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. 2023 Feb 8;14:696. doi: 10.1038/s41467-023-36345-y

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Simplified overview of the CBC and its two cofactors, ALYREF and RBM7, with relevance for the present study. See text for further detail. b Schematic outline of the tiCLIP approach (lower panel) as compared to regular steady state iCLIP (upper panel). c Histograms showing the average number of normalised mapped tiCLIP reads. Numbers from individual biological replicates are shown as circles, squares and triangles. ‘Negative’ timepoints represent controls in which blank magnetic beads were used (negative anti-GFP lanes) on unsynchronised samples. d Histograms showing average RBP binding densities (reads/kb) calculated from all exonic and intronic regions of mono- and multi-exonic transcription units (TUs) as indicated. 22,650 TUs were used in this analysis. Biological replicates are shown as in c. e Principal component analysis (PCA) plot of tiCLIP data from mono (left)- and multi (right)-exonic TUs showing the variation across libraries. In order to capture the spatial variance, whole TUs were segmented into 10 kb bins and treated as individual data points. n = number of TUs used for analyses. Biological replicates are shown as in c. Source data are provided as a Source Data file.