Welcome to HIRI
Welcome to the preliminary website of HIRI - the Helmholtz Institute for RNA-based Infection Research!
The Helmholtz Institute for RNA-based Infection Research (HIRI) was established in May 2017 as a partnership between the Helmholtz Centre for Infection Research (HZI) and the Julius-Maximilian-University of Würzburg (JMU). HIRI is the first research institution worldwide bridging the fields of RNA biology and infectious disease.
GRADUATE PROGRAM RNA & INFECTION
Application is open until October 30th, 2018
APPLY NOW
Our mission
Rising antimicrobial resistance, chronic infections, and (re-) emerging pathogens are among the major challenges facing humanity. RNA is increasingly understood to contribute to key regulatory and sensory processes in the cell, but the role of RNA in infection biology remains understudied. HIRI will combine interdisciplinary expertise with cutting-edge research infrastructure to exploit the vast potential of RNA as a diagnostic molecule, target, and drug to combat infectious diseases.
Our Team
Prof. Jörg Vogel
Department
RNA Biology of Bacterial Infections
The first HIRI department was established in June 2017 by HIRI’s founding director, Professor Jörg Vogel. The aim of his department is to develop novel procedures to understand the RNA world of bacterial pathogens and use RNA-centric approaches to target pathogens and manipulate the microbiota.
Prof. Chase Beisel
Research group
RNA Synthetic Biology
The lab of Prof. Chase Beisel (formerly North Carolina State University, USA) will investigate and harness the functional diversity of CRISPR-Cas immune systems for the development of new foundational technologies. They aim to develop a new generation of CRISPR technologies that can be employed to better understand, diagnose, and combat human infections.
Dr. Antoine-Emmanuel Saliba
Research group
Single-cell Analysis
The research of Dr. Antoine-Emmanuel Saliba (former maître de conférences, Université Strasbourg, France) and his group is dedicated to using single- cell RNA-seq approaches to study heterogeneity in host responses to infections and its impact on disease outcome.
Dr. Neva Caliskan
Research group
Recoding Mechanisms in Infections
The research of Dr. Neva Caliskan’s group aims to identify and characterize the mechanisms and regulatory implications of translational recoding in RNA viruses and pathogenic bacteria.
Dr. Lars Barquist
Research group
Integrative Informatics for Infection Biology
The group of Dr. Lars Barquist will develop systems approaches to RNA and infection, using modern visualization, data science, and machine learning technologies to integrate large-scale functional genomics data.
Jun. Prof. Alexander Westermann
Research group
Host-pathogen-microbiota interactions
The group of Alexander Westermann focuses on investigating molecular RNA-based mechanisms that allow infecting pathogens to outcompete the resident microbiota. Their research centers on the identification and functional characterization of noncoding RNA molecules in pathogens, microbiota members and the host, to identify those RNAs that may serve as biomarkers for diagnostics or as therapeutic targets.
Jun. Prof. Redmond Smyth
Research group
Genome Architecture and Evolution of RNA Viruses (GARV)
The genomes of RNA viruses are not just passive carriers of protein coding information, but active participants in the viral infection process through the action of non-coding RNA. We study the structure and function of viral non-coding RNA, with the goal of harnessing the resulting knowledge in the design of next generation RNA-based therapies.
Selected publications from HIRI scientists
Selected experimental work
Neonatally imprinted mesenteric lymph node stromal cell subsets modulate dendritic cell properties
Nature Communications In press
Müller SM, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba AE, Sebra RP, Siegel TN
Histone variants restrict chromatin organization and antigenic variation in trypanosomes
Nature In press
Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM (2018)
CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9.
Molecular Cell 69(5):893-905.e7
Available at: https://www.sciencedirect.com/science/article/pii/S1097276518300911?via%3Dihub
Holmqvist E, Li L, Bischler T, Barquist L, Vogel J (2018)
Global maps of ProQ binding in vivo reveal target recognition via RNA structure and stability control at mRNA 3' ends
Molecular Cell 70(5):971-982.e6
Available at: https://www.sciencedirect.com/science/article/pii/S1097276518303137?via%3Dihub
Marshall R, Maxwell CS, Collins SP, Jacobsen T, Luo ML, Begemann MB, Gray BN, January E, Singer A, He Y, Beisel CL, Noireaux V (2018)
Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System.
Molecular Cell 69: 113–125
Available at: http://www.cell.com/molecular-cell/fulltext/S1097-2765(17)30935-8
Caliskan N, Wohlgemuth I, Korniy N, Pearson M, Peske F, Rodnina MV (2017)
Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA.
Molecular Cell 66: 558–567.e4
Available at: http://dx.doi.org/10.1016/j.molcel.2017.04.023
Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Śmiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J (2017)
In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways.
Molecular Cell 65: 39–51
Available at: http://www.cell.com/molecular-cell/pdf/S1097-2765(16)30710-9.pdf
Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann AJ, Gunn JS, Vogel J (2017)
RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE.
PNAS 114: 201620772
Available at: http://www.pnas.org/lookup/doi/10.1073/pnas.1620772114
Smirnov A, Wang C, Drewry LL, Vogel J (2017)
Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA.
EMBO Journal 36: 1029–1045
Available at: http://emboj.embopress.org/lookup/doi/10.15252/embj.201696127
Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J (2016)
Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions.
Nature 529: 496–501
Available at: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006033
Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DAC, Schulte LN, Helaine S, Vogel J (2016)
Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella.
Nature Microbiology 2: 1–8
Available at: https://www.nature.com/articles/nmicrobiol2016206
Smirnov A, Förstner KU, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J (2016)
Grad-seq guides the discovery of ProQ as a major small RNA-binding protein.
PNAS 113: 11591–11596
Available at: http://www.pnas.org/lookup/doi/10.1073/pnas.1609981113
Chao Y, Vogel J (2016)
A 3’ UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response.
