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In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]

ABSTRACT: We performed irCLASH and HiCLIP for ADAR1-3 in HEK293 cells. In addition, we performed mRNA-seq in ADAR1-3 overexpressed HEK293 cells and control HEK293 cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE136325 | GEO | 2020/03/26

REPOSITORIES: GEO

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In vivo atlas of RNA secondary structures recognized by ADARs [RNA-Seq]

Project description:We performed irCLASH and HiCLIP for ADAR1-3 in HEK293 cells. In addition, we performed mRNA-seq in ADAR1-3 overexpressed HEK293 cells and control HEK293 cells

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In vivo atlas of RNA secondary structures recognized by ADARs

Project description:This SuperSeries is composed of the SubSeries listed below.

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In vivo atlas of RNA secondary structures recognized by ADARs

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In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]

Project description:In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]

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hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.

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Specificity of ADAR1-isoforms: RIP-seq of ADAR1p150 and ADAR1p110 in HEK293 cells

Project description:Adenosine deaminase acting on RNA (ADAR) (also known as ADAR1) promotes A-to-I conversion in double-stranded and highly structured RNAs. ADAR1 has two isoforms transcribed from different promoters: ADAR1p150, which is mainly cytoplasmic and interferon-inducible, and constitutively expressed ADAR1p110 that is primarily localized in the nucleus. Mutations in ADAR1 cause Aicardi – Goutières syndrome (AGS), a severe autoinflammatory disease in humans associated with aberrant IFN production. In mice, deletion of ADAR1 or selective knockout of the p150 isoform alone leads to embryonic lethality driven by overexpression of interferon-stimulated genes. This phenotype can be rescued by concurrent deletion of cytoplasmic dsRNA-sensor MDA5. These findings indicate that the interferon-inducible p150 isoform is indispensable and cannot be rescued by the ADAR1p110 isoform. Nevertheless, editing sites uniquely targeted by ADAR1p150 but also mechanisms of isoform- specificity remain elusive. To examine in vivo interaction between ADAR1-isoforms and its substrates, we performed RNA immunoprecipitation and sequencing (RIP-seq) in HEK293 cells. RIP-seq experiment was done with overexpressed flag-tagged ADAR1 isoforms.

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2022_de Reuver_ADAR1 +/+ vs ADAR1 Za/Za HEK293 cells (deep-seq)

Project description:ADAR1 +/+ vs ADAR1 Za/Za HEK293 cells (deep-seq)

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How do ADARs bind RNA? New protein-RNA structures illuminate substrate recognition by the RNA editing ADARs.

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