Meyer, Katja; Köster, Tino; Nolte, Christine; Weinholdt, Claus; Lewinski, Martin; Grosse, Ivo; Staiger, Dorothee: Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7. In: Genome Biology. Jg.18 H. 1. 2017
Inhalt
- Results
- Conditions for UV light crosslinking of RNA–protein complexes in Arabidopsis plants
- iCLIP of AtGRP7
- Confirmation of high-confidence binders among iCLIP targets by RIP-seq
- Validation of iCLIP and RIP-seq targets by RIP-qPCR
- Determination of the AtGRP7 binding landscape
- Impact of AtGRP7 on candidate targets
- AtGRP7 regulates circadian target transcripts
- AtGRP7 targets in the subjective morning
- Alternative splicing targets identified by iCLIP and/or RIP-seq
- Discussion
- Detection of iCLIP targets and discrimination against background
- iCLIP and RIP-seq identify an overlapping but not identical set of target transcripts
- Binding mode of AtGRP7
- Impact of AtGRP7 on targets
- Impact of AtGRP7 on circadian transcript oscillations
- Effect of AtGRP7 on RNA processing steps
- Conclusions
- Methods
- Plant material
- Plant growth
- iCLIP
- RIP-seq
- RNA-seq
- Bioinformatics
- Determination of pentamer enrichment at XL sites
- Changes in alternative splicing events
- RT-PCR and real-time PCR
- Immunoblot analysis
- Additional files
- Abbreviations
- Funding
- Availability of data and materials
- Authors’ contributions
- Ethics approval and consent to participate
- Competing interests
- Publisher’s Note
- Author details
- References