Fig. 1: HDLBP binds to ER-targeted mRNAs.

a Quantification of membrane and cytosolic mRNA localization in HEK293 cells by sequencing. Histogram of log2-transformed membrane enrichment (ratio between the membrane and cytosolic read counts, mean of two replicates). Cutoffs of 0.5 and 1.5 (gray lines) were chosen to classify membrane-bound (n = 1157), cytosolic (n = 6139) and mRNAs with undefined localization (n = 193). mRNAs with a TPM of at least ten were included in this analysis. b Quality control of mRNA-seq-derived localization. Log2-transformed membrane enrichment was compared between groups of mRNAs classified according to presence of encoded targeting signals (TS): cytosol-localized mRNAs with no targeting signals (n = 5142), mRNAs encoding mitochondrial proteins excluding mtDNA-encoded mRNAs (n = 739), mRNAs coding for post-translationally targeted tail-anchored transmembrane proteins (n = 102), mitochondrial DNA expressed mRNAs encoding mitochondrial proteins (n = 13), membrane-localized mRNAs with no known TS (n = 107), mRNAs encoding signal peptide (SignalP) containing proteins (n = 214) or transmembrane helices (n = 724) or both (n = 282). mRNAs with a TPM of at least ten were included in this analysis. The lower and upper hinges of box plots correspond to the 25th and 75th percentiles, respectively. Upper and lower whiskers extend from the hinge to the largest or smallest value no further than the 1.5× interquartile range from the hinge, respectively. Center lines of box plots depict the median values. c Distribution of HDLBP crosslinks (T-C transitions) throughout the transcriptome as detected by PAR-CLIP in HEK293 cells. d Scatter plot of normalized HDLBP cross-linking signal in CDS versus mRNA expression level in non-fractionated cells. mRNAs were classified according to their membrane enrichment in (a). Inset above shows density distributions of HDLBP cross-linking signal. e HDLBP-bound and unbound mRNAs with respect to their localization. Absolute numbers and percentages of HDLBP-bound mRNAs of total HEK293 cytosolic and membrane-bound mRNAs are shown. f HDLBP PAR-CLIP binding enrichment (mean of two biological replicates) for different mRNA classes; cytosol-localized mRNAs with no TS (n = 1578), mRNAs encoding mitochondrial proteins excluding mtDNA-expressed mRNAs (n = 251), mRNAs coding for post-translationally targeted tail-anchored transmembrane proteins (n = 30), membrane-localized mRNAs with no known TS (n = 74), mRNAs encoding signal peptide (SignalP) containing proteins (n = 138) or transmembrane helices (n = 492) or both (n = 219). The lower and upper hinges of box plots correspond to the 25th and 75th percentiles, respectively. Upper and lower whiskers extend from the hinge to the largest or smallest value no further than the 1.5× interquartile range from the hinge, respectively. Center lines of box plots depict the median values. a–f Source data are provided as a Source Data file.