Rec and np9 in normal human tissues
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR738381.fastq.gz | Fastqsanger.gz | |||
| ERR738382.fastq.gz | Fastqsanger.gz | |||
| ERR738383.fastq.gz | Fastqsanger.gz | |||
| ERR738384.fastq.gz | Fastqsanger.gz | |||
| ERR738385.fastq.gz | Fastqsanger.gz |
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Project description:HERV-K protein Rec functions as RNA transport protein shuttling unspliced viral genomic RNA from the nucleus to the cytoplasm. Rec was found to be expressed in several tumors and transformed cell lines and contributes to cell transformation by inhibiting the transcription factor Promyelocytic Leukemia Zinc Finger Protein
2019-10-12 | GSE51571 | GEO
Project description:Background: The human genome consists of considerable portions derived from retroviruses inherited for millions of years. So-called human endogenous retroviruses (HERVs) are usually severely mutated, yet some coding-competent HERVs exist. The HERV-K(HML-2) group includes evolutionarily young proviruses that still encode typical retroviral proteins. HERV-K(HML-2) has been implicated in various human diseases because transcription is often upregulated and some of the encoded proteins are known to affect cell biology. HERV-K(HML-2) Protease (Pro) has received little attention so far, although it appears expressed in some disease contexts and other retroviral proteases are known to process cellular proteins. Results: We set out to identify human cellular proteins being substrates of HERV-K(HML-2) Pro employing a modified Terminal Amine Isotopic Labeling of Substrates (TAILS) procedure. Thousands of human proteins were identified as significantly processed by HERV-K(HML-2) Pro. Identified proteins locate to various cellular compartments and participate in diverse, often disease-relevant cellular processes. We verified cleavage of a majority of selected human proteins in vitro and in vivo. Conclusions: Hundreds, if not thousands of cellular proteins are potential substrates of HERV-K(HML-2) Pro. It is conceivable that even low-level expression of HERV-K(HML-2) Pro has a functional impact on cell biology and thus relevance for human diseases. Specific studies will be required to elucidate effects of HERV-K(HML-2) Pro expression regarding human substrate proteins, cell biology and disease. Endogenous retrovirus-encoded Pro activity may also be relevant for disease development in species other than human.
2019-09-02 | PXD013296 | Pride
Project description:The human genome consists of considerable portions derived from retroviruses typically inherited already for millions of years. So-called human endogenous retroviruses (HERVs) are usually severely mutated, yet some coding-competent HERV sequences exist. The HERV-K(HML-2) group includes evolutionarily young proviruses that still encode typical retroviral proteins. HERV-K(HML-2) has been implicated in various human diseases because transcription is often upregulated and encoded proteins are known to affect cell biology. HERV-K(HML-2) protease has received little attention so far. With findings for Human Immunodeficiency Virus (HIV) protease in mind we set out to identify human cellular proteins being substrates of HERV-K(HML-2) protease employing a modified Terminal Amine Isotopic Labeling of Substrates (TAILS) procedure. Thousands of significantly processed human proteins were revealed by TAILS and we could verify cleavage of a majority of selected human proteins in vitro. Our analysis suggests that hundreds, if not thousands of cellular proteins are potential substrates of HERV-K(HML-2) protease. As identified proteins participate in diverse, often disease-relevant cellular processes, it is conceivable that expression of HERV-K(HML-2) protease has functional consequences for cell biology and thus development of human diseases. Endogenous retrovirus-encoded protease may also be relevant for disease development in species other than human.
