Publications of Interest

Xue W, Dahlman JE, Tammela T, Khan OF, Sood S, Dave A, Cai W, Chirino LM, Yang GR, Bronson R, Crowley DG, Sahay G, Schroeder A, Langer R, Anderson DG, Jacks T.  Small RNA Combination Therapy for Lung Cancer.  Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):E3553-61. doi: 10.1073/pnas.1412686111. Epub 2014 Aug 11

Ward J, Kanchagar C, Veksler-Lublinsky I, Lee RC, McGill MR, Jaeschke H, Curry SC, Ambros VR.  Circulating microRNA profiles in human patients with acetaminophen hepatotoxicity or ischemic hepatitis.  Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):12169-74. doi: 10.1073/pnas.1412608111. Epub 2014 Aug 4.

Sterling, C. H., Veksler-Lublinksy, I., & Ambros, V. (2014). An efficient and sensitive method for preparing cDNA libraries from scarce biological samples. Nucleic Acids Research. doi:10.1093/nar/gku637

Gammon DB, Duraffour S, Rozelle DK, Hehnly H, Sharma R, Sparks ME, West CC, Chen Y, Moresco JJ, Andrei G, Connor JC, Conte D, Gundersen-Rindal DE, Marshall WL, Yates J, Silverman N, Mello CC. A single vertebrate DNA virus protein disarms invertebrate immunity to RNA virus infection.  Elife. 2014 Jun 25:e02910. doi: 10.7554/eLife.02910. [Epub ahead of print]

Koh, C. S., Brilot, A. F., Grigorieff, N., & Korostelev, A. A. (2014). Taura syndrome virus IRES initiates translation by binding its tRNA-mRNA–like structural element in the ribosomal decoding center. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1406335111

Kim H, Ishidate T, Ghanta KS, Seth M, Conte D Jr, Shirayama M, Mello CC. A Co-CRISPR Strategy for Efficient Genome Editing in Caenorhabditis elegans. Genetics. 2014 May 30. pii: genetics.114.166389. [Epub ahead of print]

Shirayama M, Stanney W 3rd, Gu W, Seth M, Mello CC. The Vasa Homolog RDE-12 Engages Target mRNA and Multiple Argonaute Proteins to Promote RNAi in C. elegans. Curr Biol. 2014 Mar 26. pii: S0960-9822(14)00267-X. doi: 10.1016/j.cub.2014.03.008. [Epub ahead of print]

Moran Y, Fredman D, Praher D, Li XZ, Wee LM, Rentzsch F, Zamore PD, Technau U, Seitz H. Cnidarian microRNAs frequently regulate targets by cleavage. Genome Res. 2014 Mar 18. [Epub ahead of print]

Yang C, Wang H, Qiao T, Yang B, Aliaga L, Qiu L, Tan W, Salameh J, McKenna-Yasek DM, Smith T, Peng L, Moore MJ, Brown RH Jr, Cai H, Xu Z. Partial loss of TDP-43 function causes phenotypes of amyotrophic lateral sclerosis. Proc Natl Acad Sci U S A. 2014 Mar 10. [Epub ahead of print]

Chen W, Moore MJ. The spliceosome: disorder and dynamics defined. Curr Opin Struct Biol. 2014 Feb 11;24C:141-149. doi: 10.1016/j.sbi.2014.01.009.

Träger U, Andre R, Lahiri N, Magnusson-Lind A, Weiss A, Grueninger S, McKinnon C, Sirinathsinghji E, Kahlon S, Pfister EL, Moser R, Hummerich H, Antoniou M, Bates GP, Luthi-Carter R, Lowdell MW, Björkqvist M, Ostroff GR, Aronin N, Tabrizi SJ.  HTT-lowering reverses Huntington's disease immune dysfunction caused by NFκB pathway dysregulation. Brain. 2014 Mar;137(Pt 3):819-33. doi: 10.1093/brain/awt355. Epub 2014 Jan 22.

Fukunaga R, Colpan C, Han BW, Zamore PD. Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. 
EMBO J. Published 31 January 2014, 10.1002/embj.201387176 

Chen W, Shulha HP, Ashar-Patel A, Yan J, Green KM, Query CC, Rhind N, Weng Z, Moore MJ. Endogenous U2·U5·U6 snRNA complexes in S. pombe are intron lariat spliceosomes. RNA. 2014;  Published in Advance January 17, 2014, doi:10.1261/rna.040980.113

Kearns NA, Genga RM, Enuameh MS, Garber M, Wolfe SA, Maehr R.Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells. Development. 2014 Jan;141(1):219-223.

