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eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons.

Yang Q, Yu CH, Zhao F, Dang Y, Wu C, Xie P, Sachs MS, Liu Y.

Nucleic Acids Res. 2019 Sep 26;47(17):9243-9258. doi: 10.1093/nar/gkz710.


The cell free protein synthesis system from the model filamentous fungus Neurospora crassa.

Wu C, Dasgupta A, Shen L, Bell-Pedersen D, Sachs MS.

Methods. 2018 Mar 15;137:11-19. doi: 10.1016/j.ymeth.2017.12.003. Epub 2017 Dec 30.


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.


Synaptic vesicles isolated from the electric organ of Torpedo californica and from the central nervous system of Mus musculus contain small ribonucleic acids (sRNAs).

Li H, Wu C, Aramayo R, Sachs MS, Harlow ML.

Genom Data. 2017 Mar 8;12:52-53. doi: 10.1016/j.gdata.2017.02.015. eCollection 2017 Jun.


The Neurospora Transcription Factor ADV-1 Transduces Light Signals and Temporal Information to Control Rhythmic Expression of Genes Involved in Cell Fusion.

Dekhang R, Wu C, Smith KM, Lamb TM, Peterson M, Bredeweg EL, Ibarra O, Emerson JM, Karunarathna N, Lyubetskaya A, Azizi E, Hurley JM, Dunlap JC, Galagan JE, Freitag M, Sachs MS, Bell-Pedersen D.

G3 (Bethesda). 2017 Jan 5;7(1):129-142. doi: 10.1534/g3.116.034298.


Circadian clock regulation of mRNA translation through eukaryotic elongation factor eEF-2.

Caster SZ, Castillo K, Sachs MS, Bell-Pedersen D.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9605-10. doi: 10.1073/pnas.1525268113. Epub 2016 Aug 9.


Structure and function of the yeast listerin (Ltn1) conserved N-terminal domain in binding to stalled 60S ribosomal subunits.

Doamekpor SK, Lee JW, Hepowit NL, Wu C, Charenton C, Leonard M, Bengtson MH, Rajashankar KR, Sachs MS, Lima CD, Joazeiro CA.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4151-60. doi: 10.1073/pnas.1605951113. Epub 2016 Jul 6.


Ribosome Elongation Stall Directs Gene-specific Translation in the Integrated Stress Response.

Young SK, Palam LR, Wu C, Sachs MS, Wek RC.

J Biol Chem. 2016 Mar 18;291(12):6546-58. doi: 10.1074/jbc.M115.705640. Epub 2016 Jan 27.


Ribosome Reinitiation Directs Gene-specific Translation and Regulates the Integrated Stress Response.

Young SK, Willy JA, Wu C, Sachs MS, Wek RC.

J Biol Chem. 2015 Nov 20;290(47):28257-71. doi: 10.1074/jbc.M115.693184. Epub 2015 Oct 7.


Synaptic vesicles contain small ribonucleic acids (sRNAs) including transfer RNA fragments (trfRNA) and microRNAs (miRNA).

Li H, Wu C, Aramayo R, Sachs MS, Harlow ML.

Sci Rep. 2015 Oct 8;5:14918. doi: 10.1038/srep14918.


Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding.

Yu CH, Dang Y, Zhou Z, Wu C, Zhao F, Sachs MS, Liu Y.

Mol Cell. 2015 Sep 3;59(5):744-54. doi: 10.1016/j.molcel.2015.07.018. Epub 2015 Aug 27.


Control of mRNA Stability in Fungi by NMD, EJC and CBC Factors Through 3'UTR Introns.

Zhang Y, Sachs MS.

Genetics. 2015 Aug;200(4):1133-48. doi: 10.1534/genetics.115.176743. Epub 2015 Jun 4.


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.


Genome-wide characterization of light-regulated genes in Neurospora crassa.

Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS.

G3 (Bethesda). 2014 Jul 21;4(9):1731-45. doi: 10.1534/g3.114.012617.


Preparation of a Saccharomyces cerevisiae cell-free extract for in vitro translation.

Wu C, Sachs MS.

Methods Enzymol. 2014;539:17-28. doi: 10.1016/B978-0-12-420120-0.00002-5.


Interactions of the TnaC nascent peptide with rRNA in the exit tunnel enable the ribosome to respond to free tryptophan.

Martínez AK, Gordon E, Sengupta A, Shirole N, Klepacki D, Martinez-Garriga B, Brown LM, Benedik MJ, Yanofsky C, Mankin AS, Vazquez-Laslop N, Sachs MS, Cruz-Vera LR.

