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Culmination of a half-century quest reveals insight into mutant tRNA-mediated frameshifting after tRNA departure from the decoding site.

Atkins JF.

Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):11121-11123. doi: 10.1073/pnas.1815837115. Epub 2018 Oct 19. No abstract available.


Polyamine Control of Translation Elongation Regulates Start Site Selection on Antizyme Inhibitor mRNA via Ribosome Queuing.

Ivanov IP, Shin BS, Loughran G, Tzani I, Young-Baird SK, Cao C, Atkins JF, Dever TE.

Mol Cell. 2018 Apr 19;70(2):254-264.e6. doi: 10.1016/j.molcel.2018.03.015.


Translational autoregulation of BZW1 and BZW2 expression by modulating the stringency of start codon selection.

Loughran G, Firth AE, Atkins JF, Ivanov IP.

PLoS One. 2018 Feb 22;13(2):e0192648. doi: 10.1371/journal.pone.0192648. eCollection 2018.


Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response.

Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF.

J Biol Chem. 2018 Mar 23;293(12):4434-4444. doi: 10.1074/jbc.M117.818526. Epub 2018 Jan 31.


AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation.

Yordanova MM, Loughran G, Zhdanov AV, Mariotti M, Kiniry SJ, O'Connor PBF, Andreev DE, Tzani I, Saffert P, Michel AM, Gladyshev VN, Papkovsky DB, Atkins JF, Baranov PV.

Nature. 2018 Jan 18;553(7688):356-360. doi: 10.1038/nature25174. Epub 2018 Jan 3.


Multiple RNA structures affect translation initiation and UGA redefinition efficiency during synthesis of selenoprotein P.

Mariotti M, Shetty S, Baird L, Wu S, Loughran G, Copeland PR, Atkins JF, Howard MT.

Nucleic Acids Res. 2017 Dec 15;45(22):13004-13015. doi: 10.1093/nar/gkx982.


ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?

Dinan AM, Atkins JF, Firth AE.

Biol Direct. 2017 Oct 16;12(1):24. doi: 10.1186/s13062-017-0195-0.


Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis.

Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF.

Nucleic Acids Res. 2017 Sep 29;45(17):10156-10167. doi: 10.1093/nar/gkx690.


Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage.

Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF.

Nucleic Acids Res. 2017 Sep 29;45(17):10143-10155. doi: 10.1093/nar/gkx689.


Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity.

Ivanov IP, Wei J, Caster SZ, Smith KM, Michel AM, Zhang Y, Firth AE, Freitag M, Dunlap JC, Bell-Pedersen D, Atkins JF, Sachs MS.

MBio. 2017 Jun 27;8(3). pii: e00844-17. doi: 10.1128/mBio.00844-17.


Avoidance of reporter assay distortions from fused dual reporters.

Loughran G, Howard MT, Firth AE, Atkins JF.

RNA. 2017 Aug;23(8):1285-1289. doi: 10.1261/rna.061051.117. Epub 2017 Apr 25.


A [Cu]rious Ribosomal Profiling Pattern Leads to the Discovery of Ribosomal Frameshifting in the Synthesis of a Copper Chaperone.

Atkins JF, Loughran G, Baranov PV.

Mol Cell. 2017 Jan 19;65(2):203-204. doi: 10.1016/j.molcel.2017.01.002.


Human selenoprotein P and S variant mRNAs with different numbers of SECIS elements and inferences from mutant mice of the roles of multiple SECIS elements.

Wu S, Mariotti M, Santesmasses D, Hill KE, Baclaocos J, Aparicio-Prat E, Li S, Mackrill J, Wu Y, Howard MT, Capecchi M, Guigó R, Burk RF, Atkins JF.

Open Biol. 2016 Nov;6(11). pii: 160241.


Position-dependent termination and widespread obligatory frameshifting in Euplotes translation.

Lobanov AV, Heaphy SM, Turanov AA, Gerashchenko MV, Pucciarelli S, Devaraj RR, Xie F, Petyuk VA, Smith RD, Klobutcher LA, Atkins JF, Miceli C, Hatfield DL, Baranov PV, Gladyshev VN.

Nat Struct Mol Biol. 2017 Jan;24(1):61-68. doi: 10.1038/nsmb.3330. Epub 2016 Nov 21.


Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum.

Heaphy SM, Mariotti M, Gladyshev VN, Atkins JF, Baranov PV.

Mol Biol Evol. 2016 Nov;33(11):2885-2889. Epub 2016 Aug 8.


Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use.

Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV.

Nucleic Acids Res. 2016 Sep 6;44(15):7007-78. doi: 10.1093/nar/gkw530. Epub 2016 Jul 19. Review.


An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting.

Saffert P, Adamla F, Schieweck R, Atkins JF, Ignatova Z.

J Biol Chem. 2016 Aug 26;291(35):18505-13. doi: 10.1074/jbc.M116.744326. Epub 2016 Jul 5.


Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform.

Tzani I, Ivanov IP, Andreev DE, Dmitriev RI, Dean KA, Baranov PV, Atkins JF, Loughran G.