Seth M, Shirayama M, Gu W, Ishidate T, Conte D Jr, Mello CC. The C. elegans CSR-1 argonaute pathway counteracts epigenetic silencing to promote germline gene expression. Dev Cell. 2013 Dec 23;27(6):656-63.

Conine CC, Moresco JJ, Gu W, Shirayama M, Conte D Jr, Yates JR 3rd, Mello CC. Argonautes promote male fertility and provide a paternal memory of germline gene expression in C. elegans. Cell. 2013 Dec 19;155(7):1532-44. doi: 10.1016/j.cell.2013.11.032.

Brilot AF, Korostelev AA, Ermolenko DN, Grigorieff N. Structure of the ribosome with elongation factor G trapped in the pretranslocation state. PNAS 2013 ; published ahead of print December 9, 2013, doi:10.1073/pnas.1311423110

Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, Byron M, Monks B, Henry-Bezy M, Lawrence JB, O'Neill LA, Moore MJ, Caffrey DR, Fitzgerald KA. A long noncoding RNA mediates both activation and repression of immune response genes. Science. 2013 Aug 16;341(6147):789-92. doi: 10.1126/science.1240925. Epub 2013 Aug 1. PubMed PMID: 23907535.

Kucukural A, Ozadam H, Singh G, Moore MJ, Cenik C. ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq. Bioinformatics. 2013 Aug 12. [Epub ahead of print] PubMed PMID: 23929032.

Svidritskiy E, Ling C, Ermolenko DN, Korostelev AA. Blasticidin S inhibits translation by trapping deformed tRNA on the ribosome. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12283-8. doi: 10.1073/pnas.1304922110. Epub 2013 Jul 3. PubMed PMID: 23824292; PubMed Central PMCID: PMC3725078.

Santos N, Zhu J, Donohue JP, Korostelev AA, Noller HF. Crystal structure of the 70S ribosome bound with the Q253P mutant form of release factor RF2. Structure. 2013 Jul 2;21(7):1258-63. doi: 10.1016/j.str.2013.04.028. Epub 2013 Jun 13. PubMed PMID: 23769667.

Li XZ, Roy CK, Moore MJ, Zamore PD. Defining piRNA primary transcripts. Cell Cycle. 2013 Jun 1;12(11):1657-8. doi: 10.4161/cc.24989. Epub 2013 May 10. PubMed PMID: 23673320.

Nieuwenhuizen RP, Lidke KA, Bates M, Puig DL, Grünwald D, Stallinga S, Rieger B. Measuring image resolution in optical nanoscopy. Nat Methods. 2013 Jun;10(6):557-62. doi: 10.1038/nmeth.2448. Epub 2013 Apr 28. PubMed PMID: 23624665.

Jokhi V, Ashley J, Nunnari J, Noma A, Ito N, Wakabayashi-Ito N, Moore MJ, Budnik V. Torsin mediates primary envelopment of large ribonucleoprotein granules at the nuclear envelope. Cell Rep. 2013 Apr 25;3(4):988-95. doi: 10.1016/j.celrep.2013.03.015. Epub 2013 Apr 11. PubMed PMID: 23583177; PubMed Central PMCID: PMC3683601.

Bossé GD, Rüegger S, Ow MC, Vasquez-Rifo A, Rondeau EL, Ambros VR, Grosshans H, Simard MJ. The decapping scavenger enzyme DCS-1 controls microRNA levels in Caenorhabditis elegans. Mol Cell. 2013 Apr 25;50(2):281-7. doi: 10.1016/j.molcel.2013.02.023. Epub 2013 Mar 28. PubMed PMID: 23541767.

Crawford DJ, Hoskins AA, Friedman LJ, Gelles J, Moore MJ. Single-molecule colocalization FRET evidence that spliceosome activation precedes stable approach of 5' splice site and branch site. Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6783-8. doi: 10.1073/pnas.1219305110. Epub 2013 Apr 8. PubMed PMID: 23569281; PubMed Central PMCID: PMC3637735.

Ge DT, Zamore PD. Small RNA-directed silencing: the fly finds its inner fission yeast? Curr Biol. 2013 Apr 22;23(8):R318-20. doi: 10.1016/j.cub.2013.03.033. PubMed PMID: 23618667.

Li XZ, Roy CK, Dong X, Bolcun-Filas E, Wang J, Han BW, Xu J, Moore MJ, Schimenti JC, Weng Z, Zamore PD. An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell. 2013 Apr 11;50(1):67-81. doi: 10.1016/j.molcel.2013.02.016. Epub 2013 Mar 21. PubMed PMID: 23523368; PubMed Central PMCID: PMC3671569.

