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Run-on sequencing reveals nascent transcriptomics of the human microbiome

View ORCID ProfileAlbert C. Vill, Edward J. Rice, View ORCID ProfileIwijn De Vlaminck, View ORCID ProfileCharles G. Danko, View ORCID ProfileIlana L. Brito
doi: https://doi.org/10.1101/2022.04.22.489220
Albert C. Vill
1Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
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Edward J. Rice
2Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY
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Iwijn De Vlaminck
3Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY
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Charles G. Danko
2Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY
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Ilana L. Brito
3Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY
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  • ORCID record for Ilana L. Brito
  • For correspondence: ibrito@cornell.edu
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ABSTRACT

Precise regulation of transcription initiation and elongation enables bacteria to control cellular responses to environmental stimuli. RNAseq is the most common tool for measuring the transcriptional output of bacteria, comprising predominantly mature transcripts. To gain further insight into transcriptional dynamics, it is necessary to discriminate actively transcribed loci from those represented in the total RNA pool. One solution is to capture RNA polymerase (RNAP) in the act of transcription, but current methods are restricted to culturable and genetically tractable organisms. Here, we apply precision run-on sequencing (PRO-seq) to profile nascent transcription, a method amenable to diverse species. We find that PRO-seq is well-suited to profile small, structured, or post-transcriptionally modified RNAs, which are often excluded from RNAseq libraries. When PRO-seq is applied to the human microbiome, we identify taxon-specific RNAP pause motifs. We also uncover concurrent transcription and cleavage of guide RNAs and tRNA fragments at active CRISPR and tRNA loci. We demonstrate the specific utility of PRO-seq as a tool for exploring transcriptional dynamics in diverse microbial communities.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 22, 2022.
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Run-on sequencing reveals nascent transcriptomics of the human microbiome
Albert C. Vill, Edward J. Rice, Iwijn De Vlaminck, Charles G. Danko, Ilana L. Brito
bioRxiv 2022.04.22.489220; doi: https://doi.org/10.1101/2022.04.22.489220
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Run-on sequencing reveals nascent transcriptomics of the human microbiome
Albert C. Vill, Edward J. Rice, Iwijn De Vlaminck, Charles G. Danko, Ilana L. Brito
bioRxiv 2022.04.22.489220; doi: https://doi.org/10.1101/2022.04.22.489220

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