About the Atkins recoding research group

Codes with THE code. Signals buried within the coding sequence of a minority of mRNAs in probably all organisms stimulate a non-standard decoding event utilized for gene expression purposes. The non-standard event can be local redefinition of codon meaning, a shift of reading register or the bypassing of a block of nucleotides present in the mature mRNA. The efficiency of some of the "recoding" events is responsive to the cellular level of a component, such as polyamines or release factor 2, and these events can serve an autoregulatory function. In others there is a fixed ratio of the product of standard decoding to that of the recoding product which serves some unique function.

We are investigating the occurrence, mechanisms involved and the functions of recoding. In addition to seeking basic understanding, we are also using the potential to manipulate recoding and related aspects of protein synthesis for societal beneficial purposes. In that regards we are seeking small molecule inhibitors of Foot and Mouth Disease propagation via targeting an unusual form of recoding required for viral expression but is not utilized by viral hosts.

In 2012 together with collaborators elsewhere we discovered that the pig pathogen Porcine Reproductive and Respiratory Syndrome Virus and other arteriviruses utilize a different form of recoding, programmed -2 frameshifting, that is a potentially useful antiviral target and are searching for other novel recoding-based targets.

We are also investigating the nature of the recoding required for synthesis in mammals of the selenium transport protein and starting to employ the reagents being generated for clinical purposes. We are keen to exploit knowledge gained from recoding and related studies for the amelioration of genetic disease, to optimize protein synthesis under particular over-expression situations. 

Current research projects in the Atkins recoding research group

Coming soon...

People in the Atkins recoding research group

Current group members

Research Fellow and Lab Manager

Yensi Flores

Gary Loughran

PhD Students

Pramod Bhatt

Apoorva Nathamuni Suresh

Kate Marie O'Connor

Past Lab Members

Dmitry Andreev

Janinah Baclaocos

Pavel V. Baranov 

Catherine Buckley

Arthur Coakley

Betty Ying-Wen Chung 

Kiera Deane

Andrew E. Firth

Elaine Forbes

Gordon Garde

Ivaylo P. Ivanov 

Audrey Michel

Ming-Yuan Chou (Brno, Czech Republic)

Martin Mullins, Vice President, Whitehead Institute, affiliated with MIT

Michael O’Connor

Michelle O’Connor

Niamh O'Flynn

Sinead O’Loughlin

Daniel J. O’Mahony, Partner,  Seroba Kernel Life Science (biotech venture capital) Molesworth Street, Dublin 2.

Christophe Penno

Michael Power

Paul Saffert

John Talty

Ioanna Tzani

Martina Yordanova

Selected publications

Full list of publications

For publications 1995 to date, please visit John F. Atkins publications on PubMed.

Selected publications 2008 -2018

Books

RNA Worlds: New Tools for Deep Exploration.

T.R. Cech, J.A. Steitz and J.F. Atkins. eds. 2019.
(5th edition RNA Worlds books). 559 pages.
Cold Spring Harbor Laboratory Press, New York. In print and e-book.
Individual articles also published in the journal Cold Spring Harbor Perspectives in Biology.
ISBN:  978-1-621822-24-0.

RNA worlds: From life’s origins to diversity in gene regulation.

J. F. Atkins, R. F. Gesteland, & T. Cech (Eds.). (2011).  
New York;: Cold Spring Harbor Laboratory Press.
ISBN:  978-0-879699-46-8.

Recoding: Expansion of Decoding rules enriches gene expression.

J.F. Atkins and R.F. Gesteland.  (2010). 
New York: Springer Science+Business Media, LLC.
ISBN: 978-0-387-89381-5.
DOI: 978-0-387-89382-2.

Journal Articles

Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response.
G. Loughran, I. Jungreis, I. Tzani, M. Power, R.I. Dmitriev, I.P Ivanov, M. Kellis and J.F. Atkins.
2018. J. Biol. Chem. 293, 4434-4444.

Polyamine control of translation elongation regulates start site selection on the antizyme inhibitor mRNA via ribosome queuing.
I.P. Ivanov, B. Shin, G. Loughran, I. Tzani, S.K. Young-Baird, C. Cao, J.F. Atkins and T.E. Dever.
2018. Mol. Cell 70, 254-264.

Avoidance of reporter assay distortions from fused dual reporters.
G. Loughran, M.T. Howard, A.E. Firth and J.F. Atkins.
2017. RNA 23, 1285-1289.

Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of roles of multiple SECIS elements.
S. Wu, M. Mariotti, D. Santesmasses, K.E. Hill, J. Baclaocos, E. Aparicio-Prat, S. Li, J. Mackrill, Y. Wu, M.T. Howard, M. Capecchi, R. Guigó, R.F. Burk and J.F. Atkins.
2016. Open Biology 6.pii:160241. PMID: 27881738.

Ribosomal frameshifting and transcriptional slippage: From genetic steganography & cryptography to adventitious use.
J.F. Atkins, G. Loughran, P.R. Bhatt, A.E. Firth and P.V. Baranov.
2016. Nucl. Acids Res. 44, 7007-7078.

Coupling of mRNA structure rearrangement to ribosome movement during bypassing of non-coding regions.
J. Chen, A. Coakley, M. O’Connor, A. Petrov, S.E. O’Leary, J.F. Atkins and J.D. Puglisi.
2015.  Cell 163, 1267-1280.

Productive mRNA stem-loop mediated transcriptional slippage: crucial features in common with intrinsic terminators.
C. Penno, V. Sharma, A. Coakley, M.O’C. Motherway, D. van Sinderen, L. Lubkowska, M.L. Kireeva, M. Kashlev, P.V. Baranov and J.F. Atkins.
2015. Proc. Natl. Acad. Sci. USA 112: E1984-1993.

Antibiotic re-frames decoding.
J.F. Atkins and P.V. Baranov.
2013. Nature 503, 478-479.

Theiler’s murine encephalomyelitis and Foot-and Mouth Disease viruses in its functional utilization of the StopGo non-standard translation mechanism.
G. Loughran, J.E. Libbey, S. Uddowla, M.F. Scallan, M.D. Ryan, R.S. Fujinami, E. Rieder and J.F. Atkins.
2013. J. Gen. Virol. 94, 348-353.

An overlapping protein-coding region in Influenza A virus segment 3 modulates the host response.
B.W. Jagger et al.
2012. Science 337, 199-204.

Ribosomal frameshifting utilized in influenza A virus expression occurs within the sequence UCC_UUU_CGU and is in the +1 direction.
A.E. Firth et al.
2012.  Open Biol. 2: 120109.

Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome.
G. Loughran, A.E. Firth and J.F. Atkins.
2011. Proc. Natl. Acad. Sci. USA. 108, 1111-1119.

Translation goes global.
R.B. Weiss and J.F. Atkins.
2011. Science 334, 1509-1510.

Links

Professor John F Atkins UCC Research Profile