The epigenome in early vertebrate development

Abstract

Epigenetic regulation defines the commitment and potential of cells, including the limitations in their competence to respond to inducing signals. This review discusses the developmental origins of chromatin state in Xenopus and other vertebrate species and provides an overview of its use in genome annotation. In most metazoans the embryonic genome is transcriptionally quiescent after fertilization. This involves nucleosome-dense chromatin, repressors and a temporal deficiency in the transcription machinery. Active histone modifications such as H3K4me3 appear in pluripotent blastula embryos, whereas repressive marks such as H3K27me3 show a major increase in enrichment during late blastula and gastrula stages. The H3K27me3 modification set by Polycomb restricts ectopic lineage-specific gene expression. Pluripotent chromatin in Xenopus embryos is relatively unconstrained, whereas the pluripotent cell lineage in mammalian embryos harbors a more enforced type of pluripotent chromatin.

Figure 1

Histone modifications mark functionally different elements in the genome. A. Model of a nucleosome core particle with protruding histone tails. Each nucleosome is composed of 147 bp of DNA wrapped around the histone octamer consisting of two copies each of the four core histones H2A (blue, grey), H2B (yellow, olive), H3 (brown, dark red), H4 (green, light green). The figure is based on PDB ID 1AOI (Luger et al., 1997) with the unstructured histone tails drawn in scale. The sites of post-translational histone modifications of interest are marked by yellow circles. B. Average ChIP-seq profiles of seven histone modifications associated with active or inactive genes, promoters or enhancers in Gm12878 (lymphoblastoid) cells. These profiles were generated using raw data from the ENCODE project, downloaded from the UCSC Genome Browser.

Figure 2

Chromatin state in early Xenopus embryos. Key histone modifications such as H3K4me3 (green) and H3K27me3 (red) are newly deposited in early embryos, with major increases in enrichment at blastula and gastrula stages respectively. The genomic DNA is robustly methylated during these stages (light grey), but this methylation does not preclude transcription until the neurula stage when methylation-dependent repression (dark grey) is restored. There is a hierarchy of active and repressive chromatin; at the blastula stage embryonic chromatin is relatively uncommitted and permissive. During gastrulation H3K27me3 is deposited on spatially regulated genes to repress multi-lineage gene expression. DNA methylation-dependent repression becomes prominent during organogenesis and differentiation. Embryo drawings are from Nieuwkoop and Faber (1967).

Figure 3

Improvement of Xenopus gene annotation using epigenomic data. Shown is the canx gene locus (5′ end of gene is to the right), visualized using the UCSC Genome Browser (genome assembly JGI 4.1/xenTro2). ChIP-seq profiles of the histone modification H3K4me3 (green), the general transcription factor TBP (pink) and RNA Polymerase II (purple) are shown in the top three tracks. TSS-seq data, marking the site of transcription initiation, is shown in red and RNA-seq, showing expressed exons, in blue. Two exons are skipped at this developmental stage (left orange arrow) and an upstream start site is used (right orange arrow). The bottom track shows the JGI gene model and the experimentally validated, improved Xtev annotation based on these experimental data. Xtev gene models and visualization tracks of deep sequencing data can be obtained at www.ncmls.nl/gertjanveenstra.