Recycling of parental histones preserves the epigenetic landscape during embryonic development (STRIPE-seq)

Epigenetic inheritance during DNA replication requires an orchestrated assembly of nucleosomes from parental and newly synthesized histones. We analyzed Drosophila HisC mutant embryos harboring a deletion of all canonical histone genes, in which nucleosome assembly relies on parental histones from cell cycle 14 onwards. Lack of new histone synthesis and parental histone recycling leads to more accessible chromatin and reduced nucleosome occupancy. This leads to upregulated and spurious transcription, whereas the control of the developmental transcriptional program is partially maintained. Importantly, the genomic positions of modified parental H2A, H2B, and H3 are restored during DNA replication. Therefore, the results suggest that parental histones with active or repressive marks are recycled to preserve the epigenetic landscape during DNA replication in vivo. Overall design: Profiling of 5'capped mRNA and transcriptional initiation sites (transcription start regions) in whole Drosophila melanogaster embryos between 5.5 to 7 hours after egg laying. Wild type embryos (w1118) are compared with mutant embryos (Df(2L)HisC) lacking newly synthesized histones. Each analysis was conducted in quadruplicates or quintuplicates.