Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA350899 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We sequenced the mRNA from a stably transduced Human T-cell line expressing the HIV-1 Tat protein. The inducible Tat expression has been used to understand and compare the cellular molecules and pathways being modulated by the wild type subtype-C Tat versus its single signature amino acid residue variant. Additionaly, the HIV-1 subtype B and C Tat comparitive analysis has also been included in the study to evaluate the gene expression profile as a reponse to subtype specific Tat proteins.
2018-10-25 | GSE89266 | GEO
Project description:Over-expression of truncated FMRP with 295 amino acid residues: HEK293T cells
| PRJNA283322 | ENA
Project description:The AF4/FMR2 proteins AFF1 and AFF4 act as a scaffold to assemble the Super Elongation Complex (SEC) that strongly activates transcriptional elongation of HIV-1 and cellular genes. Although they can dimerize, it is unclear whether the dimers exist and function within a SEC in vivo. Furthermore, it is unknown whether AFF1 and AFF4 function similarly in mediating SEC-dependent activation of diverse genes. Providing answers to these questions, our current study shows that AFF1 and AFF4 reside in separate SECs that display largely distinct gene target specificities. While the AFF1-SEC is more potent in supporting HIV-1 transactivation by the viral Tat protein, the AFF4-SEC is more important for HSP70 induction upon heat shock. The functional difference between AFF1 and AFF4 in Tat-transactivation has been traced to a single amino acid variation between the two proteins, which causes them to enhance the affinity of Tat for P-TEFb, a key SEC component, with different efficiency. Finally, genome-wide analysis confirms that the genes regulated by AFF1- and AFF4-SEC are largely non-overlapping and perform distinct functions. Thus, the SEC represents a family of related complexes that exist to increase the regulatory diversity and gene control options during transactivation of diverse cellular and viral genes. RNA-seq in HeLa cells of wild-type and after RNAi of AFF1 or AFF4.
2015-05-20 | E-GEOD-69021 | biostudies-arrayexpress
Project description:Single nucleotide variants are the most frequent type of sequence changes detected in the genome and these are frequently variants of uncertain significance (VUS). VUS are changes in DNA for which disease risk association is unknown. Thus, methods that classify the functional impact of a VUS can be used as evidence for variant interpretation. In the case of the breast and ovarian cancer specific tumor suppressor protein, BRCA1, pathogenic missense variants frequently score as loss of function in an assay for homology-directed repair (HDR) of DNA double-strand breaks. We previously published functional results using a multiplexed assay for 1056 amino acid substitutions residues 2-192 in the amino terminus of BRCA1. In this study, we have re-assessed the data from this multiplexed assay using an improved analysis pipeline. These new analysis methods yield functional scores for more variants in the first 192 amino acids of BRCA1, plus we report new results for BRCA1 amino acid residues 193-302. We now present the functional classification of 2172 BRCA1 variants in BRCA1 residues 2-302 using the multiplexed HDR assay. Comparison of the functional determinations of the missense variants with clinically known benign or pathogenic variants indicated 93% sensitivity and 100% specificity for this assay. The results from BRCA1 variants tested in this assay are a resource for clinical geneticists for evidence to evaluate VUS in BRCA1.
2023-06-12 | GSE234482 | GEO
Project description:A combination of bioinformatics, RNAseq, and cell-based functional assays were used to study the changes in host cell gene expression when HIV-1 Rev, Tat, Tat and Rev or HERV-K Rec was expressed. These results suggest that HIV Rev is capable of modulating gene and mRNA isoform expression, during HIV-1 infection.
2023-10-31 | GSE160606 | GEO
Project description:A combination of bioinformatics, RNAseq, and cell-based functional assays were used to study the changes in host cell gene expression when HIV-1 Rev, Tat, Tat and Rev or HERV-K Rec was expressed. These results suggest that HIV Rev is capable of modulating gene and mRNA isoform expression, during HIV-1 infection.
2023-12-07 | GSE162852 | GEO
Project description:The AF4/FMR2 proteins AFF1 and AFF4 act as a scaffold to assemble the Super Elongation Complex (SEC) that strongly activates transcriptional elongation of HIV-1 and cellular genes. Although they can dimerize, it is unclear whether the dimers exist and function within a SEC in vivo. Furthermore, it is unknown whether AFF1 and AFF4 function similarly in mediating SEC-dependent activation of diverse genes. Providing answers to these questions, our current study shows that AFF1 and AFF4 reside in separate SECs that display largely distinct gene target specificities. While the AFF1-SEC is more potent in supporting HIV-1 transactivation by the viral Tat protein, the AFF4-SEC is more important for HSP70 induction upon heat shock. The functional difference between AFF1 and AFF4 in Tat-transactivation has been traced to a single amino acid variation between the two proteins, which causes them to enhance the affinity of Tat for P-TEFb, a key SEC component, with different efficiency. Finally, genome-wide analysis confirms that the genes regulated by AFF1- and AFF4-SEC are largely non-overlapping and perform distinct functions. Thus, the SEC represents a family of related complexes that exist to increase the regulatory diversity and gene control options during transactivation of diverse cellular and viral genes.
2015-05-20 | GSE69021 | GEO
Project description:Chemokine receptors CXCR4 and CCR5 regulate white blood cell trafficking, and are engaged by the HIV-1 envelope glycoprotein gp120 during infection. We combine directed evolution of CXCR4 and CCR5 libraries comprising nearly all ~7,000 single amino acid substitutions with deep sequencing to define sequence-fitness landscapes for surface expression and ligand interactions. Functional interaction sites are mapped based on conservation; for example, extracellular residues are conserved for binding HIV-1-blocking antibodies, as expected. Chemokine CXCL12 interacts with residues extending asymmetrically into the CXCR4 ligand-binding cavity, and distal mutations within allosteric and G protein coupling sites are identified that enhance chemokine binding. CCR5 residues conserved for gp120 interactions partially overlap with the chemokine-binding site, and gp120 binding is increased by acidic substitutions in the CCR5 N-terminus and extracellular loops. Furthermore, general features are apparent from sequence patterns, including membrane regions that are intolerant to polar mutations, and deleterious cysteine substitutions within extracellular loops.
2018-04-23 | GSE100368 | GEO
Project description: Not available
| S-EPMC2531291 | biostudies-literature
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO