Journal Club

Here are the papers that have been recently discussed at our lab journal club (most recent first):

Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis. Legnini I, Di Timoteo G, Rossi F, Morlando M, Briganti F, Sthandier O, Fatica A, Santini T, Andronache A, Wade M, Laneve P, Rajewsky N, Bozzoni I. Mol Cell. 2017 Apr 6;66(1):22-37.e9. doi: 10.1016/j.molcel.2017.02.017. Epub 2017 Mar 23.

Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain. Lintner NG, McClure KF, Petersen D, Londregan AT, Piotrowski DW, Wei L, Xiao J, Bolt M, Loria PM, Maguire B, Geoghegan KF, Huang A, Rolph T, Liras S, Doudna JA, Dullea RG, Cate JH. PLoS Biol. 2017 Mar 21;15(3):e2001882. doi: 10.1371/journal.pbio.2001882.

5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding. Jiao X, Doamekpor SK, Bird JG, Nickels BE, Tong L, Hart RP, Kiledjian M. Cell. 2017 Mar 9;168(6):1015-1027.e10. doi: 10.1016/j.cell.2017.02.019.

In vivo evidence that eIF3 stays bound to ribosomes elongating and terminating on short upstream ORFs to promote reinitiation. Mohammad MP, Munzarová Pondělíčková V, Zeman J, Gunišová S, Valášek LS. Nucleic Acids Res. 2017 Jan 23. pii: gkx049. doi: 10.1093/nar/gkx049. [Epub ahead of print]

Mitochondrial Protein Synthesis Adapts to Influx of Nuclear-Encoded Protein. Richter-Dennerlein R, Oeljeklaus S, Lorenzi I, Ronsör C, Bareth B, Schendzielorz AB, Wang C, Warscheid B, Rehling P, Dennerlein S. Cell. 2016 Oct 6;167(2):471-483.e10. doi: 10.1016/j.cell.2016.09.003.

A novel translational control mechanism involving RNA structures within coding sequences. Jungfleisch J, Nedialkova DD, Dotu I, Sloan KE, Martinez-Bosch N, Brüning L, Raineri E, Navarro P, Bohnsack MT, Leidel SA, Diez J. Genome Res. 2016 Nov 7. pii: gr.209015.116. [Epub ahead of print]

A conserved quality-control pathway that mediates degradation of unassembled ribosomal proteins. Sung MK, Porras-Yakushi TR, Reitsma JM, Huber FM, Sweredoski MJ, Hoelz A, Hess S, Deshaies RJ. Elife. 2016 Aug 23;5. pii: e19105. doi: 10.7554/eLife.19105.

Potent, Reversible, and Specific Chemical Inhibitors of Eukaryotic Ribosome Biogenesis. Kawashima SA, Chen Z, Aoi Y, Patgiri A, Kobayashi Y, Nurse P, Kapoor TM. Cell. 2016 Oct 6;167(2):512-524.e14. doi: 10.1016/j.cell.2016.08.070.

eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Lee AS, Kranzusch PJ, Doudna JA, Cate JH. Nature. 2016 Aug 4;536(7614):96-9.

Novel Intronic RNA Structures Contribute to Maintenance of Phenotype in Saccharomyces cerevisiae. Hooks KB, Naseeb S, Parker S, Griffiths-Jones S, Delneri D. Genetics. 2016 Jul;203(3):1469-81. doi: 10.1534/genetics.115.185363. Epub 2016 May 18.

Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. Iwasaki S, Floor SN, Ingolia NT. Nature. 2016 Jun 15;534(7608):558-61. doi: 10.1038/nature17978.

Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing. Chadani Y, Niwa T, Chiba S, Taguchi H, Ito K. Proc Natl Acad Sci U S A. 2016 Feb 16;113(7):E829-38. doi: 10.1073/pnas.1520560113. Epub 2016 Feb 1.

Rqc1 and Ltn1 prevent CAT-tail induced protein aggregation by efficient recruitment of Cdc48 on stalled 60S subunits. Defenouillere Q, Zhang E, Namane A, Mouaikel J, Jacquier A, Fromont-Racine M. J Biol Chem. 2016 Apr 18. pii: jbc.M116.722264.

Degradation of Gadd45 mRNA by nonsense-mediated decay is essential for viability. Nelson JO, Moore KA, Chapin A, Hollien J, Metzstein MM. Elife. 2016 Mar 8;5. pii: e12876. doi: 10.7554/eLife.12876.

Redefining the Translational Status of 80S Monosomes. Heyer EE, Moore MJ. Cell. 2016 Feb 11;164(4):757-69. doi: 10.1016/j.cell.2016.01.003.

Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity. Nedialkova DD, Leidel SA. Cell. 2015 Jun 18;161(7):1606-18. doi: 10.1016/j.cell.2015.05.022. Epub 2015 Jun 4.

