Genome binding/occupancy profiling by high throughput sequencing
Summary
We generated high-resolution maps of genome-lamina interactions for different stages of the pre-implantation mouse embryo, including oocyte, zygote, 2cell stage and 8cell stage and additionally mouse ES cells. We find that LAD domains are already present at the zygote stage, but not in the oocyte, concluding that genome-nuclear lamina interactions are not inherited from the maternal germline, but instead are established de novo rapidly after fertilisation. By using a hybrid genetic background, we were able to identify parental-specific genome-nuclear lamina interaction, allowing us to show that the parental genomes have different features, which are globally resolved at the 8-cell stage. We blocked replication in zygotes by treatment with aphidicolin and found that LAD establishment was unaffected. Moreover, we ectopically expressed Kdm5b in zygotes and show that paternal LAD formation is impaired, suggesting that this mechanism is dependent upon de novo H3K4 methylation. Altogether, our data suggest a step-wise assembly model whereby early LAD formation precedes consolidation of TADs and reveals non-inheritance of nuclear organisation from the germline.
Overall design
DamID profiles (Dam-lamin B1 and/or Dam alone) were generated for population of cells (15,20,24 cells, triplicate) and for single cells for all the stages studied (oocyte, zygote, 2cell stage and 8cell stage ES cells) and for the additional experiments (treatment with aphidicolin/DMSO, injection with WT_Kdm5b/MUTANT_Kdm5b mRNA). The libraries were sequenced using Illumina hiseq 2500 platform.
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