Kim S, Ishidate T, Sharma R, Soto MC, Conte D Jr, Mello CC, Shirayama M. Wnt and CDK-1 regulate cortical release of WRM-1/β-catenin to control cell division orientation in early Caenorhabditis elegans embryos. Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):E918-27. doi: 10.1073/pnas.1300769110. Epub 2013 Feb 19. PubMed PMID: 23431196; PubMed Central PMCID: PMC3593879.

Flores-Jasso CF, Salomon WE, Zamore PD. Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates. RNA. 2013 Feb;19(2):271-9. doi: 10.1261/rna.036921.112. Epub 2012 Dec 18. PubMed PMID: 23249751; PubMed Central PMCID: PMC3543083.

van der Bom IM, Moser RP, Gao G, Sena-Esteves M, Aronin N, Gounis MJ. Frameless multimodal image guidance of localized convection-enhanced delivery of therapeutics in the brain. J Neurointerv Surg. 2013 Jan 1;5(1):69-72. doi: 10.1136/neurintsurg-2011-010170. Epub 2011 Dec 22. PubMed PMID: 22193239; PubMed Central PMCID: PMC3533401.

Zhang Z, Theurkauf WE, Weng Z, Zamore PD. Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence. 2012 Dec 28;3(1):9. doi: 10.1186/1758-907X-3-9. PubMed PMID: 23273270; PubMed Central PMCID: PMC3552703.

D'Ambrogio A, Gu W, Udagawa T, Mello CC, Richter JD. Specific miRNA stabilization by Gld2-catalyzed monoadenylation. Cell Rep. 2012 Dec 27;2(6):1537-45. doi: 10.1016/j.celrep.2012.10.023. Epub 2012 Nov 29. PubMed PMID: 23200856; PubMed Central PMCID: PMC3534910.

Gu W, Lee HC, Chaves D, Youngman EM, Pazour GJ, Conte D Jr, Mello CC. CapSeq and CIP-TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell. 2012 Dec 21;151(7):1488-500. doi: 10.1016/j.cell.2012.11.023. PubMed PMID: 23260138; PubMed Central PMCID: PMC3581324.

Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T, Powers MA, Giles KM, Leedman PJ, Hess J, Grunwald D, Bussemaker HJ, Singer RH, Schirmacher P, Prives C. Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes. Mol Cell. 2012 Dec 14;48(5):799-810. doi: 10.1016/j.molcel.2012.09.020. Epub 2012 Oct 24. PubMed PMID: 23102701; PubMed Central PMCID: PMC3525737.

Bicknell AA, Cenik C, Chua HN, Roth FP, Moore MJ. Introns in UTRs: why we should stop ignoring them.Bioessays. 2012 Dec;34(12):1025-34. doi: 10.1002/bies.201200073. Epub 2012 Oct 26. PubMed PMID: 23108796. 

Wee LM, Flores-Jasso CF, Salomon WE, Zamore PD. Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell. 2012 Nov 21;151(5):1055-67. doi: 10.1016/j.cell.2012.10.036. Erratum in: Cell. 2013 Jan 17;152(1-2):366. PubMed PMID: 23178124; PubMed Central PMCID: PMC3595543.

Singh G, Kucukural A, Cenik C, Leszyk JD, Shaffer SA, Weng Z, Moore MJ. The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell. 2012 Nov 9;151(4):750-64. doi: 10.1016/j.cell.2012.10.007. Epub 2012 Oct 18. Erratum in: Cell. 2012 Nov 9;151(4):915-6. PubMed PMID: 23084401; PubMed Central PMCID: PMC3522173.

Aronin N, Moore M. Hunting down huntingtin. N Engl J Med. 2012 Nov;367(18):1753-4. doi: 10.1056/NEJMcibr1209595. PubMed PMID: 23113488.

Fukunaga R, Han BW, Hung JH, Xu J, Weng Z, Zamore PD. Dicer partner proteins tune the length of mature miRNAs in flies and mammals. Cell. 2012 Oct 26;151(3):533-46. doi: 10.1016/j.cell.2012.09.027. Epub 2012 Oct 11. Erratum in: Cell. 2012 Nov 9;151(4):912. PubMed PMID: 23063653; PubMed Central PMCID: PMC3609031.

