PDF《cCL》

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2 yeast total RNA total RNA UV

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2 yeast eluted poly(A)-RNA eluted poly(A)-RNA AAA cCL AAA TTT

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2 Supplementary Figure 1: UV254-induced RNA damage in S. cerevisiae Analysis of yeast RNA integrity after

254 nm crosslinking (cCL ): After irradiation of living yeast cells with

0 C 1.2 J/cm2 of UV254, RNA integrity was analyzed using a BioAnalyzer

2100 (RNA Pico Chip). The top panel displays the gel representation of in-chip electrophoresis , the bottom panel the respective diagrams including the two ribosomal RNA peaks. c HuH-7 cCL rep

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2 PAR-CL Supplementary Figure 2: Replicate mRNA interactome experiments Three biological replicates of mRNA interactome capture from yeast (a, b) and HuH-7 (c, d) are plotted against each other based on the protein enrichmen t in crosslinked over non-crosslinked samples. a b RNA binding 1.6 x

10 -43 const. of ribos. 6.1 x

10 -25 9.3 x

10 -40 mRNA binding 1.5 x

10 -17 1.8 x

10 -14 translation f. 6.1 x

10 -10 4.6 x

10 -16 RNA helicase activity 1.5 x

10 -13 5.2 x

10 -13 fold enrichment

0 20

10 10 yeast human p adj. value p adj. value core interactome RBPs GO molecular function 3.7 x

10 -99 K Homology 3.3 x

10 -9

4 x

10 -3 DEAD-like (N) 6.6 x

10 -4 3.9 x

10 -9 2.5 x

10 -18 RNP-I 4.4 x

10 -10 fold enrichment

0 20

10 10 yeast human p adj. value p adj. value core interactome RBPs Interpro domains 5.3 x

10 -18 Helicase s.1 &

2 2.1 x

10 -18 DUF1605 3.0 x

10 -1 7.0 x

10 -1 c 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 proportion residues in low complexity regions proportion of proteins yeast 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 proportion of proteins human enigmRBPs all yeast RBPs whole proteome enigmRBPs all human RBPs whole proteome yeast human 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 proportion of proteins enigmRBPs all human RBPs whole proteome 0.0 0.2 0.4 0.6 0.8 1.0 0.0 0.2 0.4 0.6 0.8 1.0 proportion residues in disordered regions proportion of proteins enigmRBPs all yeast RBPs whole proteome d transferases oxidoreductases 45% 18% 15% 10% 8% 4% ligases lyases isomerases hydrolases yeast (FDR 0.01) transferases 22% oxidoreductases 32% 19% hydrolases 16% isomerases 6% lyases 5% ligases HuH-7 (FDR 0.05) e transferases 27% oxidoreductases 27% 23% hydrolases 9% isomerases 14% lyases f core interactome Supplementary Figure 3: Characteristics of yeast and HuH-7 mRNA interactomes a, GO biochemical pathway enrichment of the core mRNA interactome. b, Protein domain enrichment of the core mRNA interactome. c, Proportions of the amino acids in low complexity regions of enigmRBPs, all interactome RBPs and whole proteomes of yeast and human. d, Proportions of the amino acids in disordered regions of enigmRBPs, all interactome RBPs and whole proteomes of yeast and human. e, EC enzyme classi cation of enzyme RBPs from yeast and HuH-7 cells. f, EC enzyme classi cation of enzyme RBPs from core mRNA interactome. a b HSD17B10 wt B HSD17B10 wt A HSD17B10 R130C B HSD17B10 R130C A 2.5 5.0 7.5 10.0 12.5 3.0 6.0 9.0 log2( counts per million + 2) log2( counts per million + 2) 2.5 5.0 7.5 10.0 log2( counts per million + 2) 3.0 6.0 9.0 12.0 log2( counts per million + 2) eGFP B eGFP A log2( counts per million + 2) log2( counts per million + 2) HSD17B10 R130C HSD17B10 wt eGFP chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr2 chr20 chr21 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chrM chrX chrY 0.0 0.5 1.0 1.5 2.0 2.5 3.0 3.5 crosslink site density chromosomes 2.5 5.0 7.5 10.0 12.5 3.0 6.0 9.0 12.0 Supplementary Figure 4: HSD17B10 iCLIP a, iCLIP replicates correlation of bound RNA species. Displayed are crosslink peaks as log2 (counts per million + 2). b, Crosslink site bar plot for iCLIP cDNA libraries after alignment to the human genome and random barcode evaluation. (mt) tRNA