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Code for Atlas of mRNA translation and decay for bacteria

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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, https://doi.org/10.1093/nargab/lqaa099 


Code deposited also at 

https://github.com/lilit-nersisyan/Atlas-of-mRNA-translation-and-decay-for-bacteria/, release version 1.0.

Funding

Swedish Foundation’s Starting Grant (Ragnar Söderberg Foundation)

Wallenberg Academy Fellowship (KAW 2016.0123)

Impact of transcriptome complexity on gene expression dynamics

Swedish Research Council

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Genomic dissection of cellular plasticity and transcriptional memory in drug tolerance.

Swedish Research Council

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Development of a novel tool for diagnosis and prevention of antimicrobial resistance

Swedish Research Council

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Roles of snoRNAs in chromatin organization, gene expression and DNA repair

Swedish Research Council

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Ribosomal frameshifts as a novel mechanism to control RNA turnover in stress

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]

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Publisher

Karolinska Institute

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