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Charpentier, EmmanuelleORCID iD iconorcid.org/0000-0002-0254-0778
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Publications (10 of 71) Show all publications
Tsatsaronis, J. A., Franch-Arroyo, S., Resch, U. & Charpentier, E. (2018). Extracellular Vesicle RNA: A Universal Mediator of Microbial Communication?. Trends in Microbiology, 26(5), 401-410
Open this publication in new window or tab >>Extracellular Vesicle RNA: A Universal Mediator of Microbial Communication?
2018 (English)In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 26, no 5, p. 401-410Article, review/survey (Refereed) Published
Abstract [en]

Both extracellular RNAs and extracellular vesicles (EVs) have recently garnered attention as novel mediators of intercellular communication in eukaryotes and prokaryotes alike. EVs not only permit export of RNA, but also facilitate delivery and trans-kingdom exchange of these and other biomolecules, for instance between microbes and their hosts. In this Opinion article, we propose that EV-mediated export of RNA represents a universal mechanism for interkingdom and intrakingdom communication that is conserved among bacterial, archaeal, and eukaryotic microbes. We speculate how microbes might use EV RNA to influence target cell gene expression or manipulate host immune responses.

Place, publisher, year, edition, pages
ELSEVIER SCI LTD, 2018
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-150717 (URN)10.1016/j.tim.2018.02.009 (DOI)000430327400004 ()29548832 (PubMedID)2-s2.0-85043450331 (Scopus ID)
Available from: 2018-08-16 Created: 2018-08-16 Last updated: 2018-08-16Bibliographically approved
Lécrivain, A.-L., Le Rhun, A., Renault, T. T., Ahmed-Begrich, R., Hahnke, K. & Charpentier, E. (2018). In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes. Proceedings of the National Academy of Sciences of the United States of America, 115(46), 11814-11819
Open this publication in new window or tab >>In vivo 3′-to-5′ exoribonuclease targetomes of Streptococcus pyogenes
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 46, p. 11814-11819Article in journal (Refereed) Published
Abstract [en]

mRNA decay plays an essential role in the control of gene expression in bacteria. Exoribonucleases (exoRNases), which trim transcripts starting from the 5′ or 3′ end, are particularly important to fully degrade unwanted transcripts and renew the pool of nucleotides available in the cell. While recent techniques have allowed genome-wide identification of ribonuclease (RNase) targets in bacteria in vivo, none of the 3′-to-5′ exoRNase targetomes (i.e., global processing sites) have been studied so far. Here, we report the targetomes of YhaM, polynucleotide phosphorylase (PNPase), and RNase R of the human pathogen Streptococcus pyogenes. We determined that YhaM is an unspecific enzyme that trims a few nucleotides and targets the majority of transcript ends, generated either by transcription termination or by endonucleolytic activity. The molecular determinants for YhaM-limited processivity are yet to be deciphered. We showed that PNPase clears the cell from mRNA decay fragments produced by endoribonucleases (endoRNases) and is the major 3′-to-5′ exoRNase for RNA turnover in S. pyogenes. In particular, PNPase is responsible for the degradation of regulatory elements from 5′ untranslated regions. However, we observed little RNase R activity in standard culture conditions. Overall, our study sheds light on the very distinct features of S. pyogenes 3′-to-5′ exoRNases.

Place, publisher, year, edition, pages
National Academy of Sciences, 2018
Keywords
3′-to-5′ exoRNase, 5′-end sequencing, 3′-end sequencing, Streptococcus pyogenes, RNA degradation
National Category
Microbiology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-153170 (URN)10.1073/pnas.1809663115 (DOI)000449934400052 ()30381461 (PubMedID)
Available from: 2018-11-08 Created: 2018-11-08 Last updated: 2018-12-17Bibliographically approved
Lécrivain, A.-L., Broglia, L., Renault, T., Hahnke, K., Ahmed-Begrich, R., Le Rhun, A. & Charpentier, E. (2018). Interplay between 3′-to-5′ exoRNases and RNase Y in Streptococcus pyogenes.
Open this publication in new window or tab >>Interplay between 3′-to-5′ exoRNases and RNase Y in Streptococcus pyogenes
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2018 (English)Manuscript (preprint) (Other academic)
National Category
Biochemistry and Molecular Biology Microbiology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-153182 (URN)
Available from: 2018-11-08 Created: 2018-11-08 Last updated: 2018-11-08
Labuhn, M., Adams, F. F., Ng, M., Knoess, S., Schambach, A., Charpentier, E. M., . . . Heckl, D. (2018). Refined sgRNA efficacy prediction improves large- and small-scale CRISPR-Cas9 applications. Nucleic Acids Research, 46(3), 1375-1385
Open this publication in new window or tab >>Refined sgRNA efficacy prediction improves large- and small-scale CRISPR-Cas9 applications
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2018 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 46, no 3, p. 1375-1385Article in journal (Refereed) Published
Abstract [en]