Wu CH, Fallini C, Ticozzi N, Keagle PJ, Sapp PC, Piotrowska K, Lowe P, Koppers M, McKenna-Yasek D, Baron DM, Kost JE, Gonzalez-Perez P, Fox AD, Adams J, Taroni F, Tiloca C, Leclerc AL, Chafe SC, Mangroo D, Moore MJ, Zitzewitz JA, Xu ZS, van den Berg LH, Glass JD, Siciliano G, Cirulli ET, Goldstein DB, Salachas F, Meininger V, Rossoll W, Ratti A, Gellera C, Bosco DA, Bassell GJ, Silani V, Drory VE, Brown RH Jr, Landers JE. Mutations in the profilin 1 gene cause familial amyotrophic lateral sclerosis. Nature. 2012 Aug 23;488(7412):499-503. doi: 10.1038/nature11280. PubMed PMID: 22801503; PubMed Central PMCID: PMC3575525. 

Li L, Gu W, Liang C, Liu Q, Mello CC, Liu Y. The translin-TRAX complex (C3PO) is a ribonuclease in tRNA processing. Nat Struct Mol Biol. 2012 Aug;19(8):824-30. doi: 10.1038/nsmb.2337. Epub 2012 Jul 8. PubMed PMID: 22773104; PubMed Central PMCID: PMC3414638.

Shirayama M, Seth M, Lee HC, Gu W, Ishidate T, Conte D Jr, Mello CC. piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell. 2012 Jul 6;150(1):65-77. doi: 10.1016/j.cell.2012.06.015. Epub 2012 Jun 25. PubMed PMID: 22738726; PubMed Central PMCID: PMC3597741. 


Lee HC, Gu W, Shirayama M, Youngman E, Conte D Jr, Mello CC. C. elegans piRNAs mediate the genome-wide surveillance of germline transcripts. Cell. 2012 Jul 6;150(1):78-87. doi: 10.1016/j.cell.2012.06.016. Epub 2012 Jun 25. PubMed PMID: 22738724; PubMed Central PMCID: PMC3410639. 


Zamore PD. RNA: methods and protocols - a new series. Silence. 2012 Jun 7;3(1):7. doi: 10.1186/1758-907X-3-7. PubMed PMID: 22676652; PubMed Central PMCID: PMC3420260. 


Speese SD, Ashley J, Jokhi V, Nunnari J, Barria R, Li Y, Ataman B, Koon A, Chang YT, Li Q, Moore MJ, Budnik V.Nuclear envelope budding enables large ribonucleoprotein particle export during synaptic Wnt signaling. Cell. 2012 May 11;149(4):832-46. doi: 10.1016/j.cell.2012.03.032. Erratum in: Cell. 2012 Oct 26;151(3):687-9. PubMed PMID: 22579286; PubMed Central PMCID: PMC3371233.

Hoskins AA, Moore MJ. The spliceosome: a flexible, reversible macromolecular machine. Trends Biochem Sci. 2012 May;37(5):179-88. doi: 10.1016/j.tibs.2012.02.009. Epub 2012 Apr 3. Review. PubMed PMID: 22480731; PubMed Central PMCID: PMC3508674.

Sapp E, Valencia A, Li X, Aronin N, Kegel KB, Vonsattel JP, Young AB, Wexler N, DiFiglia M. Native mutant huntingtin in human brain: evidence for prevalence of full-length monomer. J Biol Chem. 2012 Apr 13;287(16):13487-99. doi: 10.1074/jbc.M111.286609. Epub 2012 Feb 27. PubMed PMID: 22375012; PubMed Central PMCID: PMC3339996.

Xie J, Ameres SL, Friedline R, Hung JH, Zhang Y, Xie Q, Zhong L, Su Q, He R, Li M, Li H, Mu X, Zhang H, Broderick JA, Kim JK, Weng Z, Flotte TR, Zamore PD, Gao G. Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nat Methods. 2012 Mar 4;9(4):403-9. doi: 10.1038/nmeth.1903. PubMed PMID: 22388288; PubMed Central PMCID: PMC3420816.

Grünwald D, Singer RH. Multiscale dynamics in nucleocytoplasmic transport. Curr Opin Cell Biol. 2012 Feb;24(1):100-6. doi: 10.1016/j.ceb.2011.11.011. Epub 2011 Dec 22. Review. PubMed PMID: 22196930; PubMed Central PMCID: PMC3294057.

Khvorova A, Wolfson A. New competition in RNA regulation. Nat Biotechnol. 2012 Jan 9;30(1):58-9. doi: 10.1038/nbt.2092. PubMed PMID: 22231098.