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. 2023 Sep 28;14:6078. doi: 10.1038/s41467-023-40948-w

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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. 6 — T. gondii PRU parasites were exposed to high pH, cyst inducing conditions for 48 h prior to crosslinking and anti-FLAG immunoprecipitation (N = 3). Averages of all 3 libraries are represented here. a Venn diagram showing the overlap of: genes having significant changes (|Log2FC > 1|, Padj<0.05) in transcript abundance after exposure to BIC in vitro and found to be significantly bound by ROCY1 based on enrichment in sequenced eCLIP samples. b eCLIP data represented on two genome browser tracks showing input (top, red) and input and IP overlaid (bottom, red and blue) and significant ROCY1 peaks associated with the 5’ and 3’ UTRs and CDS of the ROCY1 transcript. c Same as for b, but at the BFD1 locus. d Same as in b, c, but for the BAG1 locus. In contrast to the ROCY1 and BFD1 transcripts, no significant ROCY1-bound peaks were detected for the BAG1 transcript. e Metagene profile of eCLIP and size-matched input reads spanning from transcriptional start site (TSS) to transcriptional end site (TES). Dotted lines indicate the borders between 5’UTR, CDS and 3’UTR. f Quantification of the total length of each transcript feature type (5’ UTR, 3’ UTR, CDS) in all genes with > 1 ROCY1 peak across the entire transcript (top stacked bar) and across only those regions with significant ROCY1 eCLIP peaks at least 11 bp in size and with a PureCLIP score of at least 50. Chisquare analysis shows a highly significant (P < 0.0001), unequal distribution of where the ROCY1 peaks are when normalized to the length of the ROCY1-targeted genes. g Mean-centered, clustered heatmap of T. gondii genes that are significantly induced by exposure to BIC including both transcript abundance (blue to yellow) and the ROCY1 PureClip score (mauve to teal). Hypothetical protein; MIC: microneme protein. PureClip scores > 4.3 are significant at P < 0.01. Grey indicates no eCLIP score above that statistical threshold were detected for that transcript. This experiment was performed once. Data are provided as a Source Data File.