Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CLIP-seq analysis of integrase-RNA interactions

ABSTRACT: Integrase CLIP-seq experiments were conducted on wild-type and eccentric HIV-1 virions generated in the presence of allosteric integrase inhibitors and IN K264/266A and R269/K273A mutations

ORGANISM(S): Human immunodeficiency virus 1

PROVIDER: GSE83588 | GEO | 2016/08/25

SECONDARY ACCESSION(S): PRJNA326435

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CLIP-seq analysis of integrase-RNA interactions

Project description:Integrase CLIP-seq experiments were conducted on wild-type and eccentric HIV-1 virions generated in the presence of allosteric integrase inhibitors and IN K264/266A and R269/K273A mutations Integrase CLIP-seq experiments were conducted by immunoprecipitation of integrase-RNA complexes from fully formed mature and eccentric virus particles. Libraries of RNA molecules bound by integrase were generated and sequenced by Illumina Hi-Seq2000 and 2500 platforms.

2016-08-25 | E-GEOD-83588 | biostudies-arrayexpress

CLIP-seq analysis of NC-RNA interactions in wild-type and eccentric particles

Project description:Nucleocapsid (NC) CLIP-seq experiments were conducted on wild-type and eccentric HIV-1 virions generated in the presence of allosteric integrase inhibitor, BI-B2.

2017-06-15 | GSE100018 | GEO

CLIP-seq analysis of hnRNPA1-RNA interactions

Project description:hnRNPA1 CLIP-seq experiments were conducted on HEK293T cells transiently expressing WT hnRNPA1 and hnRNPA1-DSB mutant

2023-12-31 | GSE238202 | GEO

A3G and A3F CLIP

Project description:APOBEC3G and APOBEC3F are cell-encoded restriction factors that have evolved to counteract virus infections. When packaged into HIV-1 particles, A3G and A3F impair reverse transcription and induce the hypermutation of viral DNA. We employed a next generation sequencing approach to identify the RNAs that these proteins bind in HIV-1 infected cells and HIV-1 virions. We then analysed the mechanism of packaging of APOBEC3 in detail.

2014-12-17 | E-MTAB-2700 | biostudies-arrayexpress

Molecular targets of HIV integrase inhibitor, MK-2048, on ATL cells

Project description:Adult T-cell Leukemia (ATL) is a highly chemoresistant malignancy of peripheral T lymphocytes, associated with retrovirus human T-cell leukemia virus type I (HTLV-1). To elucidate the complex molecular mechanism of anti-Growth effect of the HIV integrase inhibitor, MK-2048 in ATL cells, we attempted to perform gene expression profiling.

2020-01-01 | GSE113265 | GEO

HIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort.

Project description:Distinct integration patterns of different retroviruses have puzzled virologists for over 20 years. The viral integrase (IN), as part of the intasome complex, docks onto the target DNA (tDNA) and catalyzes the insertion of the viral genome into the host chromatin. We identified retroviral IN amino acids directly contacting tDNA bases and affecting the local integration site sequence biases. These residues also determine the propensity of the virus to integrate into flexible tDNA sequences. Remarkably, natural polymorphisms INS119G and INR231G retarget viral integration away from gene dense regions, without affecting the interaction with the lentiviral tethering cofactor LEDGF/p75 (PSIP1). Precisely these variants were associated with rapid disease progression in a chronic HIV-1 subtype C infection cohort. These findings link integration site selection to virulence and viral evolution but also to the host immune response and antiretroviral therapy, since HIV-1 IN119 is under selection by HLA alleles and integrase inhibitors. LEDGF/p75 (PSIP1) ChIP-Seq using A300-848 antibody (recognizes p75 isoform) and input control in primary CD4+ T-cells

2015-01-26 | E-GEOD-61003 | biostudies-arrayexpress

HIV-1 integrase variants retarget viral integration and are associated with disease progression in a chronic infection cohort.

2015-01-26 | GSE61003 | GEO

HIV integrase deep sequencing.

Project description:Identification of minority resistance mutations in the HIV-1 integrase gene using Next Generation Sequencing

| PRJEB9552 | ENA

Implementation of PAR-CLIP to characterize RNA-protein interactions in prokaryotes at nucleotide resolution

Project description:The identification of RNAs that are recognized by RNA-binding proteins (RNA-BPs) using techniques such as Crosslinking and Immunoprecipitation (CLIP) has revolutionized the genome-wide discovery of RNA-BP RNA targets. Among the different versions of CLIP that have been developed, the use of photoactivable nucleoside analogs has resulted in high efficiency photoactivable ribonucleoside-enhanced CLIP (PAR-CLIP) in vivo. Nonetheless, PAR-CLIP has not yet been applied in prokaryotes. To determine if PAR-CLIP can be used in prokaryotes, we determined suitable conditions for the incorporation of 4-thiouridine (4SU), a photoactivable nucleoside, into E. coli RNA and for the isolation of RNA crosslinked to RNA-BPs of interest. Applying this technique to Hfq, a well-characterized regulator of small RNA (sRNA)-messenger RNA (mRNA) interactions, we showed that PAR-CLIP identified most of the known sRNA targets of Hfq, as well as functionally relevant sites of Hfq-mRNA interactions at nucleotide resolution. Based on our findings, PAR-CLIP represents an improved method to identify both the RNAs and the specific regulatory sites that are recognized by RNA-BPs in prokaryotes.

2022-10-18 | MSV000090547 | MassIVE

Project description:Allosteric Integrase Inhibitor BI-D influences HIV-1 integration sites selection

| PRJNA860913 | ENA