Bartel Lab Publications

2008

Baek, D., J. Villén, C. Shin, F.D. Camargo, S.P. Gygi, and D.P. Bartel. 2008. The impact of microRNAs on protein output. Nature epub ahead of print July 30, 2008.

Stark, A., N. Bushati, C.H. Jan, P. Kheradpour, E. Hodges, J. Brennecke, D.P. Bartel, S.M. Cohen and M. Kellis. 2008. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. GenesDev 22:8-13. Supplemental Material

Müller, U.F and D.P. Bartel. 2008. Improved polymerase ribozyme efficiency on hydrophobic assemblies. RNA 14:552-62.

Okamura, K. W.J. Chung, J.G. Ruby, H. Guo, D.P. Bartel and E.C. Lai. 2008. The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs. Nature epub ahead of print May 7, 2008. Supplemental Material

Addo-Quaye, C., T.W. Eshoo, D.P. Bartel and M.J. Axtell. 2008. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis Degradome. CurrBiol epub ahead of print May 7, 2008. Supplemental Material (2)

2007

Miska, E.A., E. Alvarez-Saavedra, A.L. Abbott, N.C. Lau, A.B. Hellman, S.M. McGonagle, D.P. Bartel, V.R. Ambros and H.R. Horvitz. 2007. Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 3:e215.

Stark, A., M.F. Lin, P. Kheradpour, J.S. Pederson, L. Parts, J.W. Carlson, M.A. Crosby, M.D. Rasmussen, S. Roy, A.N. Deoras, J.G. Ruby, et al. 2007. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450:219-232.

Ruby, J.G., A. Stark, W.K. Johnston, M. Kellis, D.P. Bartel and E.C. Lai. 2007. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res. 17:1850-1864. Supplemental Material

Ruby, J.G., C.H. Jan and D.P. Bartel. 2007. Initronic microRNA precursors that bypass Drosha processing. Nature 448:83-87. Supplemental Material

Grimson, A.G., K.K. Farh, W.K. Johnston, P. Garrett-Engele, L.P. Lim and D.P. Bartel. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. MolCell 27:91-105. Supplemental Material

Axtell, M.A., J. Snyder and D.P. Bartel. 2007. Common functions for diverse small RNAs of land plants. Plant Cell 19:1750-1769. Supplemental Material

Mayr, C. M.T. Hemann and D.P. Bartel. 2007. Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation. Science 315: 1576-1579. Supplemental Material

Zhou, B., S. Wang, C. Mayr, D.P. Bartel and H.F. Lodish. 2007. miR-150, a microRNA expressed in mature B and T cells, blocks early B cell development when expressed prematurely. Proc Natl Acad Sci USA 104: 7080-7085. Supplemental Material

2006

Ruby, J.G., C. Jan, C. Player, M.J. Axtell, W. Lee, C. Nusbaum, H. Ge and D.P. Bartel. 2006. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193-1207. Supplemental Material

Rajagopalan, R., H. Vaucheret, J. Trejo and D.P. Bartel. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. GenesDev 20:3407-3425.

Axtell, M.A., C. Jan, R. Rajagopalan and D.P. Bartel. 2006. A two-hit trigger for siRNA biogenesis in plants. Cell 127: 565-577.

Lau, N.C., A.G. Seto, J. Kim, S. Kuramochi-Miyagawa, T. Nakano, D.P. Bartel and R.E. Kingston. 2006. Characterization of the piRNA complex from rat tests. Science 313: 363-367. Supplemental Material

Vaucheret, H., A.C. Mallory and D.P. Bartel. 2006. AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. Mol Cell 22:129-136.

