Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

David, Julianne K.; Maden, Sean K.; Wood, M. C.; Thompson, Reid F.; Nellore, Abhinav

doi:10.1101/2022.03.11.484016

“…To test this hypothesis, we reanalyzed data from models of induced readthrough showing that readthrough is indeed a causal inducer for the expression of gene proximal transposons after hyperosmotic stress and viral infection ( Figure 5 ). Given the technical challenges of measuring readthrough and the unreliability of intron retention detection tools ( David et al, 2022 ), our results are likely underestimating the true magnitude of correlation between readthrough and transposon expression.…”

Section: Discussionmentioning

confidence: 90%

“…5). Given the technical challenges of measuring readthrough and the unreliability of intron retention detection tools (David et al 2022) our results are likely underestimating the true magnitude of correlation between readthrough and transposon expression.…”

Section: Readthrough Read-in and Transposonsmentioning

confidence: 88%

A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence

Pabis

¹

,

Barardo

²

,

Selvarajoo

³

et al. 2024

eLife

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Aging and senescence are characterized by pervasive transcriptional dysfunction, including increased expression of transposons and introns. Our aim was to elucidate mechanisms behind this increased expression. Most transposons are found within genes and introns, with a large minority being close to genes. This raises the possibility that transcriptional readthrough and intron retention are responsible for age-related changes in transposon expression rather than expression of autonomous transposons. To test this, we compiled public RNA-seq datasets from aged human fibroblasts, replicative and drug-induced senescence in human cells and RNA-seq from aging mice and senescent mouse cells. Indeed, our reanalysis revealed a correlation between transposons expression, intron retention and transcriptional readthrough across samples and within samples. Both intron retention and readthrough increased with aging or cellular senescence and these transcriptional defects were more pronounced in human samples as compared to those of mice. In support of a causal connection between readthrough and transposon expression, analysis of models showing induced transcriptional readthrough confirmed that they also show elevated transposon expression. Taken together, our data shows that elevated transposon reads during aging seen in various RNA-seq dataset are concomitant with multiple transcriptional defects. Intron retention and transcriptional readthrough are the most likely explanation for the expression of transposable elements that lack a functional promoter.

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“…Scripts to reproduce results contained here are available on GitHub under MIT license [ 77 ] and Zenodo [ 78 ].…”

Section: Acknowledgementsmentioning

confidence: 99%

“…Our work reused short- and long-read sequencing runs from a human whole blood sample (HX1; SRP065930 on SRA) [ 47 ] and a human induced pluripotent stem cell line sample (iPSC; SRP098984 on SRA) [ 48 ]. Data and figures generated by scripts are available on GitHub [ 77 ] and Zenodo [ 78 ].…”

mentioning

confidence: 99%

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

David

¹

,

Maden

²

,

Wood

³

et al. 2022

Self Cite

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Background There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but reliable detection is complicated by overlapping genes and transcripts as well as the presence of unprocessed or partially processed RNAs. Results We compared introns detected by 8 tools using short RNA-seq reads with introns observed in long RNA-seq reads from the same biological specimens. We found significant disagreement among tools (Fleiss’ $$\kappa = 0.113$$ κ = 0.113 ) such that 47.7% of all detected intron retentions were not called by more than one tool. We also observed poor performance of all tools, with none achieving an F1-score greater than 0.26, and qualitatively different behaviors between general-purpose alternative splicing detection tools and tools confined to retained intron detection. Conclusions Short-read tools detect intron retention with poor recall and precision, calling into question the completeness and validity of a large percentage of putatively retained introns called by commonly used methods.

show abstract

A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence

Pabis

¹

,

Barardo

²

,

Selvarajoo

³

et al. 2022

Preprint

View full text Add to dashboard Cite

Aging and senescence are characterized by pervasive transcriptional dysfunction, including increased expression of transposons and introns. Our aim was to elucidate mechanisms behind this increased expression. Most transposons are found within genes and introns, with a large minority being close to genes. This raises the possibility that transcriptional readthrough and intron retention are responsible for age-related changes in transposon expression rather than expression of autonomous transposons. To test this, we compiled public RNA-seq datasets from aged human fibroblasts, replicative and drug-induced senescence in human cells and RNA-seq from aging mice and senescent mouse cells. Indeed, our reanalysis revealed a correlation between transposons expression, intron retention and transcriptional readthrough across samples and within samples. Both intron retention and readthrough increased with aging or cellular senescence and these transcriptional defects were more pronounced in human samples as compared to those of mice. In support of a causal connection between readthrough and transposon expression, analysis of models showing induced transcriptional readthrough confirmed that they also show elevated transposon expression. Taken together, our data shows that elevated transposon reads during aging seen in various RNA-seq dataset are concomitant with multiple transcriptional defects. Intron retention and transcriptional readthrough are the most likely explanation for the expression of transposable elements that lack a functional promoter.

show abstract

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Cited by 7 publications

References 81 publications

A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence

A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

A concerted increase in readthrough and intron retention drives transposon expression during aging and senescence

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