Genome-wide profiling the epigenetic landscape of histone variant TH2B in murine oocytes and pre-implantation embryos [ChIP-seq]

The testis-specific histone variant of H2B, TH2B, is enriched in the oocytes, sperm and early embryos, with levels decreasing as the embryos differentiate into pre-gastrula stages. However, the involvement of TH2B in epigenetic reprogramming in the preimplantation embryos is largely unknown. The current study mapped the genome-wide epigenetics of TH2B in MII oocytes and early embryos using ultra-low-input ChIP-seq (ULI-ChIP). We demonstrate that TH2B deposition varies greatly between gametes; however, following fertilization, TH2B from gametes is swiftly redistributed in 2-cell embryos. A considerable enrichment of TH2B at the transcription start site (TSS) was identified in sperm chromatin compared to that in oocytes. We also found some overlap between the dynamics of the sperm and the 2 cell, which contain genes related to transcription regulation. Additionally, TH2B was enriched at zygotic genome activation (ZGA) genes. H2A.Z and TH2B were associated, as was discovered in the presence of H2AK119ub1. The correct execution of ZGA and other developmental programs, such as timing the expression or repression of particular genes, may involve TH2B along with H2A.Z, and H2AK119ub1, the latter two regulating the aforementioned processes. Also, early embryos had H3K9me3 deposited at TH2B-bound loci, which is a sign of heterochromatin and functions in regulating retrotransposons. In our study, we found that TH2B was enriched in LTRs. Thus, TH2B chromatin in gametes and preimplantation embryos has distinctive properties, as highlighted by our study, and they also present fresh opportunities to investigate the epigenetic dynamics in murine preimplantation embryos. Owing to the limited cell numbers in oocyte and early embryos (2-cell and 8-cell), TH2B ultra-low-input native chromatin immunoprecipitation and sequencing (ULI-NChIP-seq) was employed. For allele specific alignment of parental TH2B dynamics SNPsplit was used.

H2B的睾丸特异性组蛋白变体TH2B在卵母细胞、精子及早期胚胎中富集，其丰度随胚胎分化至原肠胚前期逐渐降低。然而，TH2B在植入前胚胎表观重编程过程中的参与机制尚不完全明确。本研究利用超低量输入染色质免疫沉淀测序（ultra-low-input ChIP-seq, ULI-ChIP），绘制了减数分裂II期卵母细胞（MII oocytes）及早期胚胎中TH2B的全基因组表观图谱。研究证实，TH2B的沉积在配子之间差异显著；但受精后，配子来源的TH2B会在2-细胞胚胎中快速重新分布。与卵母细胞相比，精子染色质中TH2B在转录起始位点（transcription start site, TSS）处存在显著富集。我们还发现，精子与2-细胞胚胎的TH2B结合动态存在部分重叠，这些重叠区域对应的基因与转录调控相关。此外，TH2B在合子基因组激活（zygotic genome activation, ZGA）相关基因区域富集。研究还发现，TH2B与H2A.Z存在相互关联，且该关联伴随H2AK119ub1的存在。TH2B、H2A.Z及H2AK119ub1可能共同参与合子基因组激活及其他发育程序的正确执行，例如调控特定基因的时序性表达或沉默，后两者可对上述过程进行调控。此外，早期胚胎中结合TH2B的基因座存在H3K9me3沉积，这是异染色质的标志性修饰，其功能为调控逆转录转座子。本研究还发现，TH2B在长末端重复序列（LTRs）区域富集。综上，本研究表明，配子及植入前胚胎中的TH2B染色质具有独特的特性，同时为小鼠植入前胚胎的表观动力学研究提供了新的方向。由于卵母细胞及早期胚胎（2-细胞、8-细胞）的细胞数量极为有限，本研究采用了超低量输入原生染色质免疫沉淀测序（ultra-low-input native chromatin immunoprecipitation and sequencing, ULI-NChIP-seq）技术。为实现亲本TH2B动态变化的等位基因特异性比对，本研究使用了SNPsplit工具。