Ontology highlight
ABSTRACT:
PROVIDER: PRJNA720376 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by microarray profiling. Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr were transfected into control and YBX1-knockdown cells to identify YBX1-dependent targets that are modulated due to tRF loss-of-function.
2015-05-08 | E-GEOD-63564 | biostudies-arrayexpress
Project description:The interactions between proteins and nucleic acids have a fundamental function in many biological processes well beyond nuclear gene transcription and include RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins binding individual mRNAs in mammalian cells has greatly been augmented by recent surveys, no systematic study on the native proteins of human cells differentially engaging various types of nucleic acids in a non sequence-specific manner has been reported. We designed an experimental approach to cover the non sequence-specific RNA and DNA binding space broadly, including methylation, and test for its ability to interact with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high confidence direct binders, 249 of which were devoid of previous experimental evidence for binding nucleic acids. We could assign 513 specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and to individual domains. The evolutionary conserved protein YB-1, previously associated with cancer and gene regulation, is shown to bind methylated cytosine preferentially conferring YB-1 a potential epigenetic function. Collectively, the dataset represents a rich resource of experimentally determined nucleic acid-specific binding proteins in humans and, indirectly, for other species. Identification of genomic YB-1 binding sites in HEK293 cells
2013-06-18 | E-GEOD-47539 | biostudies-arrayexpress
Project description:In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by alpha-amanitine treatment, RNA extraction at time points 0 and 8hr post-treatment, and transcriptomic profiling. Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr were transfected into control and YBX1-knockdown cells to identify YBX1-dependent targets whose stabilities are modulated due to tRF loss-of-function. We used alpha-amanitine mediated inhibition of RNA-polymerase to measure transcript stability across the entire transcriptome.
2015-05-08 | E-GEOD-63565 | biostudies-arrayexpress
Project description:The interactions between proteins and nucleic acids have a fundamental function in many biological processes well beyond nuclear gene transcription and include RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins binding individual mRNAs in mammalian cells has greatly been augmented by recent surveys, no systematic study on the native proteins of human cells differentially engaging various types of nucleic acids in a non sequence-specific manner has been reported. We designed an experimental approach to cover the non sequence-specific RNA and DNA binding space broadly, including methylation, and test for its ability to interact with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high confidence direct binders, 249 of which were devoid of previous experimental evidence for binding nucleic acids. We could assign 513 specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and to individual domains. The evolutionary conserved protein YB-1, previously associated with cancer and gene regulation, is shown to bind methylated cytosine preferentially conferring YB-1 a potential epigenetic function. Collectively, the dataset represents a rich resource of experimentally determined nucleic acid-specific binding proteins in humans and, indirectly, for other species.
2013-06-18 | GSE47539 | GEO
Project description:Immunostimulatory endogenous nucleic acids drive the lesional inflammation in cutaneous lupus erythematosus
| PRJNA377232 | ENA
Project description:In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by microarray profiling.
2015-05-08 | GSE63564 | GEO
Project description:Aicardi-Goutières syndrome (AGS) is a genetically heterogeneous encephalopathy whose pathology is linked to an abnormal type I interferon response induced by self-derived nucleic acids. Data indicate that endogenous retroelements represent one source of interferon-stimulatory self-nucleic acid. No effective therapies are available for this disorder. In this pilot study involving patients with AGS due to mutations in TREX1, RNASEH2A, RNASEH2B or SAMHD1 three nucleoside analogue reverse transcriptase inhibitors (RTIs) were administered over 12 months. Transcription profiling was done by RNA-seq.
2018-12-12 | E-MTAB-7087 | biostudies-arrayexpress
Project description:In order to test whether inhibition of tRFs induced under hypoxia would counteract the YBX1-dependent reduction of target transcripts, we used transient transfection of antisense locked-nucleic acids (pooled LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr under hypoxia followed by microarray profiling. Synthetic antisense locked-nucleic acids (LNAs) targeting the YBX1 binding site on tRFAsp, tRFGly, tRFGlu, and tRFTyr were transfected (as a pool) in control and YBX1-knockdown cells under hypoxia to assess the consequences of inhibiting tRFs induced in hypoxic MDA-parental cells.
2015-05-08 | E-GEOD-63563 | biostudies-arrayexpress
Project description:In order to identify YBX1-dependent targets that are modulated upon changing the levels of endogenous tRFs, we used transient transfection of antisense locked-nucleic acids (LNAs) against tRFAsp, tRFGly, tRFGlu, and tRFTyr followed by alpha-amanitine treatment, RNA extraction at time points 0 and 8hr post-treatment, and transcriptomic profiling.
2015-05-08 | GSE63565 | GEO
Project description:Asterix/Gtsf1 has been previously been shown to be involved in the silencing of retrotransposons in animal germ cells through the piRNA pathway. During early stages of purification of mouse Gtsf1 protein in Sf9 cells for structural studies, we found that the protein was co-purifying with endogenous nucleic acids. We first characterized those RNAs by next-generation sequencing (this dataset) and then later investigated its RNA-binding in more relevant cell culture systems. In each case, we found Asterix/Gtsf1 was binding tRNAs. Given the role of tRNAs as primers for Long Terminal Repeat (LTR) transposons, this work implicates Asterix/Gtsf1 as exploiting tRNA dependence to identify transposon transcripts and promote piRNA silencing.
2021-02-20 | GSE151110 | GEO