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Series GSE135457 Query DataSets for GSE135457
Status Public on Oct 28, 2020
Title The landscape of RNA Pol II binding reveals a step-wise transition during ZGA
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Zygotic genome activation (ZGA) is the first transcription event in life. However, it is unclear how RNA polymerase is engaged in initiating ZGA in mammals. Here, by developing small-scale Tn5-assisted chromatin cleavage with sequencing (Stacc–seq), we investigated the landscapes of RNA polymerase II (Pol II) binding in mouse embryos. We found that Pol II undergoes ‘loading’, ‘pre-configuration’, and ‘production’ during the transition from minor ZGA to major ZGA. After fertilization, Pol II is preferentially loaded to CG-rich promoters and accessible distal regions in one-cell embryos (loading), in part shaped by the inherited parental epigenome. Pol II then initiates relocation to future gene targets before genome activation (pre-configuration), where it later engages in full transcription elongation upon major ZGA (production). Pol II also maintains low poising at inactive promoters after major ZGA until the blastocyst stage, coinciding with the loss of promoter epigenetic silencing factors. Notably, inhibition of minor ZGA impairs the Pol II pre-configuration and embryonic development, accompanied by aberrant retention of Pol II and ectopic expression of one-cell targets upon major ZGA. Hence, step-wise transition of Pol II occurs when mammalian life begins, and minor ZGA has a key role in the pre-configuration of transcription machinery and chromatin for genome activation.
Overall design Stacc-seq and RNA-seq were applied on mouse oocytes and pre-implantation embryos. All wild-type pre-implantation embryos were collected by crossing C57BL/6N female mice with PWK male mice.
Contributor(s) Liu B, Xu Q, Wang Q, Xie W
Citation(s) 33116310
Submission date Aug 06, 2019
Last update date Jan 03, 2021
Contact name Bofeng Liu
Organization name Tsinghua University
Department School of Life Science
Lab Xie Wei Lab
Street address Haidian District
City Beijing
ZIP/Postal code 100084
Country China
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (116)
GSM4010558 PN5_total_RNA_rep1
GSM4010559 2cell_late_total_RNA_Con_rep1
GSM4010560 2cell_late_total_RNA_mTBE_rep1
BioProject PRJNA558961
SRA SRP217544

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Supplementary file Size Download File type/resource
GSE135457_ICM_Smart_FPKM_rep12.txt.gz 235.0 Kb (ftp)(http) TXT
GSE135457_RAW.tar 3.2 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
GSE135457_total_RNA_FPKM_all.txt.gz 306.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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