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Background  Functions for RNA-binding proteins in orchestrating plant development and environmental responses are well established. However, the lack of a genome-wide view of 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 and immunoprecipitation (iCLIP) genome-wide to determine the binding repertoire of the circadian clock-regulated  Arabidopsis thaliana  glycine-rich RNA-binding protein  At GRP7.    Results  iCLIP identifies 858 transcripts with significantly enriched crosslink sites in plants expressing  At GRP7-GFP that are absent in plants expressing an RNA-binding-dead  At GRP7 variant or GFP alone. To independently validate the targets, we performed RNA immunoprecipitation (RIP)-sequencing of  At GRP7-GFP plants subjected to formaldehyde fixation. Of the iCLIP targets, 452 were also identified by RIP-seq and represent a set of high-confidence binders.  At GRP7 can bind to all transcript regions, with a preference for 3′ untranslated regions. In the vicinity of crosslink sites, U/C-rich motifs are overrepresented. Cross-referencing the targets against transcriptome changes in  At GRP7 loss-of-function mutants or  At GRP7-overexpressing plants reveals a predominantly negative effect of  At GRP7 on its targets. In particular, elevated  At GRP7 levels lead to damping of circadian oscillations of transcripts, including  DORMANCY/AUXIN ASSOCIATED FAMILY PROTEIN2  and  CCR-LIKE . Furthermore, several targets show changes in alternative splicing or polyadenylation in response to altered  At GRP7 levels.    Conclusions  We have established iCLIP for plants to identify target transcripts of the RNA-binding protein  At GRP7. This paves the way to investigate the dynamics of posttranscriptional networks in response to exogenous and endogenous cues.    Electronic supplementary material  The online version of this article (doi:10.1186/s13059-017-1332-x) contains supplementary material, which is available to authorized users.

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