Genome editing with the CRISPR-Cas9 system has enabled unprecedented efficacy for reverse genetics and gene correction approaches. While off-target effects have been successfully tackled, the effort to eliminate variability in sgRNA efficacies-which affect experimental sensitivity-is in its infancy. To address this issue, studies have analyzed the molecular features of highly active sgRNAs, but independent cross-validation is lacking. Utilizing fluorescent reporter knock-out assays with verification at selected endogenous loci, we experimentally quantified the target efficacies of 430 sgRNAs. Based on this dataset we tested the predictive value of five recently-established prediction algorithms. Our analysis revealed a moderate correlation (r = 0.04 to r = 0.20) between the predicted and measured activity of the sgRNAs, and modest concordance between the different algorithms. We uncovered a strong PAM-distal GC-content-dependent activity, which enabled the exclusion of inactive sgRNAs. By deriving nine additional predictive features we generated a linear model-based discrete system for the efficient selection (r = 0.4) of effective sgRNAs (CRISPRater). We proved our algorithms' efficacy on small and large external datasets, and provide a versatile combined on-and off-target sgRNA scanning platform. Altogether, our study highlights current issues and efforts in sgRNA efficacy prediction, and provides an easily-applicable discrete system for selecting efficient sgRNAs.

National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-145587 (URN)10.1093/nar/gkx1268 (DOI)000425294400034 ()29267886 (PubMedID)
Available from: 2018-03-20 Created: 2018-03-20 Last updated: 2018-06-09Bibliographically approved
Broglia, L., Materne, S., Lecrivain, A.-L., Hahnke, K., Le Rhun, A. & Charpentier, E. (2018). RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B. RNA Biology, 15(10), 1336-1347
Open this publication in new window or tab >>RNase Y-mediated regulation of the streptococcal pyrogenic exotoxin B
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2018 (English)In: RNA Biology, ISSN 1547-6286, E-ISSN 1555-8584, Vol. 15, no 10, p. 1336-1347Article in journal (Refereed) Published
Abstract [en]

Endoribonuclease Y (RNase Y) is a crucial regulator of virulence in Gram-positive bacteria. In the human pathogen Streptococcus pyogenes, RNase Y is required for the expression of the major secreted virulence factor streptococcal pyrogenic exotoxin B (SpeB), but the mechanism involved in this regulation remains elusive. Here, we demonstrate that the 5′ untranslated region of speB mRNA is processed by several RNases including RNase Y. In particular, we identify two RNase Y cleavage sites located downstream of a guanosine (G) residue. To assess whether this nucleotide is required for RNase Y activity in vivo, we mutated it and demonstrate that the presence of this G residue is essential for the processing of the speB mRNA 5′ UTR by RNase Y. Although RNase Y directly targets and processes speB, we show that RNase Y-mediated regulation of speB expression occurs primarily at the transcriptional level and independently of the processing in the speB mRNA 5′ UTR. To conclude, we demonstrate for the first time that RNase Y processing of an mRNA target requires the presence of a G. We also provide new insights on the speB 5′ UTR and on the role of RNase Y in speB regulation.

