Since END-1 is sufficient to induce endoderm differentiation, one possibility is that these embryos are dying due to inappropriate specification of early endodermal tissue. In order to obtain fully-penetrant embryonic lethality we optimized the RNAi protocols and achieved 100% lethality. To identify potential target genes of
hda-1, we harvested
hda-1(RNAi) and control treated embryos prior to the lethal stage, and performed DNA microarray analysis. We performed these experiments in triplicate, and averaged the resulting ratios. Our results show that, in agreement with a general role in transcriptional repression for histone deacetylases, lack of
hda-1 in the early embryo results in greater than three-fold upregulation of the expression of 95 genes. By contrast, only 10 genes are downregulated three fold or greater. Importantly, one of the most downregulated genes is
hda-1 itself, demonstrating that functional depletion of that gene product by RNAi was successful. This genome-wide approach sheds light on the function of HDACs in multicellular organisms. For instance, it shows that a single predicted HDAC could be sufficient to determine gene activity by itself during development. In addition, it reveals that a specific histone deacetylase may have an effect on tissue-specific gene products, since many of the genes that are de-repressed in the
hda-1 (RNAi) animals appear to encode potential gut- and pharynx-specific genes.