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| Status |
Public on Apr 19, 2022 |
| Title |
Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
In mammals, translational control plays critical roles during oocyte-to-embryo transition (OET) when transcription ceases. However, the underlying regulatory mechanisms remain challenging to study. Here, using low-input Ribo-seq (Ribo-lite), we investigated translational landscapes during OET using 30-150 mouse oocytes or embryos per stage. Ribo-lite can also accommodate single oocytes. Combining PAIso-seq to interrogate poly(A) tail lengths, we found a global switch of translatome that closely parallels changes of poly(A) tails upon meiotic resumption. Translation activation correlates with polyadenylation and is supported by polyadenylation signal proximal cytoplasmic polyadenylation elements (papCPEs) in 3' untranslated regions. By contrast, translation repression parallels global de-adenylation. The latter includes transcripts containing no CPEs or non-papCPEs, which encode many transcription regulators that are preferentially re-activated before zygotic genome activation. CCR4-NOT, the major de-adenylation complex, and its key adaptor protein BTG4 regulate translation downregulation often independent of RNA decay. BTG4 is not essential for global de-adenylation but is required for selective gene de-adenylation and production of very short-tailed transcripts. In sum, our data reveal intimate interplays among translation, RNA stability and poly(A) tail length regulation underlying mammalian OET.
Note: RNA-seq data for PN5 zygotes, early two-cell, late two-cell, four-cell and eight-cell stages and ICM were obtained from our previous publication (Zhang et al., Nature, 2016: Allelic reprogramming of the histone modification H3K4me3 in early mammalian development, GSE71434).
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| Overall design |
By employing Ribo-seq and RNA-seq, we systematically examined the dynamics of translatome and transcriptome of WT oocytes, WT early embryos, Cnot6l/Btg4 KO oocytes and CHX/DRB treated early embryos.
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| Contributor(s) |
Xiong Z, Xu K, Lin Z, Kong F, Wang Q, Quan Y, Li L, Xie W |
| Citation(s) |
35697785 |
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| Submission date |
Jan 29, 2021 |
| Last update date |
Jul 17, 2024 |
| Contact name |
Zhuqing Xiong |
| E-mail(s) |
lexizqxiong@gmail.com
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| Organization name |
School of Life Science, Tsinghua Univers
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| Street address |
Haidian District
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| City |
Beijing |
| State/province |
FOREIGN |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (2) |
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| Samples (105)
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| Relations |
| BioProject |
PRJNA697913 |
| SRA |
SRP303825 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE165782_E1_singlecell_all_fpkm.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE165782_E5_Btg4_ribo_RNA_fpkm.txt.gz |
711.9 Kb |
(ftp)(http) |
TXT |
| GSE165782_E6_polyAtaillength_merge.txt.gz |
131.0 Kb |
(ftp)(http) |
TXT |
| GSE165782_FGO_Ribo_rep1_r1_10bp_rpkm.bw |
14.6 Mb |
(ftp)(http) |
BW |
| GSE165782_FGO_Ribo_rep2_r1_10bp_rpkm.bw |
8.3 Mb |
(ftp)(http) |
BW |
| GSE165782_FGO_smart_rep1_10bp_rpkm.bw |
19.1 Mb |
(ftp)(http) |
BW |
| GSE165782_FGO_smart_rep2_10bp_rpkm.bw |
18.7 Mb |
(ftp)(http) |
BW |
| GSE165782_LPI_Ribo_rep1_r1_10bp_rpkm.bw |
6.7 Mb |
(ftp)(http) |
BW |
| GSE165782_LPI_Ribo_rep2_r1_10bp_rpkm.bw |
8.0 Mb |
(ftp)(http) |
BW |
| GSE165782_LPI_smart_rep1_10bp_rpkm.bw |
18.8 Mb |
(ftp)(http) |
BW |
| GSE165782_LPI_smart_rep2_10bp_rpkm.bw |
17.3 Mb |
(ftp)(http) |
BW |
| GSE165782_RAW.tar |
452.3 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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