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Preprint

Transposon analysis from RNA sequencing

HD Hossein Davarinejad
YH Yi-Chun Huang
JC Jean-François Couture
YJ Yannick Jacob

Last updated date: Oct 7, 2026 Views: 25 Forks: 0

original An abbreviated version of this protocol was published in Science
The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication
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  1. Paired-end reads were filtered and trimmed using fastp (version 0.21.0 with default parameters) (1). Reads with quality inferior to 20 were removed from the data sets
  2. Data sets were aligned against the Arabidopsis thaliana genome (TAIR10) using STAR (version 2.7.2a) allowing two mismatches (--outFilterMismatchNmax 2).
  3. Transposable elements (TEs) were defined according to Panda et al, 2016 (2). We used their TE annotation for our analysis (https://github.com/KaushikPanda1/AthalianaTETranscripts)
  4. Using featureCounts (version 1.6.4), reads were count the paired-end fragments overlapping with TEs, reads mapping on several TE weighted.
  5. We then computed TPM using the read counts obtained from featureCounts for TEs.
  6. TEs were considered to be upregulated if:
    1. mutant lines showed a 2-fold up-regulation as compared to Col in both biological replicates,
    2. and had a value of TPM ≥ 5.
  7. Heatmap was made with R using pheatmap

 

  1. S. Chen, Y. Zhou, Y. Chen, J. Gu, fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884-i890 (2018).
  2. K. Panda et al., Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biol 17, 170 (2016).
Copyright: © 2026 The Author(s); This is an open-access article under the CC BY-NC license (https://creativecommons.org/licenses/by-nc/4.0/).
How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Davarinejad, H, Huang, Y, Couture, J and Jacob, Y(2026). Transposon analysis from RNA sequencing. Bio-protocol Preprint. bio-protocol.org/prep3008.
  2. Davarinejad, H., Huang, Y., Mermaz, B., LeBlanc, C., Poulet, A., Thomson, G., Joly, V., Muñoz, M., Arvanitis-Vigneault, A., Valsakumar, D., Villarino, G., Ross, A., Rotstein, B. H., Alarcon, E. I., Brunzelle, J. S., Voigt, P., Dong, J., Couture, J. and Jacob, Y.(2022). The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication. Science 375(6586). DOI: 10.1126/science.abm5320

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