Characterizing nascent readthrough transcripts in human cells
- 1University of Michigan
Abstract
Termination of transcription by RNA polymerase II (RNAPII) is critical to appropriately define transcriptome and proteome identity; yet mechanisms of termination regulation are incompletely understood. Current models suggest critical roles for the exonuclease XRN2, which is posited to "torpedo" out RNAPII after degrading uncapped and RNAPII-tethered nascent transcripts and posit an allosteric model wherein elongating RNAPII loses its processivity downstream of the transcription end site (TES) via unknown mechanisms. Here, we used nascent RNA Bru-seq to interrogate transcription termination across 16 human cell lines of distinct lineages, as part of the ENCODE 4 project, to identify key regulatory modes. We find that > 75% of protein-coding genes engage in readthrough transcription under homeostatic conditions. Exposing human cells to oxidative stress or hyperosmotic conditions or splicing inhibitors cause an increase in readthrough transcripts globally. Using an auxin-inducible degradation approach we find that depletion of BRD4, MED14 or XRN2 increases the extent and pervasiveness of readthrough transcripts while depletion of SUPT16H results in shorter readthrough transcripts. Our study provides a comprehensive view of homeostatic readthrough transcripts in human cells and delineates key components regulating transcription termination.
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BibTeX
@misc{mcshane2026characterizing,
title = {{Characterizing nascent readthrough transcripts in human cells}},
author = {A. McShane and I. V. Narayanan and M. T. Paulsen and H. Blinkiewicz and M. Ashaka and B. Magnuson and K. Bedi and N. Yang and J. Prasad and J. N. Dudley and S. Pitchiaya and E. Seiden and P. Grohar and E. L. Aiden and T. E. Wilson and M. Ljungman},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.01.763429},
url = {https://www.biorxiv.org/content/10.64898/2026.11.01.763429v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Characterizing nascent readthrough transcripts in human cells
AU - A. McShane
AU - I. V. Narayanan
AU - M. T. Paulsen
AU - H. Blinkiewicz
AU - M. Ashaka
AU - B. Magnuson
AU - K. Bedi
AU - N. Yang
AU - J. Prasad
AU - J. N. Dudley
AU - S. Pitchiaya
AU - E. Seiden
AU - P. Grohar
AU - E. L. Aiden
AU - T. E. Wilson
AU - M. Ljungman
PY - 2026
DA - 2026/11/01
PB - bioRxiv
DO - 10.64898/2026.11.01.763429
UR - https://www.biorxiv.org/content/10.64898/2026.11.01.763429v1
AB - Termination of transcription by RNA polymerase II (RNAPII) is critical to appropriately define transcriptome and proteome identity; yet mechanisms of termination regulation are incompletely understood. Current models suggest critical roles for the exonuclease XRN2, which is posited to "torpedo" out RNAPII after degrading uncapped and RNAPII-tethered nascent transcripts and posit an allosteric model wherein elongating RNAPII loses its processivity downstream of the transcription end site (TES) via unknown mechanisms. Here, we used nascent RNA Bru-seq to interrogate transcription termination across 16 human cell lines of distinct lineages, as part of the ENCODE 4 project, to identify key regulatory modes. We find that > 75% of protein-coding genes engage in readthrough transcription under homeostatic conditions. Exposing human cells to oxidative stress or hyperosmotic conditions or splicing inhibitors cause an increase in readthrough transcripts globally. Using an auxin-inducible degradation approach we find that depletion of BRD4, MED14 or XRN2 increases the extent and pervasiveness of readthrough transcripts while depletion of SUPT16H results in shorter readthrough transcripts. Our study provides a comprehensive view of homeostatic readthrough transcripts in human cells and delineates key components regulating transcription termination.
ER -