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Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7

ABSTRACT: Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7

PROVIDER: PRJNA388894 | ENA |

REPOSITORIES: ENA

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Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7.

Project description: Not available

| S-EPMC5663106 | biostudies-literature

Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7

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

2017-09-28 | GSE99616 | GEO

Identification of AtGRP7 targets by iCLIP

Project description:A key function for RNA-binding proteins in orchestrating plant development and environmental responses is well established. However, the lack of a genome-wide view on their in vivo binding targets and binding landscapes represents a gap in understanding the mode of action of plant RNA-binding proteins. Here, we adapt individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) for genome-wide determining the binding repertoire of the circadian clock-regulated Arabidopsis thaliana glycine-rich RNA-binding protein AtGRP7. We have established iCLIP for plants to identify target transcripts of the RNA-binding protein AtGRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues.

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CTCF binding polarity determines chromatin looping

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Project description:Analysis of UNR (CSDE1) binding to RNA targets by iCLIP transcriptome-wide mapping.

2016-11-07 | E-MTAB-3818 | biostudies-arrayexpress

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Spliceosome iCLIP

Project description:The studies of spliceosomal interactions are challenging due to their dynamic nature. Here we developed spliceosome iCLIP, which immunoprecipitates SmB along with snRNPs and auxiliary RNA binding proteins (RBPs) to simultaneously map the spliceosomal binding to human snRNAs and pre-mRNAs. This identified 9 distinct regions on pre-mRNAs, which overlap with position-dependent binding patterns of 15 RBPs. Using spliceosome iCLIP, we additionally identified >50,000 branchpoints (BPs) that have canonical features, unlike those identified by RNA-seq. The iCLIP BPs generally overlap with the computationally predicted BPs, and alternative BPs are associated with extended regions of structurally accessible RNA. We find that the position and strength of BPs defines the binding patterns of SF3 and U2AF complexes, whereas the RNA structure around BPs affects the sensitivity of exons to perturbation of these complexes. Our findings introduce spliceosome iCLIP as a new method for transcriptomic studies of BPs and splicing mechanisms.

2019-08-30 | E-MTAB-6950 | biostudies-arrayexpress

hnRNP A1 iCLIP

Project description:This experiment identifies hnRNP A1 binding sites transcriptome-wide in Hela cells. HeLa cells with inducible expression of T7-tagged hnRNP A1 were grown to approximately 90% confluence and then subject to iCLIP analysis (following the protocol from Huppertz et al. 2014 (iCLIP: protein-RNA interactions at nucleotide resolution)). The iCLIP library was sequenced using Illumina's HighSeq 1500

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CTCF binding polarity determines chromatin looping [ChIP-seq]

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