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| Status |
Public on Sep 14, 2022 |
| Title |
Hybridization led to a rewired pluripotency network in Xenopus laevis [RNA-seq] |
| Organism |
Xenopus laevis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
After fertilization, maternally contributed factors to the egg initiate the transition to pluripotency, in large part by activating de novo transcription from the embryonic genome. Diverse mechanisms coordinate this transition across animals, suggesting that widespread evolutionary innovation has shaped the earliest stages of development. Here, we show that homologs of mammalian reprogramming factors OCT4 and SOX2 divergently regulate the two subgenomes of the allotetraploid Xenopus laevis, resulting in asymmetric activation of hundreds of homeologous gene pairs in the early embryo. Chromatin accessibility profiling and CUT&RUN for modified histones and transcription factor binding reveal extensive differences in enhancer architecture between the subgenomes, which likely arose after hybridization of X. laevis's diploid progenitors ~17 million years ago. However, comparison with diploid X. tropicalis shows broad conservation of embryonic gene expression levels when divergent homeolog contributions are combined, implying strong selection to maintain dosage in the pluripotency transcriptional program, amidst genomic instability following hybridization.
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| Overall design |
RNA-seq with rRNA-depletion was performed on two embryos per sample from mixed clutches of 1-2 mothers. Embryos from the same collection are labeled with capital letters (A, B, etc.). Stage 10.5 samples had GFP, mCherry, and Luciferase mRNA added as a spike-in to rRNA-depleted RNA for an unrelated purpose. Samples excluded from analysis due to likely issue with cycloheximide treatment are labeled as DISCARDED.
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| Contributor(s) |
Lee MT, Phelps WA |
| Citation(s) |
37787392 |
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| Submission date |
Jun 27, 2022 |
| Last update date |
Oct 24, 2023 |
| Contact name |
Miler T Lee |
| E-mail(s) |
miler@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Biological Sciences
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| Street address |
4249 Fifth Ave
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15260 |
| Country |
USA |
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| Platforms (2) |
| GPL21248 |
Illumina NextSeq 500 (Xenopus laevis) |
| GPL32399 |
NextSeq 2000 (Xenopus laevis) |
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| Samples (60)
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| GSM6268545 |
Stage 7 |
| GSM6268546 |
Stage 8 |
| GSM6268547 |
Stage 9 rep A1 |
| GSM6268548 |
Stage 9 rep A2 |
| GSM6268549 |
Stage 9 DMSO rep A1 |
| GSM6268550 |
Stage 9 DMSO rep A2 |
| GSM6268551 |
Stage 9 triptolide rep A1 |
| GSM6268552 |
Stage 9 triptolide rep A2 |
| GSM6268553 |
Stage 9 DMSO rep B1 |
| GSM6268554 |
Stage 9 DMSO rep B2 |
| GSM6268555 |
Stage 9 triptolide rep B1 |
| GSM6268556 |
Stage 9 triptolide rep B2 |
| GSM6268557 |
Stage 9 CHX rep B1 |
| GSM6268558 |
Stage 9 CHX rep B2 |
| GSM6268559 |
Stage 9 CHX GFP MO rep C1 |
| GSM6268560 |
Stage 9 CHX GFP MO rep C2 |
| GSM6268561 |
Stage 9 CHX pou5f3.3 MO rep C1 |
| GSM6268562 |
Stage 9 CHX pou5f3.3 MO rep C2 |
| GSM6268563 |
Stage 9 CHX sox3 MO rep C1 |
| GSM6268564 |
Stage 9 CHX sox3 MO rep C2 |
| GSM6268565 |
Stage 9 CHX pou5f3.3, sox3 MO rep C1 |
| GSM6268566 |
Stage 9 CHX pou5f3.3, sox3 MO rep C2 |
| GSM6268567 |
Stage 9 CHX GFP MO rep D1 |
| GSM6268568 |
Stage 9 CHX GFP MO rep D2 |
| GSM6268569 |
Stage 9 CHX pou5f3.3, sox3 MO high concen rep D1 |
| GSM6268570 |
Stage 9 CHX pou5f3.3, sox3 MO high concen rep D2 |
| GSM6268571 |
Stage 9 rep E1 |
| GSM6268572 |
Stage 9 GFP MO rep E1 |
| GSM6268573 |
Stage 9 pou5f3.3, sox3 MO rep E1 |
| GSM7795138 |
Stage 8 rep 2 |
| GSM7795139 |
Stage 10.5 rep 1 |
| GSM7795140 |
Stage 10.5 rep 2 |
| GSM7795141 |
Stage 9 GFP MO rep G1 |
| GSM7795142 |
Stage 9 GFP MO rep G2 |
| GSM7795143 |
Stage 9 GFP MO rep G3 |
| GSM7795144 |
Stage 9 pou5f3.3, sox3 MO rep G1 |
| GSM7795145 |
Stage 9 pou5f3.3, sox3 MO rep G2 |
| GSM7795146 |
Stage 9 pou5f3.3, sox3 MO rep G3 |
| GSM7795147 |
Stage 9 GFP MO rep F1 |
| GSM7795148 |
Stage 9 GFP MO rep F2 |
| GSM7795149 |
Stage 9 GFP MO rep F3 |
| GSM7795150 |
Stage 9 pou5f3.2, pou5f3.3 MO rep F1 |
| GSM7795151 |
Stage 9 pou5f3.2, pou5f3.3 MO rep F2 |
| GSM7795152 |
Stage 9 pou5f3.2, pou5f3.3 MO rep F3 |
| GSM7795153 |
Stage 9 pou5f3.2, pou5f3.3, sox3 MO rep F1 |
| GSM7795154 |
Stage 9 pou5f3.2, pou5f3.3, sox3 MO rep F2 |
| GSM7795155 |
Stage 9 pou5f3.2, pou5f3.3, sox3 MO rep F3 |
| GSM7795156 |
Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep F1 |
| GSM7795157 |
Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep F2 |
| GSM7795158 |
Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep F3 |
| GSM7795159 |
Stage 9 GFP MO rep H1 |
| GSM7795160 |
Stage 9 GFP MO rep H2 |
| GSM7795161 |
Stage 9 CHX GFP MO rep H1 - DISCARDED |
| GSM7795162 |
Stage 9 CHX GFP MO rep H2 - DISCARDED |
| GSM7795163 |
Stage 9 CHX GFP MO rep H3 - DISCARDED |
| GSM7795164 |
Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep H1 - DISCARDED |
| GSM7795165 |
Stage 9 CHX pou5f3.2, pou5f3.3, sox3 MO rep H2 - DISCARDED |
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| This SubSeries is part of SuperSeries: |
| GSE207027 |
Hybridization led to a rewired pluripotency network in the allotetraploid Xenopus laevis |
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| Relations |
| BioProject |
PRJNA853335 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE207026_Phelps23_exon_counts.csv.gz |
2.8 Mb |
(ftp)(http) |
CSV |
| GSE207026_Phelps23_exon_tpm.csv.gz |
4.8 Mb |
(ftp)(http) |
CSV |
| GSE207026_Phelps23_intron_counts.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE207026_Phelps23_intron_rpkm.csv.gz |
2.4 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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