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| Status |
Public on Oct 08, 2022 |
| Title |
Suppression of endogenous retroviral enhancers in somatic cell nuclear transfer embryos |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Endogenous retroviruses (ERVs) in the mammalian genome play diverse roles in embryonic development. These development-related ERVs are generally repressed in somatic cells and are therefore likely repressed in embryos derived from somatic cell nuclear transfer (SCNT). In this study, we sought to identify ERVs that are repressed in SCNT-derived morula embryos, which may consequently cause previously unexplained embryonic deaths shortly after implantation. Our transcriptome analysis revealed that, amongst ERV families, ERVK was specifically and strongly downregulated in SCNT embryos while other transposable elements including LINE and ERVL were unchanged. Among subfamilies of ERVK, RLTR45-int was most repressed in SCNT embryos despite its highest expression in control fertilized embryos. Interestingly, the nearby genes (within 5–50 kb, n = 19) of the repressed RLTR45-int loci were also repressed in SCNT embryos with a significant correlation between them. Furthermore, lysine H3K27 acetylation was enriched around the RLTR45-int loci. These findings indicate that RLTR45-int elements function as enhancers of nearby genes. Indeed, deletion of two sequential RLTR45-int loci on chromosome 4 or 18 resulted in downregulations of nearby genes at the morula stage. We also found that RLTR45-int loci, especially SCNT-low, enhancer-like loci, were strongly enriched with H3K9me3, a repressive histone mark. Importantly, these H3K9me3-enriched regions were resistant to histone demethylase Kdm4d in SCNT embryos. Thus, we identified ERVK subfamily RLTR45-int, putative enhancer elements, as a strong reprogramming barrier for SCNT. A large-scale downregulations of their regulating genes in SCNT morulae might cumulatively affect postimplantation development of SCNT embryos.
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| Overall design |
Comparative analysis of the expression of genes and transposal elements in SCNT, IVF, RLTR45-int putative null, and RLTR45-int putative non-null embryos.
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| Contributor(s) |
Shikata D, Matoba S, Inoue K, Ogura A |
| Citation missing |
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| Submission date |
Oct 05, 2022 |
| Last update date |
Oct 08, 2022 |
| Contact name |
Inoue Kimiko |
| E-mail(s) |
iden.kogaku.brc5@gmail.com
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| Organization name |
RIKEN
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| Department |
BioResource Research Center
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| Lab |
Bioresource Engineering Division
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| Street address |
3-1-1 Koyadai
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| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-0074 |
| Country |
Japan |
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| Platforms (1) |
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| Samples (63)
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| Relations |
| BioProject |
PRJNA887456 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214878_Raw.read.counts_IVF.SCNT.embryos.txt.gz |
36.7 Mb |
(ftp)(http) |
TXT |
| GSE214878_Raw.read.counts_KO.embryos.txt.gz |
46.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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