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Series GSE189100 Query DataSets for GSE189100
Status Public on Mar 31, 2022
Title Genome-wide mapping of the histone modification H3K4me3 in bovine early embryos [ChIP-seq]
Organism Bos taurus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Reprogramming of histone modification regulates gene expression and mammal preimplantation development. Trimethylation of lysine 4 on histone 3 (H3K4me3) has unique landscape in mouse oocytes and early embryos. However, the dynamics and function of H3K4me3 in livestock embryos remain unclear. To address how it is reprogrammed in domestic animals, we profiled changes of H3K4me3 during bovine early embryo development. Notably, the overall signal of H3K4me3 decreased during embryonic genome activation (EGA). By utilizing ultra-low-input native ChIP-seq (ULI-NChIP-seq) technology, we observed widespread broad H3K4me3 domains in oocytes and embryos. The signal of broad H3K4me3 began to decrease after fertilization and was lowest after EGA. Along with the removal of broad H3K4me3, deposition of H3K4me3 at promoter regions enhanced gradually. Besides, the transcriptional activity and signal of promoter H3K4me3 showed positive correlation after the erasure of broad H3K4me3 at 16-cell stage. Moreover, knocking down of demethylases KDM5A, KDM5B and KDM5C caused EGA delay and blastocyst formation failure. RNA-seq analysis revealed 47.8% down-regulated genes in knockdown embryos at 8/16-cell stage were EGA genes, and 63.1% of up-regulated genes were maternal transcripts. Particularly, the positive correlation between transcriptional activity and promoter H3K4me3 during EGA was restrained when knocking down of KDM5A, KDM5B and KDM5C. Overall, our work initiatively mapped the genomic reprogramming of H3K4me3 during bovine preimplantation development, and KDM5A/B/C played roles in modulating oocyte-to-embryonic transition (OET) through timely erasure of broad H3K4me3 domains far away from promoters.
Overall design Examination of H3K4me3 genomic distribution by ULI-NChIP-seq in bovine embryos
Contributor(s) Zhang K, Dang Y
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Submission date Nov 18, 2021
Last update date Mar 31, 2022
Contact name Kun Zhang
Organization name Zhejiang University
Street address 866 Yuhangtang Rd
City Hangzhou
ZIP/Postal code 310058
Country China
Platforms (1)
GPL26012 Illumina NovaSeq 6000 (Bos taurus)
Samples (32)
GSM5694555 GV_input1
GSM5694556 GV_input2
GSM5694557 GV_H3K4me3_IP1
This SubSeries is part of SuperSeries:
GSE189102 Genome-wide mapping and gene expression of the histone modification H3K4me3 in bovine early embryos
BioProject PRJNA781574

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Supplementary file Size Download File type/resource 130.7 Mb (ftp)(http) BW 140.5 Mb (ftp)(http) BW 138.8 Mb (ftp)(http) BW 142.4 Mb (ftp)(http) BW 118.6 Mb (ftp)(http) BW 185.1 Mb (ftp)(http) BW 149.6 Mb (ftp)(http) BW 160.2 Mb (ftp)(http) BW 81.1 Mb (ftp)(http) BW 137.6 Mb (ftp)(http) BW 114.1 Mb (ftp)(http) BW 163.6 Mb (ftp)(http) BW 166.7 Mb (ftp)(http) BW 137.1 Mb (ftp)(http) BW 127.2 Mb (ftp)(http) BW 137.8 Mb (ftp)(http) BW
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Processed data provided as supplementary file
Raw data are available on Series record

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