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Code for Atlas of mRNA translation and decay for bacteria

posted on 2023-03-30, 12:10 authored by Lilit Nersisyan, Mengjun Wu, Susanne Huch, Vicent PelechanoVicent Pelechano

Regulation of mRNA stability is a central process in gene expression. Here, report an atlas of 5´ monophosphorylated mRNA decay intermediates (5´P) in 96 species. We use those data to demonstrate that in species with 5´-3´exonuclease activity, the exoribonuclease RNase J follows the trailing ribosome, producing an in vivo single-nucleotide toeprint of its 5´ position. While in other species, ribosome position alters endonucleolytic cleavage sites. Our work demonstrates the universal connection between RNA decay and translation and paves the way for use of metadegradome sequencing to investigate post-transcriptional regulation of unculturable species present and complex microbial communities.

Here we release the code for that work.

Data was analyzed using our fivepseq software.  Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq. Lilit Nersisyan, Maria Ropat & Vicent Pelechano. NAR Genomics and Bioinformatics, Volume 2, Issue 4, December 2020, lqaa099, 

Code deposited also at, release version 1.0.


Swedish Foundation’s Starting Grant (Ragnar Söderberg Foundation)

Wallenberg Academy Fellowship (KAW 2016.0123)

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Swedish Research Council

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European Commission

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Karolinska Institutet (SciLifeLab Fellowship, SFO and KI funds)

MoESCS RA Science Committee starting grant [21SCG-1F006]

RED postdoctoral Fellowship [2021, SciLifeLab-KI]



Karolinska Institute

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