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

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

PROVIDER: PRJNA1018904 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26111853.fastq.gz	Fastqsanger.gz
	SRR26111854.fastq.gz	Fastqsanger.gz
	SRR26111855.fastq.gz	Fastqsanger.gz
	SRR26111856.fastq.gz	Fastqsanger.gz
	SRR26111857.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

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

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

| PRJNA1018907 | ENA

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]

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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]

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

The endogenous retrovirus Mtv8 which resides within the V kappa locus does not influence the mouse immunoglobulin repertoire

Project description:The vast diversity of mammalian adaptive antigen receptors allows for robust and efficient immune responses against a wide number of pathogens. The antigen receptor repertoire is built during the recombination and hypermutation of B and T cell receptor (B-, TCR) loci. V(D)J recombination rearranges these antigen receptor loci which are organized as an array of separate V, (D), and J gene segments. Which gene segments are recombined, and thus which particular antigen receptors are present in the host repertoire, depends on the three-dimensional architecture of the recombining locus. The endogenous retrovirus (ERV) mouse mammary tumor provirus (Mtv8) resides on mouse chromosome 6 interposed within the large array of light chain kappa (IgK) V gene segments. It was unknown, however, whether Mtv8 influences the BCR repertoire, as ERVs can contribute to changes in genomic architecture by driving high levels of local transcription. We generated Mtv8-deficient mice to determine if the ERV influenced V(D)J recombination and found no significant difference in the peripheral BCR repertoire of Mtv8-deficient mice compared to wildtype controls. Thus, Mtv8, the endogenous retrovirus in the Igk locus, does not influence BCR repertoires.

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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.

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Cryptic endogenous retrovirus subfamilies in the primate lineage

Project description:Cryptic endogenous retrovirus subfamilies in the primate lineage

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