Phage biology: Stuck with dU. Marine phages with DNA containing deoxyuridine discovered. Yoav S. Arava and Oded Beja (2021) Current Biology (Dispatch) 31 (16) PR898-R900
Mitochondria serve as axonal shuttle for Cox7c mRNA through mechanism that involves its mitochondrial targeting signal Bar Cohen*, Adi Golani*, Topaz Altman*, Anca F. Savulescu, Musa M. Mhlanga, Eran Perlson** and Yoav S. Arava** (2021) BioRxiv https://doi.org/10.1101/2021.05.19.444640
Comprehensive characterization of mRNA targets of yeast aminoacyl tRNA synthetases Shahar Garin1, Ofri Levi1, Megan Forrest2, Anthony Antonellis2, and Yoav S. Arava1 (2021) RNA Biology, in press
RNA modifications as a common denominator between tRNA and mRNA Ofri Levi and Yoav S. Arava (2021) Current Genetics, 67, pages545–551
Pseudouridine-mediated translation control by methionine aminoacyl tRNA synthetase, Ofri Levi and Yoav S. Arava (2021) Nucleic Acids Research, 49(1):432-443.
Localization and RNA binding of mitochondrial aminoacyl tRNA synthetases, Shahar Garin, Ofri Levi, Bar Cohen, Adi Golani and Yoav S. Arava (2020) Genes, 11(10), 1185
CytoCensus, mapping cell identity and division in tissues and organs using machine learning. Hailstone M, Waithe D, Samuels TJ, Yang L, Costello I, Arava Y, Robertson E, Parton RM, Davis I (2020) Elife. 2020 May 19;9:e51085. doi: 10.7554/eLife.51085.
Neuronal upregulation of Prospero protein is driven by alternative mRNA polyadenylation and Syncrip-mediated mRNA stabilisation Samuels TJ, Arava Y, Järvelin AI, Robertson F, Lee JY, Yang L, Yang CP, Lee T, Ish-Horowicz D, Davis I.Biol Open. 2020 May 4;9(5):bio049684. doi: 10.1242/bio.049684.
Characterization of factors involved in localized translation near mitochondria by ribosome-proximity labeling. Vardi-Oknin D. and Arava Y. (2019) Frontiers in Cell and Developmental Biology, Front. Cell Dev. Biol., 26 November 2019
Distinct RNA-binding modules in a single PUF protein cooperate to determine RNA specificity. Chen Qiu, Robert C. Dutcher, Douglas F. Porter, Yoav Arava, Marvin Wickens and Traci M. Tanaka Hall (2019) Nucleic Acids Research, 47(16):8770-8784.
mRNA association by aminoacyl tRNA synthetase occurs at a putative anticodon mimic and autoregulates translation in response to tRNA levels. Levy O. and Arava Y. (2019) PLoS Biology, 2019 May 17;17(5):e3000274
The extent of ribosome queuing in budding yeast. Diament A, Feldman A, Schochet E, Kupiec M, Arava Y, Tuller T. PLoS Comput Biol. 2018 Jan 29;14(1):e1005951.
Identification and characterization of roles for Puf1 and Puf2 proteins in the yeast response to high calcium. Haramati O, Brodov A, Yelin I, Atir-Lande A, Samra N, Arava Y. Sci Rep. 2017 Jun 8;7(1):3037
Localization of Nuclear-Encoded mRNAs to Mitochondria Outer Surface. Golani-Armon A, Arava Y. Biochemistry (Mosc). 2016 Oct;81(10):1038-1043.
The elongation factor eEF3 (Yef3) interacts with mRNA in a translation independent manner. Samra N, Atir-Lande A, Pnueli L, Arava Y. BMC Mol Biol. 2015 Sep 24;16(1):17
Localized translation near the mitochondrial outer membrane: An update. Lesnik C, Golani-Armon A, Arava Y. RNA Biol. 2015 Aug 3;12(8):801-9
Overexpression of eIF5 rescues the translational defect of tpk1w in a manner that necessitates a novel phosphorylation site. Bavli-Kertselli I, Melamed D, Bar-Ziv L, Volf H, Arava Y. FEBS J. 2015 Feb;282(3):504-20.
OM14 is a mitochondrial receptor for cytosolic ribosomes that supports co-translational import into mitochondria. Lesnik C, Cohen Y, Atir-Lande A, Schuldiner M and Arava Y. Nature Communications 2014 Dec 9;5:5711.
Isolation of mRNAs associated with yeast mitochondria to study mechanisms of localized translation. Lesnik C and Arava Y. J Vis Exp. 2014 Mar 14;(85).
