Fig. 5a–c

Identification of the cohort of mRNAs bound to the ZC3H41-Z41AP complex by RNA immunoprecipitation sequencing (RIP-seq). a MACS2 analysis of the PuREBP1/2- and ZC3H41/Z41AP-bound transcriptomes. Immunoprecipitated transcripts identified by MACS2 were ranked according to their MACS2 score. A threshold of 7000 (horizontal dashed line) was set up based on the scores of NT8 and AATP6, which are bona fide targets of the PuREBP1/2 complex. Blue dots and grey dots correspond to transcripts that are, or are not, highly likely to be genuine targets, respectively. Orange dots indicate mRNAs encoding ribosomal proteins; none was detected above threshold scores in PuREBP1/2 purifications. b Correlation analysis of RIP followed by quantitative RT-PCR obtained using TAP-Z41AP or TAP-ZC3H41 as baits (see below); values indicate percentages of immunoprecipitated transcripts relative to input RNA. c RIP followed by quantitative RT-PCR to confirm association of the indicated transcripts to either ZC3H41, Z41AP or PuREBP1 (as a negative control). AATP11 (and NT8 in ZC3H41 and Z41AP purifications) were used as non-bound controls. L38 data correspond to the Tb927.9.2020 paralog (see Additional File 8 for the Tb927.10.3280 paralog). Percentages of immunoprecipitated RNA relative to input RNA are expressed as the mean (horizontal lines) ± SEM (shaded areas) of four independent RIPs (dots). For other abbreviations, see Figs. 1, 2 and 4