2019-09-02 | PXD010159 | Pride
Project description:The biological function and disease association of human endogenous retroviral (HERV) elements remains largely elusive. We addressed the physiological role of HERV-K(HML-2) in neuronal differentiation by manipulating HERV-K(HML-2) expression levels. We used CRISPR engineering to activate or repress HERV-K(HML-2) and demonstrate that elevated HERV-K(HML-2) transcription is detrimental for development, functionality and growth of cortical neurons. Effects are cell-type specific, as dopaminergic neurons were unaffected. We further show that layer formation is altered during forebrain organoid formation following activation of HERV-K(HML-2) transcription. HERV-K(HML-2) transcriptional activation concurrently elevated Neurotrophic Tyrosine Receptor Kinase 3 (NTRK3) expression along with other neurodegeneration-related genes. Direct transcriptional activation of NTRK3 resembled the HERV-K(HML-2) activation phenotype. Intriguingly, reduction of NTRK3 levels in HERV-K(HML-2)-activated cortical neurons restored differentiated cortical neurons. Hence, our findings unravel a unique cell type-specific mechanism of HERV-K(HML-2) during cortical neuronal differentiation.
2021-03-30 | GSE171101 | GEO
Project description:We report HERV-K rec iCLIP-seq binding data, ribosome profiling data, and RNA-seq from ELF1 naïve hESC and RNA-seq from NCCIT cells. HERV-K Rec iCLIP-seq: 2 replicates in NCCIT. Ribosome profiling: 4 replicates each of Rec-overexpressing NCCIT vs. control NCCIT; RNAseq: 3 replicates each of HERV-K Rec siRNA vs. control siRNA in NCCIT; RNA-seq: 3 replicates each of ELF1 naïve hESC vs. primed hESC.
2015-04-21 | E-GEOD-63570 | biostudies-arrayexpress
Project description:Human endogenous retroviruses (hERVs) are molecular remnants of ancient retroviruses that integrated into the human germline and now make up 8% of the human genome. The human ERVK3-1 locus was recently annotated as encoding a 109-amino acid microprotein homologous to a retroviral Rec domain. ERVK3-1 is ubiquitously expressed in normal human cells and tissues. However, because this locus was thought to be non-coding until recently, it is currently unknown whether the ERVK3-1 microprotein has a function in human cells. We demonstrate that the ERVK3-1 microprotein interacts with PPHLN1, a component of the HUSH complex, and contributes to target gene repression. We thus suggest that the ERVK3-1 Rec protein may have been co-opted by human cells for molecular sensing and/or feedback regulation of hERV expression.
2025-08-25 | PXD064459 | Pride
Project description:Human endogenous retroviruses (HERVs) occupy a large portion of the human genome. Most HERVs are transcriptionally silent, but can be reactivated during pathological states such as viral infection and certain cancers. The HERV-K HML-2 clade includes elements that recently have integrated in the human germ line and often contain intact open reading frames (ORFs) that possibly support peptide and protein expression. Understanding HERV-K-host interactions and their potential as biomarkers is problematic due to the high similarity among different elements. Previously we described a long-read single molecule real-time sequencing (PacBio) strategy to analyze HERV-K RNA expression profiles in different cell types. However, identifying HERV-K HML-2 proteins accurately is difficult without robust and reliable methods and reagents. Here we present a new approach to characterize the HML-2 elements that (a) are being translated and (b) produce enough protein to be detected and identified by mass spectrometry. Our data reveal that RNA expression profiling alone cannot accurately predict which HML-2 elements are responsible for protein production, as we observe several differences between the highest expressed RNAs and the elements that are the predominant source of HERV-K HML-2 protein synthesis. These studies represent an important advance towards untangling the complexity of HERV-K-host interactions.
2025-01-08 | GSE283037 | GEO
Project description:Elevated transcript expression of the endogenous retrovirus family HERV-K (HML-2) is seen in the majority of breast cancers, although the identity of the individual loci contributing to this expression as well as their mechanism of activation is unclear. Using high-throughput next-generation sequencing techniques optimized for the capture of HML-2 expression, we produced a complete profile of the HML-2 transcriptome before and after human mammary epithelial cell transformation.
2017-10-13 | GSE84275 | GEO
Project description:glioblastoma(GBM) tissues: Tumor tissues(C) vs. Normal tissues(N)
| PRJNA431408 | ENA