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Landscape of RNA polyadenylation in E. coli
(CNRS FRE3630 (previously UPR9073) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France)
(CNRS FRE3630 (previously UPR9073) associated with University Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France)
KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). (Computational Biological Physics, CBP)
Aalto University, Finland . (Systems Biology Programme)
Vise andre og tillknytning
2016 (engelsk)Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Polyadenylation is involved in degradation and quality control of bacterial RNAs. We used a combination of 5’-tagRACE and RNA-seq to analyse the total RNA content from wild-type strain and from mutant deficient for poly(A)polymerase. We determined that 157 mRNAs were affected as well as non-coding transcripts, up- and downregulated in the mutant when compared to the wild-type strain. Antisense RNAs were also detected and differentially affected by polyadenylation.

Our results clearly reveal a correlation between the RNA folding energy and the requirement of polyadenylation to achieve the RNA decay. A new algorithm was developed to detect in both strains posttranscriptional modifications based on unmappable 3’-ends to analyse their position and composition. Therefore, any RNA 3'-end can be polyadenylated addressing them to the exoribonucleolytic machinery which is essential to degrade structured RNAs. Importantly, poly(A)polymerase was also upregulating the expression of genes related with the entire FliA regulon and numerous membrane transporters while downregulating the expression of the antigen 43 (flu), numerous sRNAs, antisense transcripts, REP sequences with the accumulation of numerous RNA fragments resulting from the processing of entire transcripts. Altogether we show here that polyadenylation has a broader spectrum of action than was suspected until now.

sted, utgiver, år, opplag, sider
Oxford University Press, 2016.
Emneord [en]
Polyadenylation, degradation, poly(A)polymerase, pcnB deficient mutant
HSV kategori
Forskningsprogram
Biologisk fysik
Identifikatorer
URN: urn:nbn:se:kth:diva-173328DOI: 10.1093/nar/gkw894ISI: 000397286600048Scopus ID: 2-s2.0-85018357344OAI: oai:DiVA.org:kth-173328DiVA, id: diva2:852512
Merknad

QC 20170119

Tilgjengelig fra: 2015-09-09 Laget: 2015-09-09 Sist oppdatert: 2018-01-11bibliografisk kontrollert
Inngår i avhandling
1. Data Analysis and Next Generation Sequencing : Applications in Microbiology.
Åpne denne publikasjonen i ny fane eller vindu >>Data Analysis and Next Generation Sequencing : Applications in Microbiology.
2015 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

Next Generation Sequencing (NGS) is a new technology that has revolutionized the way we study living organisms. Where previously only a few genes could be studied at a time through targeted direct probing, NGS offers the possibility to perform measurements for a whole genome at once. The drawback is that the amount of data generated in the process is large and extracting useful information from it requires new methods to process and analyze it.

The main contribution of this thesis is the development of a novel experimental method coined tagRNA-seq, combining 5’tagRACE, a previously developed technique, with RNA-sequencing technology. Briefly, tagRNA-seq makes it possible to identify the 5’ ends of RNAs in bacteria and directly probe for their type, primary or processed, by ligating short RNA sequences, the tags, to the beginnings of RNA molecules. We used the method to directly probe for transcription start and processing sites in two bacterial species, Escherichiacoli and Enterococcus faecalis. It was also used to study polyadenylation in E. coli, where the ability to identify processed RNA molecules proved to be useful to separate direct and indirect regulatory effects of this mechanism. We also demonstrate how data from tagRNA-seq experiments can be used to increase confidence on the discovery of anti-sense transcripts in bacteria. Analyses of RNA-seq data obtained in the context of these experiments revealed subtle artifacts in the coverage signal towards gene ends, that we were able to explain and quantify based Kolmogorov’s broken stick model. We also discovered evidences for circularization of a few RNA transcripts, both in our own data sets and publicly available data.

Designing the tags used in tagRNA-seq led us to the problem of words absent from a text. We focus on a particular subset of these, the minimal absent words (MAWs), and develop a theory providing a complete description of their size distribution in random text. We also show that MAWs in genomes from viruses and living organisms almost always exhibit a behavior different from random texts in the tail of the distribution, and that MAWs from this tail are closely related to sequences present in the genome that preferentially appear in regions with important regulatory functions.

Finally, and independently from tagRNA-seq, we propose a new approach to the problem of bacterial community reconstruction in metagenomic, based on techniques from compressed sensing. We provide a novel algorithm competing with state-of-the-art techniques in the field.

sted, utgiver, år, opplag, sider
Stockholm: KTH Royal Institute of Technology, 2015. s. xviii, 154
Serie
TRITA-CSC-A, ISSN 1653-5723 ; 2015:15
Emneord
RNA-seq, tagRNA-seq, primary and processed RNA, Enterococcus faecalis, Complex transcription, Metagenomics, 5'tagRACE, minimal absent words, compressed sensing, metagenomics, bacterial community reconstruction
HSV kategori
Forskningsprogram
Biologisk fysik
Identifikatorer
urn:nbn:se:kth:diva-173219 (URN)978-91-7595-699-2 (ISBN)
Disputas
2015-10-30, FA32, Roslagstullsbacken 21, Stockholm, 14:00 (engelsk)
Opponent
Veileder
Merknad

QC 20150930

Tilgjengelig fra: 2015-09-30 Laget: 2015-09-07 Sist oppdatert: 2018-01-11bibliografisk kontrollert

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