1 Introduction

The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The package expects a GRanges object with certain columns as input. The following columns are a requirement: tRNA_length, tRNA_type, tRNA_anticodon, tRNA_seq, tRNA_str, tRNA_CCA.end.

2 Loading tRNA information

To work with the tRNA packages, tRNA information can be retrieved in a number of ways:

  1. A GRanges object can be constructed by hand containing the required colums (see above)
  2. a tRNAscan result file can be loaded using import.tRNAscanAsGRanges() from tRNAscanImport package
  3. selected tRNA information can be retrieved using import.tRNAdb() from tRNAdbImport package

For this vignette a predefined GRanges object is loaded.

library(tRNA)
data("gr", package = "tRNA", envir = environment())

3 tRNA sequences and structures

To retrieve the sequences for individual tRNA structure elements gettRNAstructureGRanges or gettRNAstructureSeqs can be used.

# just get the coordinates of the anticodonloop
gettRNAstructureGRanges(gr,
                        structure = "anticodonLoop")
## $anticodonLoop
## IRanges object with 299 ranges and 0 metadata columns:
##           start       end     width
##       <integer> <integer> <integer>
##   TGG        31        37         7
##   TGC        32        38         7
##   CAA        31        37         7
##   AGA        31        37         7
##   TAA        31        37         7
##   ...       ...       ...       ...
##   CAT        32        38         7
##   GAA        31        37         7
##   TTA        31        37         7
##   TAC        32        38         7
##   CAT        32        38         7
gettRNAstructureSeqs(gr,
                     joinFeatures = TRUE,
                     structure = "anticodonLoop")
## $anticodonLoop
##   A DNAStringSet instance of length 299
##       width seq                                          names               
##   [1]     7 TTTGGGT                                      TGG
##   [2]     7 CTTGCAA                                      TGC
##   [3]     7 TTCAAGC                                      CAA
##   [4]     7 TTAGAAA                                      AGA
##   [5]     7 CTTAAGA                                      TAA
##   ...   ... ...
## [295]     7 CTCATAA                                      CAT
## [296]     7 TTGAAGA                                      GAA
## [297]     7 TTTTAGT                                      TTA
## [298]     7 TTTACAC                                      TAC
## [299]     7 GTCATGA                                      CAT

In addition the sequences can be returned already joined to get a fully blank padded set of sequences. The boundaries of the individual structures is returned as metadata of the RNAStringSet object.

seqs <- gettRNAstructureSeqs(gr[1:10],
                             joinCompletely = TRUE)
seqs
##   A DNAStringSet instance of length 10
##      width seq
##  [1]    85 GGGCGTGTGGTC-TAGT-GGTAT-GATTCTCG...----GCCTGGGTTCAATTCCCAGCTCGCCCC
##  [2]    85 GGGCACATGGCGCAGTT-GGT-AGCGCGCTTC...----GCATCGGTTCGATTCCGGTTGCGTCCA
##  [3]    85 GGTTGTTTGGCC-GAGC-GGTAA-GGCGCCTG...-GATGCAAGAGTTCGAATCTCTTAGCAACCA
##  [4]    85 GGCAACTTGGCC-GAGT-GGTAA-GGCGAAAG...GCCCGCGCAGGTTCGAGTCCTGCAGTTGTCG
##  [5]    85 GGAGGGTTGGCC-GAGT-GGTAA-GGCGGCAG...GTCCGCGCGAGTTCGAACCTCGCATCCTTCA
##  [6]    85 GCGGATTTAGCTCAGTT-GGG-AGAGCGCCAG...----GCCTGTGTTCGATCCACAGAATTCGCA
##  [7]    85 GGTCTCTTGGCC-CAGTTGGTAA-GGCACCGT...----ACAGCGGTTCGATCCCGCTAGAGACCA
##  [8]    85 GCGCAAGTGGTTTAGT--GGT-AAAATCCAAC...-----CCCCGGTTCGATTCCGGGCTTGCGCA
##  [9]    85 GGCAACTTGGCC-GAGT-GGTAA-GGCGAAAG...GCCCGCGCAGGTTCGAGTCCTGCAGTTGTCG
## [10]    85 GCTTCTATGGCC-AAGTTGGTAA-GGCGCCAC...----ACATCGGTTCAAATCCGATTGGAAGCA
# getting the tRNA structure boundaries
metadata(seqs)[["tRNA_structures"]]
## IRanges object with 15 ranges and 0 metadata columns:
##                           start       end     width
##                       <integer> <integer> <integer>
##   acceptorStem.prime5         1         7         7
##               Dprime5         8         9         2
##          DStem.prime5        10        13         4
##                 Dloop        14        23        10
##          DStem.prime3        24        27         4
##                   ...       ...       ...       ...
##          TStem.prime5        61        65         5
##                 Tloop        66        72         7
##          TStem.prime3        73        77         5
##   acceptorStem.prime3        78        84         7
##         discriminator        85        85         1

Be aware, that gettRNAstructureGRanges and gettRNAstructureSeqs might not be working as expected, if the tRNA sequences in questions are armless or deviate a lot from the canonical tRNA model. It was thouroughly tested using human mitochondrial tRNA and other tRNAs missing certain features. However, for fringe cases this might not be the case. Please report these cases, if you find them, with an example.

4 Subsetting tRNA sequences

The structure information can be queried for subsetting using the function hasAccpeptorStem() as an example. Please have a look at?hasAccpeptorStem for all available subsetting functions.

gr[hasAcceptorStem(gr, unpaired = TRUE)]
# mismatches and bulged are subsets of unpaired
gr[hasAcceptorStem(gr, mismatches = TRUE)]
gr[hasAcceptorStem(gr, bulged = TRUE)]
# combination of different structure parameters
gr[hasAcceptorStem(gr, mismatches = TRUE) & 
     hasDloop(gr, length = 8)]

5 Visualization

To get an overview of tRNA feature and compare different datasets, gettRNAFeaturePlots can be used. It accepts a named GRangesList as input. Internally it will calculate a list of features values based on the functions mentioned above and the data contained in the mcols of the GRanges objects. The results can be retrieved without generating plots using gettRNASummary.

# load tRNA data for E. coli and H. sapiens
data("gr_eco", package = "tRNA", envir = environment())
data("gr_human", package = "tRNA", envir = environment())

# get summary plots
grl <- GRangesList(Sce = gr,
                   Hsa = gr_human,
                   Eco = gr_eco)
plots <- gettRNAFeaturePlots(grl)
plots$length