Jones-Rhoades, M.W., D.P. Bartel and B. Bartel. 2006. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant. Biol. 57: 19-53. (Review)

2005

Lewis, B.P., C.B. Burge and D.P. Bartel. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15-20. Supplemental Material

Lim, L.P., N.C. Lau, P. Garrett-Engele, A. Grimson, J.M. Schelter, J. Castle, D.P. Bartel, P.S. Linsley and J.M. Johnson. 2005. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769-773. Supplemental Material

Farh, K.K., A.Grimson, C. Jan, B.P. Lewis, W. Johnston, L. P. Lim, C. Burge, and D.P. Bartel. 2005. The widespread impact of mammalian microRNAs on mRNA repression and evolution. Science 310:1817-1821. Supplemental Material

Baskerville, S. and D.P. Bartel. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 11:241-247. Supplemental Material

Giraldez, A.J., R.M. Cinalli, M.E. Glasner, A.J. Enright, M.J. Thomson, S. Baskerville, S.M. Hammond, D.P. Bartel, and A.F. Schier. 2005. MicroRNAs Regulate Brain Morphogenesis in Zebrafish. Science 308: 833-838. Supplemental Material

Mallory, A.C., D.P. Bartel, and B. Bartel. 2005. MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes. Plant Cell 17: 1360-1375. Supplemental Material

Axtell, M.J. and D.P. Bartel. 2005. Antiquity of microRNAs and their targets in plants. Plant Cell 17: 1658-1673. Supplemental Material

Curtis E.A.and D.P. Bartel. 2005. New catalytic structures from an existing ribozyme. Nat Struct Mol Biol. 12:994-1000. Supplemental Material

Schultes E.A., A. Spasic, U. Mohanty, and D.P.Bartel. 2005. Compact and ordered collapse of randomly generated RNA sequences. Nat Struct Mol Biol. 12:1130-1136.

Lawrence, M. and D.P. Bartel. 2005. New ligase-derived RNA polymerase ribozymes. RNA 11:1173-1180.

Gasciolli, V., A.C. Mallory, D.P. Bartel, and H. Vaucheret. 2005. Partially Redundant Functions of Arabidopsis DICER-like Enzymes and a Role for DCL4 in Producing trans-Acting siRNAs. CurrBiol 15:1494-1500.

Matranga C., Y. Tomari, C. Shin, D.P. Bartel, and P.D. Zamore. 2005. Passenger-strand cleavage facilitates assembly of siRNA into ago2-containing RNAi enzyme complexes. Cell 123:607-620. Supplemental Material

Li M., M.W. Jones-Rhoades, N.C. Lau, D.P. Bartel, and A.E. Rougvie. 2005. Regulatory mutations of mir-48, a C. elegans let-7 family microRNA, cause developmental timing defects. Dev Cell 9:415-422. Supplemental Material

Abbott A.L., E. Alvarez-Saavedra, E.A. Miska, N.C. Lau, D.P. Bartel, H.R. Horvitz, and V. Ambros. 2005. The let-7 microRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell 9:403-414. Supplemental Material

Hornstein, E., J.H. Mansfield, S.Yekta, J.K. Hu, B.D. Harfe, M.T. McManus, S. Baskerville, D.P. Bartel, and C.J. Tabin. 2005. The microRNA miR-196 acts upstream of Hoxb8 and Shh in linb development. Nature 438: 671-674. Supplemental Material

2004

Bartel, D.P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297. (Review)

Chen, C.Z., L. Li, H.F. Lodish and D.P. Bartel. 2004. MicroRNAs modulate hematopoietic lineage differentiation. Science 303:83-86.

Yekta, S., I.H. Shih, D.P. Bartel. 2004. MicroRNA-directed cleavage of HOXB8 mRNA. Science 304:594-596.

Jones-Rhoades, M.W. and D.P. Bartel. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787-799. Supplemental Material

Ohler, U., S. Yekta, L. Lim, D.P. Bartel, and C. Burge. 2004. Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA 10:1309-1322.

Mallory, A.C., B.J. Reinhart, M.W. Jones-Rhoades, G. Tang, P.D. Zamore, M.K. Barton, and D.P. Bartel. 2004. MicroRNA conrol of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region. EMBO 23: 3356-3364.

Mallory, A.C., D.V. Dugas, D.P. Bartel and B. Bartel. 2004. MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol 14:1035-1046.