A molecular cryptosystem for images by DNA computing Shoshani S, Piran R, Arava Y, Keinan E. Angew Chem Int Ed Engl.. 2012 Mar 19;51(12):2883-7.
The protein chaperone Ssa1 affects mRNA localization to the mitochondria. Eliyahu E*, Lesnik C* and Arava Y. FEBS Lett. 2012 Jan 2;586(1):64-9.
Divergent RNA binding specificity of yeast Puf2p. Yosefzon Y, Koh YY, Chritton JJ, Lande A, Leibovich L, Barziv L, Petzold C, Yakhini Z, Mandel-Gutfreund Y, Wickens M, Arava Y. RNA. 2011 Aug;17(8):1479-88.
Genome-wide analysis of RNA extracted from isolated mitochondria. Eliyahu E, Melamed D, Arava Y. Methods Mol Biol. 2011;714:287-99.
SpRET: highly sensitive and reliable spectral measurement of absolute FRET efficiency. Levy S, Wilms CD, Brumer E, Kahn J, Pnueli L, Arava Y, Eilers J, Gitler D. Microsc Microanal. 2011 Apr;17(2):176-90. Epub 2011 Feb 21.
Asc1 supports cell-wall integrity near bud sites by a Pkc1 independent mechanism. Melamed D, Bar-Ziv L, Truzman Y, Arava Y. PLoS One 2010 jun;5(6):e11389
Tom20 mediates localization of mRNAs to mitochondria in a translation-dependent manner Eliyahu E, Pnueli L, Melamed D, Scherrer T, Gerber AP, Pines O, Rapaport D, Arava Y. Mol Cell Biol. 2010 Oct 26.
Compaction of polyribosomal mRNA. Arava Y. RNA Biol. 2009 Sep-Oct;6(4):399-401.
Exploring translation regulation by global analysis of ribosomal association. Melamed D. Eliyahu E, Arava Y. Methods. 2009 Jul;48(3):301-5.
Identification and characterization of extensive intra-molecular associations between 3’-UTRs and their ORFs. Eldad N, Yosefzon Y, Arava Y. Nucleic Acids Res. 2008 Dec;36(21):6728-38.
Yeast translational response to high salinity: Global analysis reveals regulation at multiple levels. Melamed D, Pnueli L, Arava Y. RNA. 2008 Jul;14(7):1337-51.
The 3′-UTR mediates the cellular localization of an mRNA encoding a short plasma membrane protein. Loya A, Pnueli L, Yosefzon Y, Wexler Y, Ziv-Ukelson M, Arava Y. RNA. 2008 Jul;14(7):1352-65.
A ribosomal density-mapping procedure to explore ribosome positions along translating mRNAs. Eldad N, Arava Y. Methods Mol Biol. 2008;419:231-42.
Genome-wide analysis of mRNA polysomal profiles with spotted DNA microarrays. Melamed D, Arava Y. Methods Enzymol. 2007;431:177-201.
Detecting ribosomal association with the 5′ leader of mRNAs by Ribosome Density Mapping (RDM). Eldad N, Arava Y. Methods Enzymol. 2007;431:163-75.
Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9 Pnueli L, Arava Y. BMC Genomics. 2007 Aug 21;8:285.
Dissecting eukaryotic translation and its control by ribosome density mapping. Arava Y, Boas FE, Brown PO, Herschlag D. Nucleic Acids Res. 2005 Apr 28;33(8):2421-32. Print 2005.
Genome-wide analysis of pre-mRNA splicing: intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. Sapra AK, Arava Y, Khandelia P, Vijayraghavan U. J Biol Chem. 2004 Dec 10;279(50):52437-46.
Isolation of polysomal RNA for microarray analysis. Arava Y. Methods Mol Biol. 2003;224:79-87 .
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D. Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3889-94.
GRFbeta, a novel regulator of calcium signaling, is expressed in pancreatic beta cells and brain. Arava Y, Seger R, Walker MD. J Biol Chem. 1999 Aug 27;274(35):24449-52.
Specific gene expression in pancreatic beta-cells: cloning and characterization of differentially expressed genes. Arava Y, Adamsky K, Ezerzer C, Ablamunits V, Walker MD. Diabetes. 1999 Mar;48(3):552-6.
Differential expression of the protein kinase A regulatory subunit (RIalpha) in pancreatic endocrine cells. Arava Y, Adamsky K, Belleli A, Shaltiel S, Walker MD. FEBS Lett. 1998 Mar 20;425(1):24-8. pdf
An activation domain of the helix-loop-helix transcription factor E2A shows cell type preference in vivo in microinjected zebra fish embryos. Argenton F, Arava Y, Aronheim A, Walker MD. Mol Cell Biol. 1996 Apr;16(4):1714-21.