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Scientists at the HIRI develop RNA-centric approaches to unravel the mechanisms associated with infectious diseases.

Dr Redmond Smyth

Our research and approach

The research group led by Redmond Smyth investigated how RNA viruses use RNA structure during their replication and evolution. They sought to exploit knowledge of RNA genomic architecture to advance the development of highly targeted RNA-based therapeutics.

RNA viruses are an important class of emerging infectious diseases. Currently, the majority of antivirals and pharmaceuticals function at protein level. However, RNA structures within viral genomes interact with cellular/viral proteins and nucleic acids to provide a novel surface for pharmaceutical intervention. A detailed understanding of these processes is necessary for the development of novel RNA-based therapeutics.

Redmond Smyth’s group studied RNA-based mechanisms of RNA virus replication and evolution. Their work employed a combination of molecular virology, RNA biochemistry and mathematical modelling. They sought to identify essential RNA structures as new antiviral targets, and to understand how RNA structure regulates viral evolution for better vaccine and pandemic preparedness.

Their investigations focused on single molecule and single virion analyses using high-throughput, genome-wide chemical probing technologies and mutation based functional screens. They also developed new technologies including RNA-RNA-seq, single molecule RNA structural probing and sequencing coupled microscopy. The group’s overarching goal was to exploit knowledge of RNA virus genome architecture to advance RNA-based therapies.

Team members

Redmond Smyth

Dr Redmond Smyth

Group Leader

Research projects

Publications

2024

Isoform-specific RNA structure determination using Nano-DMS-MaP

Gribling-Burrer AS, Bohn P, Smyth RP (2024)

Nature Protocols 19 (6): 1835-1865

NEAT1 promotes genome stability via m6A methylation-dependent regulation of CHD4

Mamontova V, Trifault B, Gribling-Burrer AS, Bohn P, Boten L, Preckwinkel P, Gallant P, Solvie D, Ade CP, Papadopoulos D, …, Smyth RP, Burger K (2024)

Genes & Development 38 (17-20): 915-930

Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network

Sung PY, Phelan JE, Luo D, Kulasegaran-Shylini R, Bohn P, Smyth RP, Roy P (2024)P., Roy P (2024)

Nucleic Acids Research 52 (14): 8500-8514

Sequencing accuracy and systematic errors of nanopore direct RNA sequencing

Liu-Wei W, van der Toorn W, Bohn P, Hölzer M, Smyth RP, von Kleist M (2024)

BMC Genomics 25 (1): 528

2023

Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function

Pekarek L, Zimmer MM, Gribling-Burrer AS, Buck S, Smyth RP, Caliskan N (2023)

Nucleic Acids Research 51 (2): 728–743

SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9

Schmidt N, Ganskih S, Wei Y, Gabel A, Zielinski S, Keshishian H, Lareau CA, Zimmermann L, Makroczyova J, Pearce C, …, Erhard F, Munschauer M (2023)

Cell 186 (22): 4834-4850.e23

Advanced fluorescence microscopy in respiratory virus cell biology

Xie E, Ahmad S, Smyth RP, Sieben C (2023)

Advances in Virus Research 116: 123-172

Sequential disruption of SPLASH-identified vRNA-vRNA interactions challenges their role in influenza A virus genome packaging

Jakob C, Lovate GL, Desirò D, Gießler L, Smyth RP, Marquet R, Lamkiewicz K, Marz M, Schwemmle M, Bolte H (2023)

Nucleic Acids Research 51 (12): 6479-6494

Nano-DMS-MaP allows isoform-specific RNA structure determination

Bohn P, Gribling-Burrer AS, Ambi UB, Smyth RP (2023)

Nature Methods 20 (6): 849-859

2022

Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging

Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP (2022)

Nature Structural & Molecular Biology 29 (4): 306-319

2021

The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

Zimmer MM, Kibe A, Rand U, Pekarek L, Ye L, Buck S, Smyth RP, Cicin-Sain L, Caliskan N (2021)

Nature Communications 12 (1): 7193

RNA Structures and Their Role in Selective Genome Packaging

Ye L, Ambi UB, Olguin-Nava M, Gribling-Burrer AS, Ahmad S, Bohn P, Weber MM, Smyth RP (2021)

Viruses 13 (9): 1788

2019

The evolution of RNA structural probing methods: From gels to next-generation sequencing

Mailler E, Paillart J, Marquet R, Smyth RP, Vivet-Boudou V (2019)

Wiley Interdisciplinary Reviews: RNA 10 (2): e1518

2018

In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

Smyth RP, Smith MR, Jousset A, Despons L, Laumond G, Decoville T, Cattenoz P, Moog C, Jossinet F, Mougel M, …, Kleist M, Marquet R (2018)

Nucleic Acids Research 46 (9): e57

RNA Structure - A Neglected Puppet Master for the Evolution of Virus and Host Immunity

Smyth RP, Negroni M, Lever AM, Mak J, Kenyon JC (2018)

Frontiers in Immunology 9: 2097

Structural and Functional Motifs in Influenza Virus RNAs

Ferhadian D, Contrant M, Printz-Schweigert A, Smyth RP, Paillart J, Marquet R (2018)

Frontiers in Microbiology 9: 559

2017

HIV-1 Pr55Gag binds genomic and spliced RNAs with different affinity and stoichiometry

