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Series GSE235547 Query DataSets for GSE235547
Status Public on Apr 02, 2024
Title Detection of newly synthesized RNA reveals transcriptional reprogramming during ZGA and a role of Obox3 in totipotency acquisition
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Zygotic genome activation (ZGA) after fertilization is a conserved transcriptional activation process that enables the maternal-to-zygotic transition. However, the global view of ZGA, particularly at the initiation, is not yet completely understood. Here, we develop a method to capture and sequence newly synthesized RNA in the early mouse embryos, which provides a view of transcriptional reprogramming events during ZGA. Our data demonstrate that gene activation associated with major ZGA, previously thought to occur exclusively during the mid-to-late 2-cell stage, is already initiated in zygotes. Furthermore, we identify a set of genes activated during minor ZGA and observe an enrichment of the homeobox-containing Obox factor motif at the promoters of minor ZGA genes. Among several Obox factors, Obox3 overexpression in mouse embryonic stem cells activates ZGA genes. Notably, the expression of Obox3 is severely impaired in somatic cell nuclear transfer (SCNT) embryos, and restoring its expression corrects the ZGA profile and greatly improves SCNT embryo development. Hence, our study reveals the dynamic transcriptional reprogramming during ZGA and underscores the crucial role of Obox3 in facilitating totipotency acquisition.
 
Overall design RNA-seq for newly synthesized RNAs, total RNA-seq and CUT&RUN were performed using mouse early embryos or mESCs.
 
Contributor(s) Ishiuchi T, Sakamoto M
Citation(s) 38619966
Submission date Jun 22, 2023
Last update date Apr 15, 2024
Contact name Mizuki Sakamoto
E-mail(s) g23dib04@yamanashi.ac.jp
Organization name University of Yamanashi
Street address 4-4-37,Takeda
City Kofu
ZIP/Postal code 400-8510
Country Japan
 
Platforms (2)
GPL21273 HiSeq X Ten (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (88)
GSM7504964 MII oocyte total RNA rep1
GSM7504965 MII oocyte total RNA rep2
GSM7504966 Zygote EU+ RNA rep1
Relations
BioProject PRJNA986450

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE235547_4C_EU_merged_unique.bw 19.1 Mb (ftp)(http) BW
GSE235547_4C_UnlabeledRNA_merged_unique.bw 24.5 Mb (ftp)(http) BW
GSE235547_8C_EU_merged_unique.bw 15.1 Mb (ftp)(http) BW
GSE235547_8C_UnlabeledRNA_merged_unique.bw 47.0 Mb (ftp)(http) BW
GSE235547_Aphi2C_EU_merged_unique.bw 53.6 Mb (ftp)(http) BW
GSE235547_Aphi2C_UnlabeledRNA_merged_unique.bw 25.5 Mb (ftp)(http) BW
GSE235547_Blastocyst_EU_merged_unique.bw 51.3 Mb (ftp)(http) BW
GSE235547_Blastocyst_UnlabeledRNA_merged_unique.bw 66.5 Mb (ftp)(http) BW
GSE235547_ES_RNAseq_TPM.txt.gz 5.0 Mb (ftp)(http) TXT
GSE235547_L2C_EU_merged_unique.bw 53.5 Mb (ftp)(http) BW
GSE235547_L2C_UnlabeledRNA_merged_unique.bw 22.1 Mb (ftp)(http) BW
GSE235547_MII_total_merged_unique.bw 38.8 Mb (ftp)(http) BW
GSE235547_Morula_EU_merged_unique.bw 35.0 Mb (ftp)(http) BW
GSE235547_Morula_UnlabeledRNA_merged_unique.bw 64.6 Mb (ftp)(http) BW
GSE235547_RAW.tar 1.2 Gb (http)(custom) TAR (of BW)
GSE235547_SCNT_RNAseq_TPM.txt.gz 1.8 Mb (ftp)(http) TXT
GSE235547_Zyg_A485_merged_unique.bw 26.8 Mb (ftp)(http) BW
GSE235547_Zyg_DMSO_merged_unique.bw 61.5 Mb (ftp)(http) BW
GSE235547_Zyg_EU_merged_unique.bw 63.3 Mb (ftp)(http) BW
GSE235547_Zyg_TSA_merged_unique.bw 34.2 Mb (ftp)(http) BW
GSE235547_Zyg_UnlabeledRNA_merged_unique.bw 19.6 Mb (ftp)(http) BW
GSE235547_e2C_EU_merged_unique.bw 83.0 Mb (ftp)(http) BW
GSE235547_e2C_UnlabeledRNA_merged_unique.bw 33.9 Mb (ftp)(http) BW
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Raw data are available in SRA
Processed data provided as supplementary file

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