DDX6 Orchestrates Mammalian Progenitor Function through the mRNA Degradation and Translation Pathways. Wang Y, Arribas-Layton M, Chen Y, Lykke-Andersen J, Sen GL. Mol Cell. 2015 Oct 1;60(1):118-30. doi: 10.1016/j.molcel.2015.08.014. Epub 2015 Sep 24.

Mutations in a translation initiation factor identify the target of a memory-enhancing compound. Sekine Y, Zyryanova A, Crespillo-Casado A, Fischer PM, Harding HP, Ron D. Science. 2015 May 29;348(6238):1027-30. doi: 10.1126/science.aaa6986. Epub 2015 Apr 9.

Structural basis for stop codon recognition in eukaryotes. Brown A, Shao S, Murray J, Hegde RS, Ramakrishnan V. Nature. 2015 Aug 27;524(7566):493-6. doi: 10.1038/nature14896. Epub 2015 Aug 5.

Rolling Circle Translation of Circular RNA in Living Human Cells. Abe N, Matsumoto K, Nishihara M, Nakano Y, Shibata A, Maruyama H, Shuto S, Matsuda A, Yoshida M, Ito Y, Abe H. Sci Rep. 2015 Nov 10;5:16435. doi: 10.1038/srep16435.

Aven recognition of RNA G-quadruplexes regulates translation of the mixed lineage leukemia protooncogenes. Thandapani P, Song J, Gandin V, Cai Y, Rouleau SG, Garant JM, Boisvert FM, Yu Z, Perreault JP, Topisirovic I, Richard S. Elife. 2015 Aug 12;4. doi: 10.7554/eLife.06234.

5′ UTR m6A Promotes Cap-Independent Translation. Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian S-B, Jaffrey SR. Cell. doi: 10.1016/j.cell.2015.10.012. Epub 2015 Oct 22.

Rli1/ABCE1 Recycles Terminating Ribosomes and Controls Translation Reinitiation in 3'UTRs In Vivo. Young DJ, Guydosh NR, Zhang F, Hinnebusch AG, Green R. Cell. 2015 Aug 13;162(4):872-84. doi: 10.1016/j.cell.2015.07.041.

Protein synthesis by ribosomes with tethered subunits. Orelle C, Carlson ED, Szal T, Florin T, Jewett MC, Mankin AS. Nature. 2015 Aug 6;524(7563):119-24. doi: 10.1038/nature14862. Epub 2015 Jul 29.

The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins. Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ. Mol Cell. 2015 Jul 2;59(1):35-49. doi: 10.1016/j.molcel.2015.04.026. Epub 2015 Jun 4.

Cotranslational targeting of XBP1 protein to the membrane promotes cytoplasmic splicing of its own mRNA. Yanagitani K, Imagawa Y, Iwawaki T, Hosoda A, Saito M, Kimata Y, Kohno K. Mol Cell. 2009 Apr 24;34(2):191-200. doi: 10.1016/j.molcel.2009.02.033.

A potassium ion-dependent RNA structural switch regulates human pre-miRNA 92b maturation. Mirihana Arachchilage G, Dassanayake AC, Basu S. Chem Biol. 2015 Feb 19;22(2):262-72. doi: 10.1016/j.chembiol.2014.12.013. Epub 2015 Jan 29.

A role for REP sequences in regulating translation. Liang W, Rudd KE, Deutscher MP. Mol Cell. 2015 May 7;58(3):431-9. doi: 10.1016/j.molcel.2015.03.019. Epub 2015 Apr 16.

An RNA biosensor for imaging the first round of translation from single cells to living animals. Halstead JM, Lionnet T, Wilbertz JH, Wippich F, Ephrussi A, Singer RH, Chao JA. Science. 2015 Mar 20;347(6228):1367-671. doi: 10.1126/science.aaa3380.

Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Colussi TM, Costantino DA, Zhu J, Donohue JP, Korostelev AA, Jaafar ZA, Plank TD, Noller HF, Kieft JS. Nature. 2015 Mar 5;519(7541):110-3. doi: 10.1038/nature14219. Epub 2015 Feb 4.

mTORC1-mediated translational elongation limits intestinal tumour initiation and growth. Faller WJ, Jackson TJ, Knight JR, Ridgway RA, Jamieson T, Karim SA, Jones C, Radulescu S, Huels DJ, Myant KB, Dudek KM, Casey HA, Scopelliti A, Cordero JB, Vidal M, Pende M, Ryazanov AG, Sonenberg N, Meyuhas O, Hall MN, Bushell M, Willis AE, Sansom OJ. Nature. 2015 Jan 22;517(7535):497-500. doi: 10.1038/nature13896. Epub 2014 Nov 5.

RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation. Xue S, Tian S, Fujii K, Kladwang W, Das R, Barna M. Nature. 2015 Jan 1;517(7532):33-8. doi: 10.1038/nature14010. Epub 2014 Nov 19.