1 Available resources

EpiTxDb.Hs.hg38 contains post-transcriptional RNA modifications from RMBase v2.0 (Xuan et al. 2017), tRNAdb (Jühling et al. 2009) and snoRNAdb (Lestrade and Weber 2006) and can be accessed through the functions EpiTxDb.Hs.hg38.tRNAdb(), EpiTxDb.Hs.hg38.snoRNAdb() and EpiTxDb.Hs.hg38.RMBase()

library(EpiTxDb.Hs.hg38)
etdb <- EpiTxDb.Hs.hg38.tRNAdb()
## snapshotDate(): 2020-03-31
## downloading 1 resources
## retrieving 1 resource
## loading from cache
etdb
## EpiTxDb object:
## # Db type: EpiTxDb
## # Supporting package: EpiTxDb
## # Data source: tRNAdb
## # Organism: Homo sapiens
## # Genome: hg38
## # Coordinates: per Transcript
## # Checked against sequence: Yes
## # Nb of modifications: 1843
## # Db created by: EpiTxDb package from Bioconductor
## # Creation time: 2020-02-26 10:35:24 +0100 (Wed, 26 Feb 2020)
## # EpiTxDb version at creation time: 0.99.0
## # RSQLite version at creation time: 2.2.0
## # DBSCHEMAVERSION: 1.0

Modification information can be accessed through the typical function for an EpiTxDb object, for example modifications():

modifications(etdb)
## GRanges object with 1843 ranges and 3 metadata columns:
##                   seqnames    ranges strand |    mod_id    mod_type
##                      <Rle> <IRanges>  <Rle> | <integer> <character>
##      [1] tRNA-Ala-AGC-11-1        10      + |         1         m2G
##      [2] tRNA-Ala-AGC-15-1        10      + |         2         m2G
##      [3]  tRNA-Ala-AGC-8-1        10      + |         3         m2G
##      [4]  tRNA-Ala-AGC-8-2        10      + |         4         m2G
##      [5] tRNA-Ala-AGC-11-1        17      + |         5           D
##      ...               ...       ...    ... .       ...         ...
##   [1839]   ENST00000386347        50      + |      2546        f5Cm
##   [1840]   ENST00000386347        56      + |      2547         m5U
##   [1841]   ENST00000386347        57      + |      2548           Y
##   [1842]   ENST00000386347        60      + |      2549         m1A
##   [1843]   ENST00000387449        23      + |      2550         t6A
##                          mod_name
##                       <character>
##      [1] m2G_10_tRNA-Ala-AGC-11-1
##      [2] m2G_10_tRNA-Ala-AGC-15-1
##      [3]  m2G_10_tRNA-Ala-AGC-8-1
##      [4]  m2G_10_tRNA-Ala-AGC-8-2
##      [5]   D_17_tRNA-Ala-AGC-11-1
##      ...                      ...
##   [1839]  f5Cm_50_ENST00000386347
##   [1840]   m5U_56_ENST00000386347
##   [1841]     Y_57_ENST00000386347
##   [1842]   m1A_60_ENST00000386347
##   [1843]   t6A_23_ENST00000387449
##   -------
##   seqinfo: 160 sequences from hg38 genome; no seqlengths

For a more detailed overview and explanation of the functionality of the EpiTxDb class, have a look at the EpiTxDb package.

2 Chain files for rRNA

The rRNA sequence annotation for ribosomal RNA has undergone some clarification processes in recent years. Therefore some of the annotation of modification refer to an older rRNA annotation.

In order to help using and updating older information, a chain file was generated for use with liftOver, which allows conversion of hg19 coordinates to hg38 coordinates and back. The resources can be loaded via chain.rRNA.hg19Tohg38() and chain.rRNA.hg38Tohg19().

cf <- chain.rRNA.hg19Tohg38()
## snapshotDate(): 2020-03-31
## downloading 1 resources
## retrieving 1 resource
## loading from cache
## require("rtracklayer")
cf
## Chain of length 3
## names(3): 5.8S 18S 28S

The following example illustrate a use case, in which data from the Modomics (“MODOMICS: A Database of Rna Modification Pathways. 2017 Update” 2018) database will be used. The sequence data currently stored, is the hg19 version. First we load the sequence as ModRNAStringSet.