Place, publisher, year, edition, pages
Taylor & Francis, 2018
Keywords
Streptococcus pyogenes, speB, RNase Y, virulence, 5' untranslated region, transcriptional regulation
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-154094 (URN)10.1080/15476286.2018.1532253 (DOI)000450608900008 ()30290721 (PubMedID)
Funder
Göran Gustafsson Foundation for Research in Natural Sciences and MedicineThe Kempe FoundationsSwedish Research Council, K2013-57X-21436-04-3
Available from: 2018-12-11 Created: 2018-12-11 Last updated: 2018-12-11Bibliographically approved
Charpentier, E. (2018). Spotlight on... Emmanuelle Charpentier. FEMS Microbiology Letters, 365(4), Article ID fnx271.
Open this publication in new window or tab >>Spotlight on... Emmanuelle Charpentier
2018 (English)In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 365, no 4, article id fnx271Article in journal, Editorial material (Other academic) Published
Place, publisher, year, edition, pages
Oxford University Press, 2018
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-147365 (URN)10.1093/femsle/fnx271 (DOI)000429769700001 ()
Available from: 2018-05-03 Created: 2018-05-03 Last updated: 2018-06-09Bibliographically approved
Hille, F., Richter, H., Wong, S. P., Bratovic, M., Ressel, S. & Charpentier, E. (2018). The Biology of CRISPR-Cas: Backward and Forward. Cell, 172(6), 1239-1259
Open this publication in new window or tab >>The Biology of CRISPR-Cas: Backward and Forward
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2018 (English)In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 172, no 6, p. 1239-1259Article, review/survey (Refereed) Published
Abstract [en]

In bacteria and archaea, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system against phages and other foreign genetic elements. Here, we review the biology of the diverse CRISPR-Cas systems and the major progress achieved in recent years in understanding the underlying mechanisms of the three stages of CRISPR-Cas immunity: adaptation, crRNA biogenesis, and interference. The ecology and regulation of CRISPR-Cas in the context of phage infection, the roles of these systems beyond immunity, and the open questions that propel the field forward are also discussed.

Place, publisher, year, edition, pages
Elsevier, 2018
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-146443 (URN)10.1016/j.cell.2017.11.032 (DOI)000427482100026 ()29522745 (PubMedID)
Available from: 2018-05-04 Created: 2018-05-04 Last updated: 2018-06-09Bibliographically approved
Reimer, J., Knoess, S., Labuhn, M., Charpentier, E. M., Goehring, G., Schlegelberger, B., . . . Heckl, D. (2017). CRISPR-Cas9-induced t(11;19)/MLL-ENL translocations initiate leukemia in human hematopoietic progenitor cells in vivo. Haematologica, 102(9), 1558-1566
Open this publication in new window or tab >>CRISPR-Cas9-induced t(11;19)/MLL-ENL translocations initiate leukemia in human hematopoietic progenitor cells in vivo
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2017 (English)In: Haematologica, ISSN 0390-6078, E-ISSN 1592-8721, Vol. 102, no 9, p. 1558-1566Article in journal (Refereed) Published
Abstract [en]

Chromosomal translocations that generate oncogenic fusion proteins are causative for most pediatric leukemias and frequently affect the MLL/ KMT2A gene. In vivo modeling of bona fide chromosomal translocations in human hematopoietic stem and progenitor cells is challenging but essential to determine their actual leukemogenic potential. We therefore developed an advanced lentiviral CRISPR-Cas9 vector that efficiently transduced human CD34(+) hematopoietic stem and progenitor cells and induced the t(11; 19)/MLL-ENL translocation. Leveraging this system, we could demonstrate that hematopoietic stem and progenitor cells harboring the translocation showed only a transient clonal growth advantage in vitro. In contrast, t(11; 19)/MLL-ENL-harboring CD34(+) hematopoietic stem and progenitor cells not only showed longterm engraftment in primary immunodeficient recipients, but t(11; 19)/ MLL-ENL also served as a first hit to initiate a monocytic leukemia-like disease. Interestingly, secondary recipients developed acute lymphoblastic leukemia with incomplete penetrance. These findings indicate that environmental cues not only contribute to the disease phenotype, but also to t(11; 19)/ MLL-ENL-mediated oncogenic transformation itself. Thus, by investigating the true chromosomal t(11; 19) rearrangement in its natural genomic context, our study emphasizes the importance of environmental cues for the pathogenesis of pediatric leukemias, opening an avenue for novel treatment options.

