Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites

Abstract

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.

Hedgehog signalling acts upstream of Laminin alpha1 transcription in the zebrafish paraxial mesoderm

“…Data mining of a genome-wide study of histone modification marks found in 24hpf zebrafish embryos revealed a sequence marked by H3K4me3 overlapping with the transcriptional start site of zebrafish lama1 [42], consistent with the known association of H3K4me3 histone modifications with promoter elements and the presence of the lama1…”

“…Histone methylation marks were extracted from the ChIPSeq data performed by Aday et al on 24hpf zebrafish embryos, mapped on the zebrafish genome (zv7) and uploaded on the UCSD genome browser server [42].…”

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation

“…2012). TSSs marked with H3K4me3, a modification associated with transcriptionally active promoters (Aday et al 2011), were significantly earlier replicating than TSSs lacking H3K4me3 (Fig. 3C).…”

Multiple layers of complexity in cis‐regulatory regions of developmental genes

“…Histone marks and chromatin remodeling complexes modify chromatin conformation, regulating the accessibility of transcription factors to cis-regulatory regions. Some epigenetic marks have been associated with specific groups of regulatory elements; in humans (Heintzman et al, 2009), zebrafish (Aday et al, 2011), and flies (Negre et al, 2011) the mono-methylation of histone H3 lysine 4 (H3K4me1) is usually found in active enhancer regions, close to areas of open chromatin. A recent study showed that the activity of the protein LSD1 (a demethylase of H3K4 and H3K9) is essential for differentiation of mouse embryonic stem cells (Whyte et al, 2012).…”