SRA

Using the frog Xenopus laevis as a model system we profile epigenetic features of sperm and spermatid to study how they relate to gene expression in embryos. We observe that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks, at fertilization, deregulates gene expression in the resulting embryos in a paternal chromatin dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits. Overall design: 48 samples, single-ended ChIP-seq libraries from sperm- and spermatid-derived haploid embryos pulling down H3K4me2, H3K4me3, H3K27me3 and H3K9me3, 3 replicates for each histone modification pull-down. 14 samples of both single-ended and pair-ended RNA-seq libraries for sperm- and spermatid-derived embryos. 3 replicates of single-ended RNA-seq libraries for spermatid cells. 22 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm5b 16 samples of single-ended RNA-seq form sperm- and spermatid-derived embryos overexpressing Kdm6b 6 samples of single-ended MNase-seq from sperm and spermatid chromatin 12 samples of MBD-seq from sperm and spermatid chromatin