Vazquez, F., H. Vaucheret, R. Rajagopalan, C. Lepers, V. Gasciolli, A.C. Mallory, J.-L. Hilbert, D.P. Bartel and P. Crete. 2004. Endogenous trans-acting siRNAs regaulte the acccumulation of Arabidopsis mRNAs. MolCell 16:69-79.

Bergman N.H., N.C. Lau, V. Lehnert, E. Westhof, and D.P. Bartel. 2004. The three-dimensional architecture of the class I ligase ribozyme. RNA 10:176-184.

Vaucheret, H.V.F. Vazquez, P. Crete, and D.P. Bartel. 2004. The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development. Genes Dev 18: 1187-1197.

Bartel, D.P. and C.Z. Chen. 2004. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs.
Nat Rev Genet. 5:396-400. (Opinion)

2003

Lim, L.P., N.C. Lau, E.G. Weinstein, A. Abdelhakim, S. Yekta, M.W. Rhoades, C.B. Burge, and D.P. Bartel. 2003. The microRNAs of Caenorhabditis elegans. Genes Dev. 17:991. Supplemental Material

Lim L.P., M.E. Glasner, S. Yekta, C.B. Burge, and D.P. Bartel. 2003. Vertebrate microRNA genes. Science 299:1540.

Lewis B. P., I.H. Shih, M.W. Jones-Rhoades, D.P. Bartel and C.B. Burge. 2003. Prediction of mammalian microRNA targets. Cell 115:787-798. Supplemental Material TargetScan Web Server

Bartel, B. and D.P. Bartel. 2003. MicroRNAs: At the Root of Plant Development? Plant Physiology 132:709-717.

Lawrence, M.S. and D.P. Bartel. 2003. Processivity of ribozyme-catalyzed RNA polymerization. Biochemistry 42:8748-8755.

Lau, N.C. and D.P. Bartel. 2003. Censors of the Genome. Sci Am 289: 34-41.

Chapple, K.E., Bartel, D.P. and P.J. Unrau. 2003. Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme. RNA 9:1208-1220.

Muller, U.F. and D.P. Bartel. 2003. Substrate 2'-hydroxyl groups required for ribozyme-catalyzed polymerization. Chem. Biol. 10: 799-806.

Unrau, P.J. and D.P. Bartel. 2003. An oxocarbenium-ion intermediate of a ribozyme reaction indicated by kinetic isotope effects. Proc Natl Acad Sci USA 100:15393-15397.

Tang, G., B.J. Reinhart, D.P. Bartel, and P.D. Zamore. 2003. A biochemical framework for RNA silencing in plants. Genes Dev. 17:49.

Ambros V., B. Bartel, D.P. Bartel, C.B. Burge, J.C. Carrington, X. Chen, G. Dreyfuss, S.R. Eddy, S. Griffiths-Jones, M. Marshall, M. Matzke, G. Ruvkun, and T. Tuschl. 2003. A uniform system for microRNA annotation. RNA 9:277-279.

2002

Reinhart, B.J., E.G. Weinstein, M.W. Rhoades, B. Bartel, and D.P. Bartel. 2002. MicroRNAs in plants. Genes Dev. 16:1616-1626.

Rhoades, M.W., B.J. Reinhart, L.P. Lim, C.B. Burge, B. Bartel and D.P. Bartel. 2002. Prediction of plant microRNA targets. Cell 110: 513-520.

Reinhart, B.J. and D.P. Bartel. 2002. Small RNAs correspond to centromere heterochromatic repeats. Science 297: 1831.

Glasner, M.E., N.H. Bergman, and D.P. Bartel. 2002. Metal ion requirements for structure and catalysis of an RNA ligase ribozyme. Biochemistry 41:8103-8112.

Merryman, C., E. Weinstein, S.F. Wnuk, and D.P. Bartel. 2002. A bifunctional tRNA for in vitro selection. Chem. Biol.9:741-746.

Baskerville, S. and D.P. Bartel. 2002. A ribozyme that ligates RNA to protein. PNAS 99: 9154-9159.

