DOI: 10.5061/dryad.f4qrfj723
title: Data from: Antibody production relies on the tRNA inosine wobble modification to meet biased codon demand

description: Antibodies are produced at high rates to provide immunoprotection, which
 puts pressure on the B cell translational machinery. Here, we identified a
 pattern of codon usage conserved across antibody genes. One feature
 thereof is the hyperutilization of codons which lack genome-encoded
 Watson–Crick tRNAs, instead relying on the post-transcriptional tRNA
 modification inosine (I34), which expands the decoding capacity of
 specific tRNAs through wobbling. Antibody-secreting cells had increased
 I34 levels and were more reliant on I34 for protein production than naive
 B cells. Furthermore, antibody I34-dependent codon usage may influence B
 cell passage through regulatory checkpoints. Our work elucidates the
 interface between the tRNA pool and protein production in the immune
 system and has implications for the design and selection of antibodies for
 vaccines and therapeutics.
description: tRNA sequences from J558, MPC11, WEHI231, and Bcl clone 5b1b. See
 Methods and Materials, sections on "RNA extraction" and
 "tRNA sequencing". The raw, unpaired sequence FASTQ files are
 provided.
description: # Antibody production relies on the tRNA inosine wobble modification to
 meet biased codon demand tRNA sequencing of murine B cell lines ##
 Description of the data and file structure tRNA sequencing (2 independent
 sequencing runs) Raw sequencing files from small RNA extracts processed
 using the AQRNAseq pipeline. RNA extracted from two PC-like murine cell
 lines (J558, MPC11) and two NBC-like murine cell lines (WEHI231, Bcl clone
 5b1b) Samples are numbered as follows: | run\_date | cell | type |
 file\_tag | | :-------- | :------ | :--- | :------------------ | |
 22-04-05 | bcl5b1b | nbc | 220405Bat\_D22-4079 | | 22-04-05 | bcl5b1b |
 nbc | 220405Bat\_D22-4080 | | 22-04-05 | j558 | pc | 220405Bat\_D22-4081 |
 | 22-04-05 | j558 | pc | 220405Bat\_D22-4082 | | 22-04-05 | j558 | pc |
 220405Bat\_D22-4083 | | 22-04-05 | j558 | pc | 220405Bat\_D22-4084 | |
 22-04-05 | j558 | pc | 220405Bat\_D22-4085 | | 22-04-05 | j558 | pc |
 220405Bat\_D22-4086 | | 22-04-05 | mpc11 | pc | 220405Bat\_D22-4089 | |
 22-04-05 | mpc11 | pc | 220405Bat\_D22-4090 | | 22-04-05 | mpc11 | pc |
 220405Bat\_D22-4091 | | 22-04-05 | mpc11 | pc | 220405Bat\_D22-4092 | |
 22-04-05 | wehi231 | nbc | 220405Bat\_D22-4094 | | 22-04-05 | wehi231 |
 nbc | 220405Bat\_D22-4095 | | 22-04-05 | wehi231 | nbc |
 220405Bat\_D22-4096 | | 22-04-05 | wehi231 | nbc | 220405Bat\_D22-4097 | |
 22-04-05 | wehi231 | nbc | 220405Bat\_D22-4098 | | 21-08-25 | j558 | pc |
 210825Bat\_D21-7956 | | 21-08-25 | j558 | pc | 210825Bat\_D21-7957 | |
 21-08-25 | j558 | pc | 210825Bat\_D21-7958 | | 21-08-25 | mpc11 | pc |
 210825Bat\_D21-7959 | | 21-08-25 | mpc11 | pc | 210825Bat\_D21-7960 | |
 21-08-25 | mpc11 | pc | 210825Bat\_D21-7961 | | 21-08-25 | wehi231 | pc |
 210825Bat\_D21-7962 | | 21-08-25 | wehi231 | pc | 210825Bat\_D21-7963 | |
 21-08-25 | wehi231 | pc | 210825Bat\_D21-7964 | Sequencing files are
 unpaired, the \_1 or \_2 following the file tag number represents the
 pairing info. ## Code/Software As described in the "Analysis of tRNA
 sequences by the AQRNA-seq pipeline" section of Methods and
 Materials: Broadly, sequences underwent quality control, then were
 assembled using PEAR v0.9.6 and trimmed with fastxtoolkit. Assembled
 sequences were aligned to a reference library composed of the GtRNAdb Mus
 musculus (GRCm38/mm10) high confidence tRNA gene set with Bowtie2.
 Parameters were as follows: bowtie2 -x db-tRNAgenome -k 100
 --very-sensitive --ignore-quals --np 5 --reorder -p 20 -U seq.fa -f &gt;
 seq_bt2.fa For identification of wobble position mismatches, reads were
 aligned to the high confidence tRNA gene set using Python:
 pairwise2.align.globalms(trna, read, 2, 1, -8, -0.5,
 penalize_end_gaps=False) using the Bio.pairwise2 module. The highest
 scoring alignment was chosen. Differential expression was calculated using
 DESeq2.