Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation

Abstract

Chromatin remodeling is essential for epigenome reprogramming after fertilization. However, the underlying mechanisms of chromatin remodeling remain to be explored. Here, we investigated the dynamic changes in nucleosome occupancy and positioning in pronucleus-stage zygotes using ultra low-input MNase-seq. We observed distinct features of inheritance and reconstruction of nucleosome positioning in both paternal and maternal genomes. Genome-wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 h after the injection of sperm into ooplasm. The nucleosome positioning pattern was continually rebuilt to form nucleosome-depleted regions (NDRs) at promoters and transcription factor (TF) binding sites with differential dynamics in paternal and maternal genomes. NDRs formed more quickly on the promoters of genes involved in zygotic genome activation (ZGA), and this formation is closely linked to histone acetylation, but not transcription elongation or DNA replication. Importantly, we found that NDR establishment on the binding motifs of specific TFs might be associated with their potential pioneer functions in ZGA. Further investigations suggested that the predicted factors MLX and RFX1 played important roles in regulating minor and major ZGA, respectively. Our data not only elucidate the nucleosome positioning dynamics in both male and female pronuclei following fertilization, but also provide an efficient method for identifying key transcription regulators during development.

Aberrant nucleosome organization in mouse SCNT embryos revealed by ULI-MNase-seq

“…The lengths of the mapped reads were mainly enriched at approximately 147 bp, which is the DNA size in mononucleosomes ( Figure S1 D). After fertilization, the nucleosome occupancy of the paternal genome undergoes a dramatic increase, while this rapid de novo establishment process does not occur in the maternal genome ( Wang et al., 2022 ). Similar to female pronuclei (PN) in fertilized embryos, the nucleosome occupation rate showed little change, and the enrichment of nucleosomes on different genomic elements was also relatively stable during SCNT embryonic development ( Figures S1 F and S1G).…”

“…We found that the NDRs and precisely positioned +1 and −1 nucleosomes around TSSs disappeared as early as 1 hpi and were rebuilt until 6 h after activation of the SCNT embryos ( Figure 1 B). However, the NDR pattern around TSSs appears much earlier in fertilized embryos, with male PN at 1.5 h post-fertilization (hpf) and female PN at 3 hpf ( Wang et al., 2022 ). Previous studies have shown that nucleosome arrangement is associated with the cell cycle, with fuzzier organization during S and M phases ( Deniz et al., 2016 ).…”

“…Next, we investigated the potential factors that affect nucleosome repositioning during the reprogramming of SCNT embryos. Our recent study has shown that histone acetylation influences the establishment of NDRs in male PN after fertilization ( Wang et al., 2022 ). Therefore, we defined NT-specific high NDR genes (NT-high) and NT-specific low NDR genes (NT-low) by comparing the NDR scores of promoters between SCNT and fertilized embryos at the early-2-cell or late-2-cell stage ( Figures S5 A and S5B).…”

“…The cytoplasm of oocytes can reprogram the chromatin of sperm, with the protamine replaced by histones rapidly after fertilization ( Wang et al., 2022 ). Histone replacement also occurs in SCNT embryos ( Wen et al., 2014 ), which may promote the rapid nucleosome position changes.…”

“…Nucleosome remodeling occurs quickly after fertilization, which is necessary for embryonic development ( Oliva, 2006 ; Wang et al., 2022 ). This process also occurs during SCNT embryonic development ( Tao et al., 2017 ; Wen et al., 2014 ), but how the nucleosome position changes after the donor cell nucleus is transferred into enucleated oocytes and the underlying mechanism is largely unexplored.…”