Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gag proteins encoded by endogenous retroviruses are required for zebrafish development

ABSTRACT: Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. The process by which TEs become coopted remains obscure because most cases involve ancient, transpositionally inactive elements. Reports of active TEs serving beneficial functions are scarce and often contentious due to difficulties in manipulating repetitive sequences. Here we show that recently active TEs in zebrafish encode products critical for embryonic development. Knockdown and rescue experiments demonstrate that the endogenous retrovirus family BHIKHARI-1 (Bik-1) encodes a Gag protein essential for mesoderm development. Mechanistically, Bik-1 Gag associates with the cell membrane and its ectopic expression in chicken embryos alters cell migration. Similarly, depletion of BHIKHARI-2 Gag, a relative of Bik-1, causes defects in neural crest development in zebrafish. We propose an “addiction” model to explain how active TEs can be integrated into conserved developmental processes.

ORGANISM(S): Danio rerio

PROVIDER: GSE263091 | GEO | 2024/04/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Collagen-GAG Biocompatibility Tests

Project description:All mRNA was isolated after 8 hours of culture time in each of three culture conditions. (1) TCPS Plate, (2) Collagen-GAG 2 dimensional coated plate and (3) collagen-GAG three dimensional mesh. Keywords: ordered

2004-11-09 | GSE1937 | GEO

Transcription profiling of human fibroblasts grown on TCPS plates, Collagen-GAG 2 D plate and Collagen-GAG 3D mesh

2008-06-11 | E-GEOD-1937 | biostudies-arrayexpress

RNA Sequencing of Novel HIV RNA TAR-gag and Host Genome of EVs from HIV-1 Infected Cells

Project description:We performed a 3' RACE of a novel HIV RNA TAR-gag in order to determine the sequence of the RNA at the 3' end. Our data had shown that TAR-gag was potentially a noncoding RNA and our hypothesis was that TAR-gag ended somewhere prior to the end of the gag region of the HIV genome. The 3' RACE experiment showed that TAR-gag actually consists of four different RNA clusters, the longest of which ends at 615 bases from the transcription start site; this is in the middle of the p17 region of the gag gene. In addition, we sequenced all host RNAs in the EVs.

2017-08-09 | GSE102364 | GEO

Determination of Gag stoichiometry for different production platforms by PRM analysis

Project description:In this work we established an analytical method of characterization for the Gag protein core and clarify the current variability of Gag stoichiometry in HIV-1 VLPs depending on the cell-based production platform, directly determining the number of Gag molecules per VLP in each case. Three Gag peptides have been validated to quantify the number of monomers using parallel reaction monitoring (PRM)

2022-12-07 | PXD021278 | Pride

CpG dinucleotides introduced into gag can inhibit HIV-1 gene expression by modulating pre-mRNA splicing

Project description:Progressively longer regions of the gag gene sequence in HIV-1 were codon-optimized, which introduced 11, 18 or 26 CpGs (CM22-165: codon-optimized gag from nucleotide 22 to 165, adding 11 CpGs; CM22-261: 18 CpGs; CM22-378: 26 CpGs).

2019-11-07 | GSE134159 | GEO

Transcriptome Profiles of Gag-Specific CD8+ T Cells Induced by Live Attenuated SIV Vaccine

Project description:SIVmac239Δnef (SIVΔnef) live attenuated vaccine (LAV) induces the best protection among all the vaccine modalities tested in rhesus macaque model of HIV-1 infection. Time-dependent protection is a unique feature of this vaccine: macaques are not protected at 3-5 weeks post vaccination (WPV), whereas immune protection emerges between 15 and 20 WPV. To elucidate the protection mechanisms induced by SIVΔnef vaccine, we longitudinally compared the global gene expression profiles of SIV Gag-CM9+ CD8+ (Gag-specific CD8+) T cells from peripheral blood of Mamu-A*01 rhesus macaques at 3 and 20 WPV using rhesus microarray. We found that gene expression profiles of Gag-specific CD8+ T cells at 20 WPV are qualitatively different from those at 3 WPV. At 20 WPV, the most significant transcriptional changes of Gag-specific CD8+ T cells were genes involved in cell activation, differentiation and maturation toward central memory cells. Our study indicates that a higher quality of SIV-specific CD8+ T cells elicited by SIVΔnef over time may contribute to the maturation of time dependent protection.

2015-12-02 | GSE75567 | GEO

Structural basis for spumavirus GAG tethering to chromatin

Project description:The interactions between a retrovirus and host cell chromatin that underlie integration and provirus expression are poorly understood. The prototype foamy virus (PFV) structural protein GAG associates with chromosomes via a chromatin-binding sequence (CBS) located within its C-terminal region. Here, we show that the PFV CBS is essential and sufficient for a direct interaction with nucleosomes, and present a crystal structure of the CBS bound to a mono-nucleosome. The CBS interacts with the histone octamer, engaging the H2A-H2B acidic patch, in a manner similar to other acidic patch binding proteins such as herpesvirus latency-associated nuclear antigen (LANA). Substitutions of the invariant arginine anchor residue in GAG result in global re-distribution of PFV and macaque simian foamy virus (SFVmac) integration sites towards centromeres, dampening the resulting proviral expression without affecting the overall efficiency of integration. Our findings underscore the importance of retroviral structural proteins for integration site selection and the avoidance of genomic junkyards.

2017-05-10 | GSE97973 | GEO

RNA immunoprecipitation sequencing (RIP-seq) of human Dicer-bound miRNAs in HIV-1 Gag replicating cells.

Project description:Micro (mi)RNAs are critical regulators of gene expression in human cells, whose functions can be affected during viral replication. We showed that the Human Immunodeficiency Virus type 1 (HIV-1) Gag protein interacts with the human miRNA processor Dicer and modifies its retention of specific miRNAs without affecting the enzyme’s pre-miRNA processing activity. This sequencing experiment was performed to elucidate whether the presence of Gag in human cells has an effect on the distribution of miRNAs loaded onto Dicer.

2022-04-28 | GSE201502 | GEO

Appressorial proteomics analysis of the wild-type and GAG biosynthetic mutant of Metarhizium robertsii

Project description:Exopolysaccharide galactosaminogalactan (GAG) is a fungal cell wall component composed of α-1,4 linked galactose, N-acetyl galactosamine and galactosamine, which has been demonstrated in Aspergillus fumigatus in association with fungal adhesion, biofilm formation and virulence. The gene cluster responsible for GAG biosynthesis has only been characterized in Aspergillus fungi. We found that the highly conserved gene cluster for GAG biosynthesis is also present in the insect pathogenic fungi Metarhizium species. Functional investigations in M. robertsii revealed that GAG is only produced on fungal cell wall during fungal germination, filamentation and the formation of the infection structure appressoria. Gene deletions revealed that, relative to the wild-type (WT), the appressorial mucilage production was abolished in the null mutant of M. robertsii. Since multiple enzymes are produced in appressorial mucilages, appressorial samples of the WT and mutant formed on cicada wings were collected and subjected to iTRAQ comparative proteomic analysis. We found that different protein families were up- or down-regulated in the null mutant when compared with the WT.

2021-06-07 | PXD019301 | Pride

Expression of enzymes involved in gag synthesis and degradation in cartilage aging and arthritis

Project description:Glycoarrays are used to identify differences in the expression of enzymes involved in gag synthesis and degradation in cartilage aging and arthritis. This experiment includes 3 samples from donors with and without growth factor stimulation. Samples are from human biopsy/necropsy origin.

2011-02-17 | GSE27350 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data