Molecular Cell 61: 352–363
Available at: https://www.sciencedirect.com/science/article/pii/S1097276515010059
Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016)
Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo.
EMBO Journal 35: 991–1011
Available at: http://emboj.embopress.org/lookup/doi/10.15252/embj.201593360
Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL (2016)
Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems.
Molecular Cell 62: 137–147
Available at: http://dx.doi.org/10.1016/j.molcel.2016.02.031
Miyakoshi M, Chao Y, Vogel J (2015)
Crosstalk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA.
EMBO Journal 34:1478-92
Available at: http://emboj.embopress.org/content/embojnl/34/11/1478.full.pdf
Luo ML, Mullis AS, Leenay RT, Beisel CL (2015)
Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression
Nucleic Acids Research 43(1):674-81
Available at: https://academic.oup.com/nar/article/43/1/674/2903426
Papenfort K, Espinosa E, Casadesús J, Vogel J (2015)
Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella.
PNAS 112: E4772–E4781
Available at: http://www.pnas.org/lookup/doi/10.1073/pnas.1507825112
Caliskan N, Katunin VI, Belardinelli R, Peske F, Rodnina MV (2014)
Programmed -1 frameshifting by kinetic partitioning during impeded translocation.
Cell 157: 1619–1631
Available at: http://dx.doi.org/10.1016/j.cell.2014.04.041
Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J (2013)
Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis.
Cell 153: 426–437
Available at: https://doi.org/10.1016/j.cell.2013.03.003
Papenfort K, Podkaminski D, Hinton JCD, Vogel J (2012)
The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair.
PNAS 109: E757–E764
Available at: http://www.pnas.org/cgi/doi/10.1073/pnas.1119414109
Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011)
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III.
Nature 471: 602–607
Available at: https://www.nature.com/articles/nature09886
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J (2010)
The primary transcriptome of the major human pathogen Helicobacter pylori.
Nature 464: 250–255
Available at: https://www.nature.com/articles/nature08756
Selected Review Articles
Holmqvist E, Vogel J (2018)
RNA-binding proteins in bacteria
Nature Reviews Microbiology doi: 10.1038/s41579-018-0049-5
Available at: https://www.nature.com/articles/s41579-018-0049-5
Hör J, Gorski SA, Vogel J (2018)
Bacterial RNA Biology on a Genome Scale.
Molecular Cell doi: 10.1016/j.molcel.2017.12.023
Available at: http://www.cell.com/molecular-cell/fulltext/S1097-2765(17)30980-2
Gorski SA, Vogel J, Doudna JA (2017)
RNA-based Recognition and targeting: Sowing the seeds of specificity.
Nature Reviews Molecular Cell Biology 18:215-228
Available at: https://www.nature.com/articles/nrm.2016.174
Westermann AJ, Barquist L & Vogel J (2017)
Resolving host–pathogen interactions by dual RNA-seq.
PLoS Pathogens 13: 1–19
Available at: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1006033
Caliskan N, Peske F, Rodnina MV (2015)
Changed in translation: MRNA recoding by -1 programmed ribosomal frameshifting.
Trends in Biochemical Sciences 40: 265–274
Available at: https://www.sciencedirect.com/science/article/pii/S0968000415000444?via%3Dihub
Barquist L, Vogel J (2015)
Accelerating discovery and functional analysis of small RNAs with new technologies.
Annual Review of Genetics 49:367-94
Available at: https://www.annualreviews.org/doi/full/10.1146/annurev-genet-112414-054804?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed
Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)
Single-cell RNA-seq: advances and future challenges.
Nucleic Acids Research 42:8845-60
Available at: https://academic.oup.com/nar/article/42/14/8845/1269819
Westermann AJ, Gorski SA, Vogel J (2012)
Dual RNA-seq of pathogen and host.
Nature Reviews Microbiology 10:618-30
Available at: http://dx.doi.org/10.1038/nrmicro2852
Vogel J, Luisi BF (2011)
Hfq and its constellation of RNA.
Nature Reviews Microbiology 9:578-89
Available at: https://www.nature.com/articles/nrmicro2615
OUR RNA SEMINAR
-NEXT SEMESTER STARTING OCT 16th-
Our invited speakers
- Fabian Theis (Helmholtz Center Munich)
- Peter Nielsen (University of Copenhagen, Denmark)
- Renate König (Paul Ehrlich Institute, Langen)
- Demián Cazalla (University of Utah, USA)
- Blake Wiedenheft (Montana State University, USA)
- Tom Cooper (Baylor College of Medicine, USA)
- Susan Carpenter (UC Santa Cruz, USA)
- Ciarán Condon (CNRS, Paris, France)
- Thorsten Stafforst (University Tübingen)
- Noam Stern-Ginossar (Weizmann Institute of Science, Israel)
We would like to welcome you
to the seminar and the following scientific exchange.
HIRI is hiring
Your chance to become part of the future of RNA & Infection! We are currently seeking talented and motivated scientific and non-scientific staff at all levels to advance our mission to investigate the role of RNA in infection.
PhD Positions and Postdoctoral Fellowships
PhD Bacterial RNA Biology in the Gut Microbiota
Graduate Program
RNA is our world
„Advances in RNA biology continue to highlight the importance of this central biomolecule. At HIRI, we aim to make the next generation of discoveries and translate them into the future of disease detection and treatment.“
- Prof Jörg Vogel -
Contact
With easy connections to major German transport hubs like the Frankfurt and Nuremberg International Airports, Würzburg is readily accessible by car, train, and airplane.
Visit us in beautiful Würzburg and enjoy the Mainfranken area with its special mix of culture, world heritage, and wine festivals.
Address
Building D15
97080 Würzburg