Bernacchi S, Abd El-Wahab EW, Dubois N, Hijnen M, Smyth RP, Mak J, Marquet R, Paillart J (2017)

RNA Biology 14 (1): 90-103

2016

HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells

Cromer D, Schlub TE, Smyth RP, Grimm AJ, Chopra A, Mallal S, Davenport MP, Mak J (2016)

Viruses 8 (4): 118

A step forward understanding HIV-1 diversity

Smyth RP, Negroni M (2016)

Retrovirology 13: 27

The Life-Cycle of the HIV-1 Gag-RNA Complex

Mailler E, Bernacchi S, Marquet R, Paillart J, Vivet-Boudou V, Smyth RP (2016)

Viruses 8 (9): E248

MIMEAnTo: profiling functional RNA in mutational interference mapping experiments

Smith MR, Smyth RP, Marquet R, Kleist M (2016)

Bioinformatics 32 (21): 3369-3370

2015

Mutational interference mapping experiment (MIME) for studying RNA structure and function

Smyth RP, Despons L, Huili G, Bernacchi S, Hijnen M, Mak J, Jossinet F, Weixi L, Paillart J, Kleist M, Marquet R (2015)

Nature Methods 12 (9): 866-72

Evaluation of anti-HIV-1 mutagenic nucleoside analogues

Vivet-Boudou V, Isel C, El Safadi Y, Smyth RP, Laumond G, Moog C, Paillart J, Marquet R (2015)

The Journal of Biological Chemistry 290 (1): 371-83

Properties of HIV-1 associated cholesterol in addition to raft formation are important for virus infection

Hawkes D, Jones KL, Smyth RP, Pereira CF, Bittman R, Jaworowski A, Mak J (2015)

Virus Research 210: 18-21

2014

Specific recognition of the HIV-1 genomic RNA by the Gag precursor

Abd El-Wahab EW, Smyth RP, Mailler E, Bernacchi S, Vivet-Boudou V, Hijnen M, Jossinet F, Mak J, Paillart J, Marquet R (2014)

Nature Communications 5: 4304

Identifying recombination hot spots in the HIV-1 genome

Smyth RP, Schlub TE, Grimm AJ, Waugh C, Ellenberg P, Chopra A, Mallal S, Cromer D, Mak J, Davenport MP (2014)

Journal of Virology 88 (5): 2891-902

Fifteen to twenty percent of HIV substitution mutations are associated with recombination

Schlub TE, Grimm AJ, Smyth RP, Cromer D, Chopra A, Mallal S, Venturi V, Waugh C, Mak J, Davenport MP (2014)

Journal of Virology 88 (7): 3837-49

2013

Improved quantification of HIV-1-infected CD4+ T cells using an optimised method of intracellular HIV-1 gag p24 antigen detection

Yang H, Yorke E, Hancock G, Clutton G, Sande N, Angus B, Smyth RP, Mak J, Dorrell L (2013)

Journal of Immunological Methods 391 (1-2): 174-8

Intracellular Dynamics of HIV Infection

Petravic J, Ellenberg P, Chan M, Paukovics G, Smyth RP, Mak J, Davenport MP (2013)

Journal of Virology 88 (2): 1113-24

A functional sequence-specific interaction between influenza A virus genomic RNA segments

Gavazzi C, Yver M, Isel C, Smyth RP, Rosa-Calatrava M, Lina B, Moulès V, Marquet R (2013)

PNAS 110 (41): 16604-9

2012

The Origin of Genetic Diversity in HIV-1

Smyth RP, Davenport MP, Mak J (2012)

Virus Research 169 (2): 415-29

2011

8-Modified-2'-deoxyadenosine analogues induce delayed polymerization arrest during HIV-1 reverse transcription

Vivet-Boudou V, Isel C, Sleiman M, Smyth RP, Ben Gaied N, Barhoum P, Laumond G, Bec G, Götte M, Mak J, …, Burger A, Marquet R (2011)

PLOS One 6 (11): e27456

Early events of HIV-1 infection: can signaling be the next therapeutic target?

Jones KL, Smyth RP, Pereira CF, Cameron PU, Lewin SR, Jaworowski A, Mak J (2011)

Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology 6 (2): 269-83

Labeling of multiple HIV-1 proteins with the biarsenical-tetracysteine system

Pereira CF, Ellenberg PC, Jones KL, Fernandez TL, Smyth RP, Hawkes DJ, Hijnen M, Vivet-Boudou V, Marquet R, Johnson I, Mak J (2011)

PLOS One 6 (2): e17016

2010

Accurately measuring recombination between closely related HIV-1 genomes

Schlub TE, Smyth RP, Grimm AJ, Mak J, Davenport MP (2010)

PLOS Computational Biology 6 (4): e1000766

Reducing chimera formation during PCR amplification to ensure accurate genotyping

Smyth RP, Schlub TE, Grimm A, Venturi V, Chopra A, Mallal S, Davenport MP, Mak J (2010)

Gene 469 (1-2): 45-51

2009

The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA

Keating CP, Hill MK, Hawkes DJ, Smyth RP, Isel C, Le S, Palmenberg AC, Marshall JA, Marquet R, Nabel GJ, Mak J (2009)

Nucleic Acids Research 37 (3): 945-56