An organism's genome sequence serves as a blueprint for the proteins and 
regulatory RNAs essential for cellular function. The genome also harbors 
cis-acting non-coding sequences that control gene expression and are essential 
to coordinate regulatory programs during embryonic development. However, the 
genome sequence is largely identical between cell types within a multi-cellular 
organism indicating that factors such as DNA accessibility and chromatin 
structure play a crucial role in governing cell-specific gene expression. Recent 
studies have identified particular chromatin modifications that define 
functionally distinct cis regulatory elements. Among these are forms of histone 
3 that are mono- or tri-methylated at lysine 4 (H3K4me1 or H3K4me3, 
respectively), which bind preferentially to promoter and enhancer elements in 
the mammalian genome. In this work, we investigated whether these modified 
histones could similarly identify cis regulatory elements within the zebrafish 
genome. By applying chromatin immunoprecipitation followed by deep sequencing, 
we find that H3K4me1 and H3K4me3 are enriched at transcriptional start sites in 
the genome of the developing zebrafish embryo and that this association 
correlates with gene expression. We further find that these modifications 
associate with distal non-coding conserved elements, including known active 
enhancers. Finally, we demonstrate that it is possible to utilize H3K4me1 and 
H3K4me3 binding profiles in combination with available expression data to 
computationally identify relevant cis regulatory sequences flanking 
syn-expressed genes in the developing embryo. Taken together, our results 
indicate that H3K4me1 and H3K4me3 generally mark cis regulatory elements within 
the zebrafish genome and indicate that further characterization of the zebrafish 
using this approach will prove valuable in defining transcriptional networks in 
this model system.