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Distinct sequence patterns in the active postmortem transcriptome

Peter A Noble, View ORCID ProfileAlexander E. Pozhitkov
doi: https://doi.org/10.1101/293589
Peter A Noble
1Department of Periodontics, University of Washington, Box 357444, Seattle, WA USA 98195
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  • For correspondence: panoble2017@gmail.com
Alexander E. Pozhitkov
2City of Hope, Information Sciences - Beckman Research Institute, 4920 Rivergrade Rd., Irwindale, CA 91706.
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ABSTRACT

Our previous study found more than 500 transcripts significantly increased in abundance in the zebrafish and mouse several hours to days postmortem relative to live controls. The current literature suggests that most mRNAs are post-transcriptionally regulated in stressful conditions, we rationalized that the postmortem transcripts must contain sequence features (3 to 9 mers) that are unique from those in the rest of the transcriptome – specifically, binding sites for proteins and/or non-coding RNAs involved in regulation. Our new study identified 5117 and 2245 over-represented sequence features in the mouse and zebrafish, respectively. Some of these features were disproportionately distributed along the transcripts with high densities in the 3-UTR region of the zebrafish (0.3 mers/nt) and the ORFs of the mouse (0.6 mers/nt). Yet, the highest density (2.3 mers/nt) occurred in the ORFs of 11 mouse transcripts that lacked UTRs. Our results suggest that these transcripts might serve as ‘molecular sponges’ that sequester RNA binding proteins and/or microRNAs, increasing the stability and gene expression of other transcripts. In addition, some features were identified as binding sites for Rbfox and Hud proteins that are also involved in increasing transcript stability and gene expression. Hence, our results are consistent with the hypothesis that transcripts involved in responding to extreme stress have sequence features that make them different from the rest of the transcriptome, which presumably has implications for post-transcriptional regulation in disease, starvation, and cancer.

UTR
untranslated regions
ORFs
open reading frames
OP
overabundant transcript pool
CP
control transcript pool
FP
false positive
RBP
RNA binding proteins
ncRNA
non-coding RNA
miRNA
microRNA
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted April 02, 2018.
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Distinct sequence patterns in the active postmortem transcriptome
Peter A Noble, Alexander E. Pozhitkov
bioRxiv 293589; doi: https://doi.org/10.1101/293589
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Distinct sequence patterns in the active postmortem transcriptome
Peter A Noble, Alexander E. Pozhitkov
bioRxiv 293589; doi: https://doi.org/10.1101/293589

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