Nucleic Acids Res. 2014 Jan;42(2):1245-56. doi: 10.1093/nar/gkt923. Epub 2013 Oct 16.


Reconstruction and validation of a genome-scale metabolic model for the filamentous fungus Neurospora crassa using FARM.

Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE.

PLoS Comput Biol. 2013;9(7):e1003126. doi: 10.1371/journal.pcbi.1003126. Epub 2013 Jul 18.


Non-optimal codon usage affects expression, structure and function of clock protein FRQ.

Zhou M, Guo J, Cha J, Chae M, Chen S, Barral JM, Sachs MS, Liu Y.

Nature. 2013 Mar 7;495(7439):111-5. doi: 10.1038/nature11833. Epub 2013 Feb 17.


The stringency of start codon selection in the filamentous fungus Neurospora crassa.

Wei J, Zhang Y, Ivanov IP, Sachs MS.

J Biol Chem. 2013 Mar 29;288(13):9549-62. doi: 10.1074/jbc.M112.447177. Epub 2013 Feb 8.


The arginine attenuator peptide interferes with the ribosome peptidyl transferase center.

Wei J, Wu C, Sachs MS.

Mol Cell Biol. 2012 Jul;32(13):2396-406. doi: 10.1128/MCB.00136-12. Epub 2012 Apr 16.


The antidepressant sertraline provides a promising therapeutic option for neurotropic cryptococcal infections.

Zhai B, Wu C, Wang L, Sachs MS, Lin X.

Antimicrob Agents Chemother. 2012 Jul;56(7):3758-66. doi: 10.1128/AAC.00212-12. Epub 2012 Apr 16.


Arginine changes the conformation of the arginine attenuator peptide relative to the ribosome tunnel.

Wu C, Wei J, Lin PJ, Tu L, Deutsch C, Johnson AE, Sachs MS.

J Mol Biol. 2012 Mar 2;416(4):518-33. doi: 10.1016/j.jmb.2011.12.064. Epub 2012 Jan 5.


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.


Crucial elements that maintain the interactions between the regulatory TnaC peptide and the ribosome exit tunnel responsible for Trp inhibition of ribosome function.

Martínez AK, Shirole NH, Murakami S, Benedik MJ, Sachs MS, Cruz-Vera LR.

Nucleic Acids Res. 2012 Mar;40(5):2247-57. doi: 10.1093/nar/gkr1052. Epub 2011 Nov 21.


Nascent polypeptide sequences that influence ribosome function.

Cruz-Vera LR, Sachs MS, Squires CL, Yanofsky C.

Curr Opin Microbiol. 2011 Apr;14(2):160-6. doi: 10.1016/j.mib.2011.01.011. Epub 2011 Feb 20. Review.


Initiation context modulates autoregulation of eukaryotic translation initiation factor 1 (eIF1).

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

Proc Natl Acad Sci U S A. 2010 Oct 19;107(42):18056-60. doi: 10.1073/pnas.1009269107. Epub 2010 Oct 4.


Sequence requirements for ribosome stalling by the arginine attenuator peptide.

Spevak CC, Ivanov IP, Sachs MS.

J Biol Chem. 2010 Dec 24;285(52):40933-42. doi: 10.1074/jbc.M110.164152. Epub 2010 Sep 30.


Evolutionary roles of upstream open reading frames in mediating gene regulation in fungi.

Hood HM, Neafsey DE, Galagan J, Sachs MS.

Annu Rev Microbiol. 2009;63:385-409. doi: 10.1146/annurev.micro.62.081307.162835. Review.


Characterization of chromosome ends in the filamentous fungus Neurospora crassa.

Wu C, Kim YS, Smith KM, Li W, Hood HM, Staben C, Selker EU, Sachs MS, Farman ML.

Genetics. 2009 Mar;181(3):1129-45. doi: 10.1534/genetics.107.084392. Epub 2008 Dec 22.


A high-density single nucleotide polymorphism map for Neurospora crassa.

Lambreghts R, Shi M, Belden WJ, Decaprio D, Park D, Henn MR, Galagan JE, Bastürkmen M, Birren BW, Sachs MS, Dunlap JC, Loros JJ.

Genetics. 2009 Feb;181(2):767-81. doi: 10.1534/genetics.108.089292. Epub 2008 Nov 17.


Dissection of a co-translational nascent chain separation event.

Doronina VA, de Felipe P, Wu C, Sharma P, Sachs MS, Ryan MD, Brown JD.

