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Data from: Antibody production relies on the tRNA inosine wobble modification to meet biased codon demand

Cite this dataset

Giguère, Sophie et al. (2023). Data from: Antibody production relies on the tRNA inosine wobble modification to meet biased codon demand [Dataset]. Dryad. https://doi.org/10.5061/dryad.f4qrfj723

Abstract

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.

README: 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 > 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.

Methods

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.

Funding

National Institutes of Health, Award: UM1 AI144462

Bill & Melinda Gates Foundation, Award: INV046626

Bill & Melinda Gates Foundation, Award: INV009585

Ragon Institute of MGH, MIT and Harvard

Herchel Smith Fellowship

The Collaboration for AIDS Vaccine Discovery CAVD, Award: INV009585

The Collaboration for AIDS Vaccine Discovery CAVD, Award: INV046626