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| Status |
Public on Aug 16, 2024 |
| Title |
Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [BiSulfite-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Long terminal repeats (LTRs), which comprise promoter and enhancer region of intact endogenous retroviruses (ERVs), are known to be co-opted for fine-tuning host-coding gene expression as cis-regulatory elements. Since LTRs are mainly silenced by the deposition of repressive epigenetic marks, a substantial activation of LTRs have been found in human cells after treatment with epigenetic inhibitors. Although LTR12C family had highest relative abundance of transcripts among the de-repressed ERV families, functional consequences of the activated LTR12C for host-coding genes remain uncover due to genome-wide alteration of epigenetic landscape resulting in broad transcriptional changes after the epigenetic inhibitor treatments. Here, we transactivated more than 600 LTR12C elements by using single guide RNA-based dCas9-Suntag-VP64, which is a kind of the site-specific targeting technology CRISPR activation system, with minimal off-target events. Interestingly, most of transactivated LTR12C elements acquired H3K27ac-marked enhancer feature, while 20% of them along with enrichment of H3K4me3-marked promoter feature. The enrichment of H3K4me3 signal was likely brought about by downstream regions of LTR12C, such as internal regions of intact ERV9 or other type of retrotransposons.
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| Overall design |
To investigate DNA methylation changes in HEK293T after CRISPRa, we performed WGBS.
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| Contributor(s) |
Ohtani H, Liang G, Jones PA |
| Citation(s) |
38874474 |
| |
| Submission date |
Sep 19, 2023 |
| Last update date |
Aug 16, 2024 |
| Contact name |
Hitoshi Ohtani |
| E-mail(s) |
otani@agr.nagoya-u.ac.jp
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| Organization name |
Nagoya University
|
| Department |
Graduate School of Bioagricultural Sciences
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| Lab |
Laboratory of Genome and Epigenome Dynamics
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| Street address |
Furo-cho
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| City |
Chikusa-ku |
| State/province |
Nagoya |
| ZIP/Postal code |
464-8601 |
| Country |
Japan |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE243551 |
Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer |
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| Relations |
| BioProject |
PRJNA1018907 |