Open Biol. 2016 May;6(5). pii: 150203. doi: 10.1098/rsob.150203. Epub 2016 May 25.


Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.

Chen J, Coakley A, O'Connor M, Petrov A, O'Leary SE, Atkins JF, Puglisi JD.

Cell. 2015 Nov 19;163(5):1267-1280. doi: 10.1016/j.cell.2015.10.064.


Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning.

Baranov PV, Atkins JF, Yordanova MM.

Nat Rev Genet. 2015 Sep;16(9):517-29. doi: 10.1038/nrg3963. Epub 2015 Aug 11. Review.


Transcriptional slippage in the positive-sense RNA virus family Potyviridae.

Olspert A, Chung BY, Atkins JF, Carr JP, Firth AE.

EMBO Rep. 2015 Aug;16(8):995-1004. doi: 10.15252/embr.201540509. Epub 2015 Jun 25.


A Nascent Peptide Signal Responsive to Endogenous Levels of Polyamines Acts to Stimulate Regulatory Frameshifting on Antizyme mRNA.

Yordanova MM, Wu C, Andreev DE, Sachs MS, Atkins JF.

J Biol Chem. 2015 Jul 17;290(29):17863-78. doi: 10.1074/jbc.M115.647065. Epub 2015 May 21.


Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators.

Penno C, Sharma V, Coakley A, O'Connell Motherway M, van Sinderen D, Lubkowska L, Kireeva ML, Kashlev M, Baranov PV, Atkins JF.

Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):E1984-93. doi: 10.1073/pnas.1418384112. Epub 2015 Apr 6.


Transcriptional frameshifting rescues Citrobacter rodentium type VI secretion by the production of two length variants from the prematurely interrupted tssM gene.

Gueguen E, Wills NM, Atkins JF, Cascales E.

PLoS Genet. 2014 Dec 4;10(12):e1004869. doi: 10.1371/journal.pgen.1004869. eCollection 2014 Dec.


Human DNA tumor viruses generate alternative reading frame proteins through repeat sequence recoding.

Kwun HJ, Toptan T, Ramos da Silva S, Atkins JF, Moore PS, Chang Y.

Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):E4342-9. doi: 10.1073/pnas.1416122111. Epub 2014 Sep 30.


High-efficiency translational bypassing of non-coding nucleotides specified by mRNA structure and nascent peptide.

Samatova E, Konevega AL, Wills NM, Atkins JF, Rodnina MV.

Nat Commun. 2014 Jul 21;5:4459. doi: 10.1038/ncomms5459.


Evidence of efficient stop codon readthrough in four mammalian genes.

Loughran G, Chou MY, Ivanov IP, Jungreis I, Kellis M, Kiran AM, Baranov PV, Atkins JF.

Nucleic Acids Res. 2014 Aug;42(14):8928-38. doi: 10.1093/nar/gku608. Epub 2014 Jul 10.


Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli.

Sharma V, Prère MF, Canal I, Firth AE, Atkins JF, Baranov PV, Fayet O.

Nucleic Acids Res. 2014 Jun;42(11):7210-25. doi: 10.1093/nar/gku386. Epub 2014 May 29.


Cryptic MHC class I-binding peptides are revealed by aminoglycoside-induced stop codon read-through into the 3' UTR.

Goodenough E, Robinson TM, Zook MB, Flanigan KM, Atkins JF, Howard MT, Eisenlohr LC.

Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5670-5. doi: 10.1073/pnas.1402670111. Epub 2014 Mar 31.


Sepp1(UF) forms are N-terminal selenoprotein P truncations that have peroxidase activity when coupled with thioredoxin reductase-1.

Kurokawa S, Eriksson S, Rose KL, Wu S, Motley AK, Hill S, Winfrey VP, McDonald WH, Capecchi MR, Atkins JF, Arnér ES, Hill KE, Burk RF.

Free Radic Biol Med. 2014 Apr;69:67-76. doi: 10.1016/j.freeradbiomed.2014.01.010. Epub 2014 Jan 14.


Nailing fingerprints in the stars.

Atkins JF, Baranov PV.

Nature. 2013 Nov 28;503(7477):437. No abstract available.


Molecular biology: Antibiotic re-frames decoding.

Atkins JF, Baranov PV.

Nature. 2013 Nov 28;503(7477):478-9. doi: 10.1038/503478a. No abstract available.


Identification of the nature of reading frame transitions observed in prokaryotic genomes.

Antonov I, Coakley A, Atkins JF, Baranov PV, Borodovsky M.

Nucleic Acids Res. 2013 Jul;41(13):6514-30. doi: 10.1093/nar/gkt274. Epub 2013 May 6.


rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments.

O'Connor PB, Li GW, Weissman JS, Atkins JF, Baranov PV.

Bioinformatics. 2013 Jun 15;29(12):1488-91. doi: 10.1093/bioinformatics/btt184. Epub 2013 Apr 19.


Ribosomal frameshifting used in influenza A virus expression occurs within the sequence UCC_UUU_CGU and is in the +1 direction.

