XB-ART-40368Dev Cell. September 1, 2009; 17 (3): 425-34.
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.
Epigenetic mechanisms set apart the active and inactive regions in the genome of multicellular organisms to produce distinct cell fates during embryogenesis. Here, we report on the epigenetic and transcriptome genome-wide maps of gastrula-stage Xenopus tropicalis embryos using massive parallel sequencing of cDNA (RNA-seq) and DNA obtained by chromatin immunoprecipitation (ChIP-seq) of histone H3 K4 and K27 trimethylation and RNA Polymerase II (RNAPII). These maps identify promoters and transcribed regions. Strikingly, genomic regions featuring opposing histone modifications are mostly transcribed, reflecting spatially regulated expression rather than bivalency as determined by expression profile analyses, sequential ChIP, and ChIP-seq on dissected embryos. Spatial differences in H3K27me3 deposition are predictive of localized gene expression. Moreover, the appearance of H3K4me3 coincides with zygotic gene activation, whereas H3K27me3 is predominantly deposited upon subsequent spatial restriction or repression of transcriptional regulators. These results reveal a hierarchy in the spatial control of zygotic gene activation.
PubMed ID: 19758566
PMC ID: PMC2746918
Article link: Dev Cell.
Grant support: 5 R01 HD054356 NICHD NIH HHS , R01 HD054356-01 NICHD NIH HHS , R01 HD054356-02 NICHD NIH HHS , R01 HD054356-03 NICHD NIH HHS , R01 HD054356 NICHD NIH HHS
Genes referenced: polr2a
Antibodies referenced: Ezh2 Ab1 Polr2a Ab7 Tri-Methyl H3f3a Ab19 Tri-Methyl H3f3a Ab20