library(rtracklayer)
library(Modstrings)
files <- c(system.file("extdata","Modomics.LSU.Hs.txt",
                       package = "EpiTxDb.Hs.hg38"),
           system.file("extdata","Modomics.SSU.Hs.txt",
                       package = "EpiTxDb.Hs.hg38"))
seq <- lapply(files,readLines,encoding = "UTF-8")
seq <- unlist(seq)
names <- seq[seq.int(1L,6L,2L)]
seq <- seq[seq.int(2L,6L,2L)]
seq <- ModRNAStringSet(sanitizeFromModomics(gsub("-","",seq)))
names(seq) <- c("28S","5.8S","18S")
mod <- separate(seq)

The position for the one m7G and two m6A are of for the current rRNA sequences. This is also the case for the other modifications.

mod[mod$mod == "m7G" | mod$mod == "m6A"]
## GRanges object with 3 ranges and 1 metadata column:
##       seqnames    ranges strand |         mod
##          <Rle> <IRanges>  <Rle> | <character>
##   [1]      28S      4180      + |         m6A
##   [2]      18S      1640      + |         m7G
##   [3]      18S      1833      + |         m6A
##   -------
##   seqinfo: 3 sequences from an unspecified genome; no seqlengths

Using the chain file we can liftOver the coordinates, which matches the expected coordinates.

mod_new <- unlist(liftOver(mod,cf))
mod_new[mod_new$mod == "m7G" | mod_new$mod == "m6A"]
## GRanges object with 3 ranges and 1 metadata column:
##       seqnames    ranges strand |         mod
##          <Rle> <IRanges>  <Rle> | <character>
##   [1]      28S      4220      + |         m6A
##   [2]      18S      1639      + |         m7G
##   [3]      18S      1832      + |         m6A
##   -------
##   seqinfo: 3 sequences from an unspecified genome; no seqlengths

In addition, the ModRNAStringSet object can be update with the current sequence.

rna <- readDNAStringSet(system.file("extdata","rRNA_hg38.fasta",
                                    package = "EpiTxDb.Hs.hg38")) 
seqtype(rna) <- "RNA"
seq_new <- combineIntoModstrings(rna,mod_new)
seq_new
##   A ModRNAStringSet instance of length 3
##     width seq                                               names               
## [1]  5070 CGCGACCUCAGAUCAGACGUGGC...AGCCCUCGACACAAGGGUUUGUC 28S
## [2]  1869 UACCUGGUUGAUCCUGCCAGUAG...GUGζζCCUGCGGAAGGAUCAUUA 18S
## [3]   157 CGACUCUUAGCGGJGGAUCACUC...CUACGCCUGUCUGAGCGUCGCUU 5.8S

