Profiling dynamic RNA-protein interactions using small molecule-inducible RNA editing
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE207005 | GEO | 2023/04/28
REPOSITORIES: GEO
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Project description:Profiling dynamic RNA-protein interactions using small molecule-inducible RNA editing
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Project description:Programmed RNA Editing with an Evolved Bacterial Adenosine Deaminase
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Project description:Programmed RNA Editing with an Evolved Bacterial Adenosine Deaminase I
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Project description:Programmed RNA Editing with an Evolved Bacterial Adenosine Deaminase II
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Project description:High-throughput sequencing screens suggest that RNA editing, which consists in the substitution of adenosine with inosine by the RNA-specific adenosine deaminase (ADAR) enzyme, occurs at several thousand positions across the human genome. Recent evidences have shown that RNA-editing could promote proliferation and carcinogenesis; however, the general principles of ADAR activity on the transcriptome and how ADAR is controlled in cancers remain to be established. The main aim of this project was to investigate the phenomenon of RNA editing in breast and other cancers. The frequency of A-to-I editing was evaluated in 58 breast cancers equally distributed among the different molecular subtypes and 10 normal breast tissues. The analysis was focused on defining: the relationship between the global amount of editing and ADAR expression; the ability to predict the level of editability of specific sites; the distribution of editing in normal and tumour samples and among different breast cancer subtypes; and the clinical, pathological and genomic factors affecting editing.
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Project description:Most current methods to identify cell-specific RNA binding protein (RBP) targets require analyzing an extract, a strategy that is problematic with small amounts of material. We previously addressed this issue by developing TRIBE, a method that expresses an RBP of interest fused to the catalytic domain (cd) of the RNA editing enzyme ADAR. TRIBE performs Adenosine-to-Inosine editing on candidate RNA targets of the RBP. However, target identification is limited by the efficiency of the ADARcd. Here we describe HyperTRIBE, which carries a previously characterized hyperactive mutation (E488Q) of the ADARcd. HyperTRIBE identifies dramatically more editing sites than TRIBE, many of which are also edited by TRIBE but at a much lower editing frequency. The data have mechanistic implications for the enhanced editing activity of the HyperADARcd as part of a RBP fusion protein and also indicate that HyperTRIBE more faithfully recapitulates the known binding specificity of its RBP than TRIBE.
2017-08-19 | GSE102814 | GEO
Project description:RNA-binding proteins (RBPs) are essential for posttranscriptional gene regulation, but it remains a challenge to identify RNA targets of RBPs from specific cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I RNA deaminases to RBPs. We benchmark the method and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs involved in diverse biological functions. Bulk PIE-Seq reveals canonical binding features and target genes for RBPs such as PUM2 and NOVA1, and nominates new target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Integrative analyses show that homologous RBPs frequently bind to comparable sequences and target gene sets while different RBP families bind to distinct targets, indicating that PIE-Seq is robust to uncovering RBP targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes. In summary, the dual-deaminase PIE-Seq joins the editable nucleotide space for single editors and provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.
2023-05-17 | GSE155844 | GEO
Project description:RNA editing has been shown to implicate in cardiovascular diseases, including dysregulated RNA editing in endothelial cell (EC) that involves Adenosine Deaminase Acting on RNA1 (ADAR1). However, the specific function of ADAR1 in EC at physiologic condition has not been established and the mechanism remains to be defined. This study is to determine the specific physiologic role of ADAR1 in EC and reveal its molecular and cellular mechanisms.
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Project description:Studies in epitranscriptomics indicates that RNA is modified by a variety of enzymes. Among these RNA modifications, A-to-I RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA-seq data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNAEditor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affects the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncover that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands are examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, HuR, was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme ADAR compared to the control—suggesting that the presence of RNA editing islands influences HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP-RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.
2019-11-30 | GSE141095 | GEO