Firth AE, Jagger BW, Wise HM, Nelson CC, Parsawar K, Wills NM, Napthine S, Taubenberger JK, Digard P, Atkins JF.

Open Biol. 2012 Oct;2(10):120109. doi: 10.1098/rsob.120109.


Theiler's murine encephalomyelitis virus contrasts with encephalomyocarditis and foot-and-mouth disease viruses in its functional utilization of the StopGo non-standard translation mechanism.

Loughran G, Libbey JE, Uddowla S, Scallan MF, Ryan MD, Fujinami RS, Rieder E, Atkins JF.

J Gen Virol. 2013 Feb;94(Pt 2):348-53. doi: 10.1099/vir.0.047571-0. Epub 2012 Oct 24.


Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein.

Fang Y, Treffers EE, Li Y, Tas A, Sun Z, van der Meer Y, de Ru AH, van Veelen PA, Atkins JF, Snijder EJ, Firth AE.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):E2920-8. doi: 10.1073/pnas.1211145109. Epub 2012 Oct 4.


Production of selenoprotein P (Sepp1) by hepatocytes is central to selenium homeostasis.

Hill KE, Wu S, Motley AK, Stevenson TD, Winfrey VP, Capecchi MR, Atkins JF, Burk RF.

J Biol Chem. 2012 Nov 23;287(48):40414-24. doi: 10.1074/jbc.M112.421404. Epub 2012 Oct 4.


An overlapping protein-coding region in influenza A virus segment 3 modulates the host response.

Jagger BW, Wise HM, Kash JC, Walters KA, Wills NM, Xiao YL, Dunfee RL, Schwartzman LM, Ozinsky A, Bell GL, Dalton RM, Lo A, Efstathiou S, Atkins JF, Firth AE, Taubenberger JK, Digard P.

Science. 2012 Jul 13;337(6091):199-204. doi: 10.1126/science.1222213. Epub 2012 Jun 28.


Observation of dually decoded regions of the human genome using ribosome profiling data.

Michel AM, Choudhury KR, Firth AE, Ingolia NT, Atkins JF, Baranov PV.

Genome Res. 2012 Nov;22(11):2219-29. doi: 10.1101/gr.133249.111. Epub 2012 May 16.


Alternative reading frame selection mediated by a tRNA-like domain of an internal ribosome entry site.

Ren Q, Wang QS, Firth AE, Chan MM, Gouw JW, Guarna MM, Foster LJ, Atkins JF, Jan E.

Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):E630-9. doi: 10.1073/pnas.1111303109. Epub 2012 Jan 13.


Molecular biology. Translation goes global.

Weiss RB, Atkins JF.

Science. 2011 Dec 16;334(6062):1509-10. doi: 10.1126/science.1216974. No abstract available.


Stringency of start codon selection modulates autoregulation of translation initiation factor eIF5.

Loughran G, Sachs MS, Atkins JF, Ivanov IP.

Nucleic Acids Res. 2012 Apr;40(7):2898-906. doi: 10.1093/nar/gkr1192. Epub 2011 Dec 7.


Ribosomal frameshifting into an overlapping gene in the 2B-encoding region of the cardiovirus genome.

Loughran G, Firth AE, Atkins JF.

Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):E1111-9. doi: 10.1073/pnas.1102932108. Epub 2011 Oct 24.


A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.

Sharma V, Firth AE, Antonov I, Fayet O, Atkins JF, Borodovsky M, Baranov PV.

Mol Biol Evol. 2011 Nov;28(11):3195-211. doi: 10.1093/molbev/msr155. Epub 2011 Jun 14.


Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC).

Baranov PV, Wills NM, Barriscale KA, Firth AE, Jud MC, Letsou A, Manning G, Atkins JF.

RNA Biol. 2011 Jul-Aug;8(4):637-47. doi: 10.4161/rna.8.4.15395. Epub 2011 Jul 1.


Stimulation of stop codon readthrough: frequent presence of an extended 3' RNA structural element.

Firth AE, Wills NM, Gesteland RF, Atkins JF.

Nucleic Acids Res. 2011 Aug;39(15):6679-91. doi: 10.1093/nar/gkr224. Epub 2011 Apr 27.


The interplay of mRNA stimulatory signals required for AUU-mediated initiation and programmed -1 ribosomal frameshifting in decoding of transposable element IS911.

Prère MF, Canal I, Wills NM, Atkins JF, Fayet O.

J Bacteriol. 2011 Jun;193(11):2735-44. doi: 10.1128/JB.00115-11. Epub 2011 Apr 8.


Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production.

Firth AE, Zevenhoven-Dobbe JC, Wills NM, Go YY, Balasuriya UB, Atkins JF, Snijder EJ, Posthuma CC.

J Gen Virol. 2011 May;92(Pt 5):1097-106. doi: 10.1099/vir.0.029264-0. Epub 2011 Feb 9.


Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences.

Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV.

Nucleic Acids Res. 2011 May;39(10):4220-34. doi: 10.1093/nar/gkr007. Epub 2011 Jan 25.

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