3 Sessioninfo

sessionInfo()
## R Under development (unstable) (2020-04-01 r78128)
## Platform: x86_64-apple-darwin17.7.0 (64-bit)
## Running under: macOS High Sierra 10.13.6
## 
## Matrix products: default
## BLAS:   /Users/ka36530_ca/R-stuff/bin/R-devel/lib/libRblas.dylib
## LAPACK: /Users/ka36530_ca/R-stuff/bin/R-devel/lib/libRlapack.dylib
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats4    parallel  stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] rtracklayer_1.47.0     GenomicRanges_1.39.3   GenomeInfoDb_1.23.16  
##  [4] EpiTxDb.Hs.hg38_0.99.3 EpiTxDb_0.99.5         Modstrings_1.3.12     
##  [7] Biostrings_2.55.7      XVector_0.27.2         AnnotationDbi_1.49.1  
## [10] IRanges_2.21.8         S4Vectors_0.25.14      Biobase_2.47.3        
## [13] AnnotationHub_2.19.9   BiocFileCache_1.11.4   dbplyr_1.4.2          
## [16] BiocGenerics_0.33.3    BiocStyle_2.15.6      
## 
## loaded via a namespace (and not attached):
##  [1] matrixStats_0.56.0            bitops_1.0-6                 
##  [3] assertive.models_0.0-2        bit64_0.9-7                  
##  [5] progress_1.2.2                httr_1.4.1                   
##  [7] assertive.datetimes_0.0-2     tools_4.1.0                  
##  [9] R6_2.4.1                      colorspace_1.4-1             
## [11] DBI_1.1.0                     assertive.data_0.0-3         
## [13] assertive.reflection_0.0-4    tidyselect_1.0.0             
## [15] prettyunits_1.1.1             bit_1.1-15.2                 
## [17] curl_4.3                      compiler_4.1.0               
## [19] cli_2.0.2                     assertive.properties_0.0-4   
## [21] xml2_1.3.0                    DelayedArray_0.13.8          
## [23] assertive.files_0.0-2         bookdown_0.18                
## [25] scales_1.1.0                  tRNA_1.5.2                   
## [27] askpass_1.1                   rappdirs_0.3.1               
## [29] stringr_1.4.0                 digest_0.6.25                
## [31] Rsamtools_2.3.7               rmarkdown_2.1                
## [33] assertive.numbers_0.0-2       pkgconfig_2.0.3              
## [35] htmltools_0.4.0               fastmap_1.0.1                
## [37] rlang_0.4.5                   RSQLite_2.2.0                
## [39] assertive_0.3-5               shiny_1.4.0.2                
## [41] BiocParallel_1.21.2           dplyr_0.8.5                  
## [43] RCurl_1.98-1.1                magrittr_1.5                 
## [45] GenomeInfoDbData_1.2.2        Matrix_1.2-18                
## [47] munsell_0.5.0                 Rcpp_1.0.4                   
## [49] fansi_0.4.1                   lifecycle_0.2.0              
## [51] stringi_1.4.6                 assertive.base_0.0-7         
## [53] yaml_2.2.1                    SummarizedExperiment_1.17.5  
## [55] zlibbioc_1.33.1               grid_4.1.0                   
## [57] blob_1.2.1                    promises_1.1.0               
## [59] crayon_1.3.4                  lattice_0.20-41              
## [61] tRNAdbImport_1.5.6            assertive.code_0.0-3         
## [63] GenomicFeatures_1.39.7        hms_0.5.3                    
## [65] knitr_1.28                    pillar_1.4.3                 
## [67] assertive.sets_0.0-3          codetools_0.2-16             
## [69] biomaRt_2.43.4                XML_3.99-0.3                 
## [71] glue_1.3.2                    BiocVersion_3.11.1           
## [73] Structstrings_1.3.5           evaluate_0.14                
## [75] BiocManager_1.30.10           vctrs_0.2.4                  
## [77] httpuv_1.5.2                  gtable_0.3.0                 
## [79] openssl_1.4.1                 purrr_0.3.3                  
## [81] assertive.strings_0.0-3       assertthat_0.2.1             
## [83] ggplot2_3.3.0                 xfun_0.12                    
## [85] mime_0.9                      xtable_1.8-4                 
## [87] assertive.types_0.0-3         later_1.0.0                  
## [89] assertive.data.uk_0.0-2       tibble_3.0.0                 
## [91] GenomicAlignments_1.23.2      memoise_1.1.0                
## [93] assertive.matrices_0.0-2      ellipsis_0.3.0               
## [95] assertive.data.us_0.0-2       interactiveDisplayBase_1.25.0

References

Jühling, Frank, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler, and Joern Pütz. 2009. “TRNAdb 2009: Compilation of tRNA Sequences and tRNA Genes.” Nucleic Acids Research 37: D159–D162. https://doi.org/10.1093/nar/gkn772.

Lestrade, Laurent, and Michel J. Weber. 2006. “snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs.” Nucleic Acids Research 34 (January): D158–D162. https://doi.org/10.1093/nar/gkj002.

“MODOMICS: A Database of Rna Modification Pathways. 2017 Update.” 2018. Nucleic Acids Research 46 (D1): D303–D307. https://doi.org/10.1093/nar/gkx1030.

Xuan, Jia-Jia, Wen-Ju Sun, Peng-Hui Lin, Ke-Ren Zhou, Shun Liu, Ling-Ling Zheng, Liang-Hu Qu, and Jian-Hua Yang. 2017. “RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data.” Nucleic Acids Research 46 (D1): D327–D334. https://doi.org/10.1093/nar/gkx934.