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.
Akkers
Robert C
RC
Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, 6500 HB Nijmegen, The Netherlands.
van Heeringen
Simon J
SJ
Jacobi
Ulrike G
UG
Janssen-Megens
Eva M
EM
Françoijs
Kees-Jan
KJ
Stunnenberg
Hendrik G
HG
Veenstra
Gert Jan C
GJ
D000818:Animals; D044127:Epigenesis, Genetic; D005775:Gastrula / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D006657:Histones / Q000378:metabolism*; D006801:Humans; D051379:Mice; D008954:Models, Biological; D008957:Models, Genetic; D009707:Nucleosomes / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D013997:Time Factors; D014981:Xenopus / Q000196:embryology; D014982:Xenopus laevis / Q000196:embryology
D006657:Histones; D009707:Nucleosomes