The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis

The high confidence editing sites identified by the bioinformatics pipeline are listed on the first sheet of the excel document (RNA-seq Identified Sites). The chromosome number (Column A) and coordinate in ce11 reference genome (Column B) are given for each predicted editing site. The approximate editing percentage (Column C) based on the frequency of reads with guanosine at that coordinate within unique reads as well as the number of unique reads covering that position (Column D) is listed. The predicted editing site was assigned (described in detail in the methods section) to a genic region (Column E) and a gene (Column F and G). A list of editing sites identified using Sanger sequencing editing assays from mRNAs identified by the bioinformatics pipeline are listed on the second sheet of the excel document (Sanger-seq Verification). Gene-specific reverse transcription followed by PCR amplification and Sanger sequencing was used to examine editing events in the indicated genes (Column A). The chromosome number (Column B) and coordinate in ce11 reference genome (Column C) are given for each adenosine to inosine detected as well as the percent editing as determined using the RNA-seq data (Column D). The methods used to detect the A-to-I change was listed (Column D and E) as well as confirmation (yes), decline (no), or inability to accurately determine (ND) the presence of A-to-I editing at a given adenosine. A list of all genes and the novel genes identified by the pipeline as edited are listed on the third sheet of the excel document (Edited Genes). All edited genes (Column A and B) were aligned with a document containing all identified editing sites in C. elegans from numerous published RNA-seq data sets (Supplementary file 3 [Goldstein et al., 2017]). Novel edited genes identified in this study are listed (Column C and D). Genes identified as edited by SAILOR were queried using Wormbase to identify genes that regulate chemotaxis and/or locomotion and these genes are listed on sheet four of the excel document (Locomotion and Chemotaxis Genes). The wormbase IDs and gene names (Column A and B) are listed for genes identified as regulators of this biological process. The genes were then aligned with an unpublished RNA-seq data set of RNAs bound by ADR-1 (Column C).

Genes whose transcripts exhibited ≥2 fold change in expression between wild-type and adr-2(-) neural cells are listed. Upregulated (Sheet 1) and downregulated (Sheet 2) genes are listed by gene name (Column A) and Wormbase ID (Column B). The base Mean, or mean expression of each gene normalized to sequencing depth for all samples is listed (Column C), as well as the fold change in expression observed when comparing the wild-type to adr-2(-) (Column D) and the adjusted p-value from DESeq2 (Column E). Genes whose expression was examined by qRT-PCR are marked with yellow and listed as verified (Column F). The four edited genes are listed as Edited (Column G).