National Category
Hematology
Identifiers
urn:nbn:se:umu:diva-140947 (URN)10.3324/haematol.2017.164046 (DOI)000408743300024 ()
Available from: 2017-11-13 Created: 2017-11-13 Last updated: 2018-06-09Bibliographically approved
Elsholz, A. K. W., Birk, M. S., Charpentier, E. & Turgay, K. (2017). Functional Diversity of AAA plus Protease Complexes in Bacillus subtilis. Frontiers in Molecular Biosciences, 4, Article ID 44.
Open this publication in new window or tab >>Functional Diversity of AAA plus Protease Complexes in Bacillus subtilis
2017 (English)In: Frontiers in Molecular Biosciences, ISSN 2296-889X, Vol. 4, article id 44Article, review/survey (Refereed) Published
Abstract [en]

Here, we review the diverse roles and functions of AAA+ protease complexes in protein homeostasis, control of stress response and cellular development pathways by regulatory and general proteolysis in the Gram-positive model organism Bacillus subtilis. We discuss in detail the intricate involvement of AAA+ protein complexes in controlling sporulation, the heat shock response and the role of adaptor proteins in these processes. The investigation of these protein complexes and their adaptor proteins has revealed their relevance for Gram-positive pathogens and their potential as targets for new antibiotics.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2017
Keywords
AAA plus protease complexes, Hsp100/Clp proteins, Bacillus subtilis, protein quality control, chaperones, regulatory proteolysis, McsB, adaptor proteins
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-157321 (URN)10.3389/fmolb.2017.00044 (DOI)000455311400009 ()28748186 (PubMedID)2-s2.0-85039775261 (Scopus ID)
Funder
Göran Gustafsson Foundation for Research in Natural Sciences and MedicineGerman Research Foundation (DFG)
Available from: 2019-03-14 Created: 2019-03-14 Last updated: 2019-03-14Bibliographically approved
Hurwitz, J. L., Jones, B. G., Charpentier, E. & Woodland, D. L. (2017). Hypothesis: RNA and DNA Viral Sequence Integration into the Mammalian Host Genome Supports Long-Term B Cell and T Cell Adaptive Immunity. Viral immunology, 30(9), 628-632
Open this publication in new window or tab >>Hypothesis: RNA and DNA Viral Sequence Integration into the Mammalian Host Genome Supports Long-Term B Cell and T Cell Adaptive Immunity
2017 (English)In: Viral immunology, ISSN 0882-8245, E-ISSN 1557-8976, Vol. 30, no 9, p. 628-632Article in journal, Editorial material (Other academic) Published
Abstract [en]

Viral sequence integration into the mammalian genome has long been perceived as a health risk. In some cases, integration translates to chronic viral infection, and in other instances, oncogenic gene mutations occur. However, research also shows that animal cells can benefit from integrated viral sequences (e.g., to support host cell development or to silence foreign invaders). Here we propose that, comparable with the clustered regularly interspaced short palindromic repeats that provide bacteria with adaptive immunity against invasive bacteriophages, animal cells may co-opt integrated viral sequences to support immune memory. We hypothesize that host cells express viral peptides from open reading frames in integrated sequences to boost adaptive B cell and T cell responses long after replicating viruses are cleared. In support of this hypothesis, we examine previous literature describing (1) viruses that infect acutely (e.g., vaccinia viruses and orthomyxoviruses) followed by unexplained, long-term persistence of viral nucleotide sequences, viral peptides, and virus-specific adaptive immunity, (2) the high frequency of endogenous viral genetic elements found in animal genomes, and (3) mechanisms with which animal host machinery supports foreign sequence integration.

Place, publisher, year, edition, pages
MARY ANN LIEBERT, INC, 2017
Keywords
viral sequence integration, CRISPR, hypothesis
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-142262 (URN)10.1089/vim.2017.0099 (DOI)000414394200002 ()29028182 (PubMedID)
Available from: 2017-12-06 Created: 2017-12-06 Last updated: 2018-06-09Bibliographically approved
Projects
RNA and Infection Biology: Small regulatory RNA molecules in the human pathogen Group A streptococcus [2009-03829_VR]; Umeå UniversityCRISPR/CAS: AN ADAPTIVE IMMUNE SYSTEM AGAINST GENOME INVADERS [2011-05752_VR]; Umeå UniversityRNA-INTERACTING PROTEINS: FUNCTIONS AND MODES OF ACTION IN THE HUMAN PATHOGEN STREPTOCOCCUS PYOGENES [2012-01903_VR]; Umeå University
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-0254-0778

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