Biochem Soc Trans. 2008 Aug;36(Pt 4):712-6. doi: 10.1042/BST0360712.


Site-specific release of nascent chains from ribosomes at a sense codon.

Doronina VA, Wu C, de Felipe P, Sachs MS, Ryan MD, Brown JD.

Mol Cell Biol. 2008 Jul;28(13):4227-39. doi: 10.1128/MCB.00421-08. Epub 2008 May 5.


The use of fungal in vitro systems for studying translational regulation.

Wu C, Amrani N, Jacobson A, Sachs MS.

Methods Enzymol. 2007;429:203-25.


Translation factor control of ribosome conformation during start codon selection.

Asano K, Sachs MS.

Genes Dev. 2007 Jun 1;21(11):1280-7. No abstract available.


Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons.

Tian C, Kasuga T, Sachs MS, Glass NL.

Eukaryot Cell. 2007 Jun;6(6):1018-29. Epub 2007 Apr 20.


Enabling a community to dissect an organism: overview of the Neurospora functional genomics project.

Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Baştürkmen M, Altamirano L, Xu J.

Adv Genet. 2007;57:49-96. Review.


her-2 upstream open reading frame effects on the use of downstream initiation codons.

Spevak CC, Park EH, Geballe AP, Pelletier J, Sachs MS.

Biochem Biophys Res Commun. 2006 Dec 1;350(4):834-41. Epub 2006 Oct 2.


Evolutionary changes in the fungal carbamoyl-phosphate synthetase small subunit gene and its associated upstream open reading frame.

Hood HM, Spevak CC, Sachs MS.

Fungal Genet Biol. 2007 Feb;44(2):93-104. Epub 2006 Sep 18.


Regulatory protein that inhibits both synthesis and use of the target protein controls flagellar phase variation in Salmonella enterica.

Aldridge PD, Wu C, Gnerer J, Karlinsey JE, Hughes KT, Sachs MS.

Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11340-5. Epub 2006 Jul 14.


Early nonsense: mRNA decay solves a translational problem.

Amrani N, Sachs MS, Jacobson A.

Nat Rev Mol Cell Biol. 2006 Jun;7(6):415-25. Review.


Downstream control of upstream open reading frames.

Sachs MS, Geballe AP.

Genes Dev. 2006 Apr 15;20(8):915-21. No abstract available.


Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae.

Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D'Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW.

Nature. 2005 Dec 22;438(7071):1105-15.


A nascent polypeptide domain that can regulate translation elongation.

Fang P, Spevak CC, Wu C, Sachs MS.

Proc Natl Acad Sci U S A. 2004 Mar 23;101(12):4059-64. Epub 2004 Mar 12.


Lessons from the genome sequence of Neurospora crassa: tracing the path from genomic blueprint to multicellular organism.

Borkovich KA, Alex LA, Yarden O, Freitag M, Turner GE, Read ND, Seiler S, Bell-Pedersen D, Paietta J, Plesofsky N, Plamann M, Goodrich-Tanrikulu M, Schulte U, Mannhaupt G, Nargang FE, Radford A, Selitrennikoff C, Galagan JE, Dunlap JC, Loros JJ, Catcheside D, Inoue H, Aramayo R, Polymenis M, Selker EU, Sachs MS, Marzluf GA, Paulsen I, Davis R, Ebbole DJ, Zelter A, Kalkman ER, O'Rourke R, Bowring F, Yeadon J, Ishii C, Suzuki K, Sakai W, Pratt R.

Microbiol Mol Biol Rev. 2004 Mar;68(1):1-108. Review.


Redundancy of the two dicer genes in transgene-induced posttranscriptional gene silencing in Neurospora crassa.

Catalanotto C, Pallotta M, ReFalo P, Sachs MS, Vayssie L, Macino G, Cogoni C.

Mol Cell Biol. 2004 Mar;24(6):2536-45.


The genome sequence of the filamentous fungus Neurospora crassa.

Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read ND, Jaffe D, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Endrizzi M, Qui D, Ianakiev P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Mauceli E, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Cogoni C, Macino G, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CP, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaupt G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C, Birren B.

Nature. 2003 Apr 24;422(6934):859-68.


Biochemistry. Sense and sensitivity--controlling the ribosome.

Sachs MS, Geballe AP.

Science. 2002 Sep 13;297(5588):1820-1. No abstract available.


Neurospora crassa supersuppressor mutants are amber codon-specific.

Fang P, Wu C, Sachs MS.

Fungal Genet Biol. 2002 Aug;36(3):167-75.


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