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Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [BiSulfite-seq]

ABSTRACT: Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [BiSulfite-seq]

PROVIDER: PRJNA1018907 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26113673_1.fastq.gz	Fastqsanger.gz
	SRR26113673_2.fastq.gz	Fastqsanger.gz
	SRR26113674_1.fastq.gz	Fastqsanger.gz
	SRR26113674_2.fastq.gz	Fastqsanger.gz

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Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer

Project description:Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer

| PRJNA1018902 | ENA

Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [BiSulfite-seq]

Project description: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.

2024-08-16 | GSE243548 | GEO

Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [RNA-seq]

Project description:Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [RNA-seq]

| PRJNA1018900 | ENA

Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [ChIP-seq]

Project description:Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [ChIP-seq]

| PRJNA1018904 | ENA

Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [RNA-seq]

2024-08-16 | GSE243546 | GEO

Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [ChIP-seq]

2024-08-16 | GSE243547 | GEO

Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-08-16 | GSE243551 | GEO

Methods for estimating human endogenous retrovirus activities from EST databases.

Project description:BackgroundHuman endogenous retroviruses (HERVs) are surviving traces of ancient retrovirus infections and now reside within the human DNA. Recently HERV expression has been detected in both normal tissues and diseased patients. However, the activities (expression levels) of individual HERV sequences are mostly unknown.ResultsWe introduce a generative mixture model, based on Hidden Markov Models, for estimating the activities of the individual HERV sequences from EST (expressed sequence tag) databases. We use the model to estimate the relative activities of 181 HERVs. We also empirically justify a faster heuristic method for HERV activity estimation and use it to estimate the activities of 2450 HERVs. The majority of the HERV activities were previously unknown.Conclusion(i) Our methods estimate activity accurately based on experiments on simulated data. (ii) Our estimate on real data shows that 7% of the HERVs are active. The active ones are spread unevenly into HERV groups and relatively uniformly in terms of estimated age. HERVs with the retroviral env gene are more often active than HERVs without env. Few of the active HERVs have open reading frames for retroviral proteins.

| S-EPMC1892069 | biostudies-literature

Cryptic endogenous retrovirus subfamilies in the primate lineage

Project description:Cryptic endogenous retrovirus subfamilies in the primate lineage

| PRJNA1029531 | ENA

Germline piRNAs counteract endogenous retrovirus invasion from somatic cells

Project description:Germline piRNAs counteract endogenous retrovirus invasion from somatic cells

| PRJNA988107 | ENA