Supplementary MaterialsFigure S1: Figure S1, linked to Numbers 2 and ?and3. and mapping percentages. NIHMS767511-supplement-Table_S3.xlsx (16K) GUID:?D8C788DE-C0DF-4F46-B34A-487192413E5A Desk S4: Desk S4, Linked to Shape 2A. Sites in adverse settings Editing sites determined in crazy type S2 cells and in cells expressing the just the catalytic site of dADAR. NIHMS767511-supplement-Table_S4.xlsx (50K) GUID:?A4E33DC5-0687-4157-807B-875F9F267B2A Desk S5: Desk S5, Related to Figures 2,?,33,?,44,?,55,?,66,?,7.7. TRIBE sites TRIBE editing sites from all experiments supplied in bedgraph format, with information on chromosomal coordinate, sequencing depth, editing percentages and gene names. NIHMS767511-supplement-Table_S5.xlsx (6.7M) GUID:?3DBD1313-9348-4A85-80FE-44C6E6169319 Figure S2: Figure S2, related to Figure 2. Motif analysis of Hrp48, Hrp48-ADARcd CLIP and Hrp48-TRIBE editing events Significant motifs found by MEME analysis are shown. Motifs found by in vitro selection (SELEX, (Blanchette et al., 2009)) or CLIP (endogenous Hrp48 and Hrp48-ADARcd) (A, B, C). Motifs found in regions surrounding Hrp-ADARcd TRIBE editing sites (D, E). For Hrp48-ADARcd TRIBE editing events in S2 cells, an area +/? 20 and 100 bp around the edited base was used for analysis (FDR 0.001). NIHMS767511-supplement-Figure_S2.pdf (214K) GUID:?B475932C-6EEE-4142-89B5-60287D43ABFE Figure S3: Figure S3, related to Figures 2 and ?and3.3. RNA structure prediction around TRIBE Apixaban inhibition editing sites Predicted double-strandedness around TRIBE editing sites (orange) or CLIP binding sites that lack TRIBE editing sites (grey) (A). Single nucleotide resolution for Hrp48 binding location was achieved by performing CIMS analysis (Cross Linking induced Mutation Site) on CLIP data. A flanking region of 250nt both 5 and 3 of the site (501nt in total) was folded with UNAFold, base pairing was counted in the predicted minimum free energy (MFE) and suboptimal structures (within G=5Kcal/mol of the MFE), and the profile is averaged per. All sites were then averaged to yield this plot (mean +/? Apixaban inhibition SEM, n = 17 TRIBE editing sites). B) Schematic modified from Eifler et al, 2013. RNA structure around the sites edited by the catalytic domain of human ADAR2 in yeast resemble the intermediate complex formed when ADAR2 distorts local dsRNA and the sequences flanking the edited adenosine are optimal for deaminase domain binding. Data shown is from Hrp48 TRIBE. NIHMS767511-supplement-Figure_S3.pdf (41K) GUID:?D1476B70-87F8-4BFE-B6D9-F073BA3BCF7F Figure S4: Figure S4, related to Figures 4 and ?and7.7. Mouse homologs of cell dFMR1-TRIBE targets are enriched for higher CLIP rankings Mouse homologs of dFMR1-TRIBE targets Apixaban inhibition in S2 cells are enriched for higher CLIP ranking targets of FMRP (A). Similarly, the mouse homologs of neuronal dFMR1 TRIBE targets are enriched for higher CLIP rankings. (B). Approximately 50% of the fly homologs of robust mouse brain FMRP CLIP targets are also TRIBE targets in excitatory fly neurons (Cha) (C). Mouse FMRP CLIP data are from Darnell et al, 2011. NIHMS767511-supplement-Figure_S4.pdf (51K) GUID:?EAA13F8D-1519-4517-9DE8-F4F62F3202CF Figure S5: Figure S5, related to Figures 2, ?,3,3, ?,44 and ?and5.5. Sequencing depth and number of TRIBE editing sites detected The amount of editing and enhancing sites recognized in S2 cells expressing Hrp48 TRIBE at different sequencing depths (million mapped reads), utilizing different insurance coverage thresholds for the recognition of an editing and enhancing sites (A). The greater stringent threshold of 20 reads was used throughout this scholarly study. The amount of editing sites recognized in S2 cells expressing different RBP TRIBE constructs (B) The amount of sites for confirmed sequencing depth differs by RBP (data for 20 read threshold editing sites are demonstrated). NIHMS767511-supplement-Figure_S5.pdf (31K) GUID:?66F114F9-C322-4808-9916-3D40B7D94B98 Figure S6: Figure S6, linked to Figure 5. TRIBE identifies intronic Rabbit polyclonal to VPS26 focuses on in mRNA A) NonA. A modest upsurge in A to G Apixaban inhibition editing occasions can be seen in mRNA upon induction from the fusion proteins in S2 cells (data also demonstrated, along with nascent RNA in Shape 4a). B) Editing percentage can be correlated at provided sites between natural repeats (R2 = 0.88). C) Classification of editing and enhancing Apixaban inhibition sites predicated on refseq annotation. Many intronic sites.