Mallory, A.C., B.J. Reinhart, D.P. Bartel, V.B. Vance, and L.H. Bowman. 2002. A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and microRNAs in tobacco. PNAS 99: 15228-15233.

2001

Johnston, W.K., P.J. Unrau, M.S. Lawrence, M.E. Glasner, and D.P. Bartel. 2001. RNA-catalyzed RNA- polymerization: Accurate and general RNA -templated primer extension. Science 292:1319-1325. Supplemental Material

Lau, N.C., L.P. Lim, E.G. Weinstein, and D.P. Bartel. 2001. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858-862. Supplemental Material

Tuschl, T., P.A. Sharp, and D.P. Bartel. 2001. A ribozyme selected from variants of U6 promotes 2',5'-branch formation. RNA 7:29-43.

Szostak, J.W., D.P. Bartel, and L. Luisi. 2001. Synthesizing life. Nature 409:387-439.

Curtis, E.A. and D.P. Bartel. 2001. The hammerhead cleavage reaction in monovalent cations. RNA 7:546-552.

2000

Bergman, N.H., W.K. Johnston, and D.P. Bartel. 2000. Kinetic framework for ligation by an efficient RNA ligase ribozyme. Biochemistry 39:3115-3123.

Zamore, P.D., T. Tuschl, P.A. Sharp, and D.P. Bartel. 2000. RNAi: dsRNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101:25-33.

Schultes, E.A and D.P. Bartel. 2000. One sequence, two ribozymes: Implications for the emergence of new ribozyme folds. Science 289(5478):448-452.

Glasner M.E., C.C. Yen, E.H. Ekland, and D.P. Bartel. 2000. Recognition of nucleoside triphosphates during RNA-catalyzed primer extension. Biochemistry 39:15556-62.

1999

Bartel, D.P. 1999. Re-creating an RNA replicase. In The RNA World II. Gesteland, R.F., T.R. Cech, and J.F. Atkins, eds. (Cold Spring Harbor Laboratory Press), pp.143-161.

Zamore, P.D., D.P. Bartel, R. Lehmann, and J.R. Williamson. 1999. The PUMILIO-RNA interaction: A single RNA-binding domain monomer recognizes a bipartite target sequence. Biochemistry 38: 596-604.

Williams, P.K., K.A. Martindale and D.P. Bartel. 1999. Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO J. 18:5423-5433.

Bartel, D.P. and P.J. Unrau. 1999. Constructing an RNA world. Trends Biochem. Sci. 24:M9-12; Trends Cell Biol. 9:M9-12; Trends Genet. 15:M9-12 (joint issue).

Tuschl, T., P.D. Zamore, R. Lehmann, D.P. Bartel and P.A. Sharp. 1999. Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev. 13:3191-7.

1998

Williams, K.P. and D.P. Bartel. 1998. The tmRNA website. Nucleic Acids Res. 26:163-165.

Tuschl, T., P.A. Sharp, and D.P. Bartel. 1998. Selection in vitro of novel ribozymes from a partially randomized U2 and U6 snRNA library. EMBO J. 17:2637-2650.

Unrau, P.J. and D.P. Bartel. 1998. RNA-catalyzed nucleotide synthesis. Nature 395:260-263.

1997

Williams, K.P., X.-H. Liu, T.N.M. Schumacher, H.Y. Lin, D.A. Ausiello, P.S. Kim, and D.P. Bartel. 1997. Bioactive and nuclease-resistant l-DNA ligand of vasopressin. PNAS 94:11285-11290.

Sabeti, P.C., P.J. Unrau and D.P. Bartel. 1997. Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem. Biol. 4:767-774.

1996

Williams, K.P. and D.P. Bartel. 1996. In vitro selection of catalytic RNA. In Nucleic Acids and Molecular Biology, Vol. 10, F. Eckstein and D.M.J. Lilley, eds. (Springer-Verlag) pp 367-381.

Williams, K.P. and D.P. Bartel. 1996. Phylogenetic analysis of tmRNA secondary structure. RNA 2:1306-1310.

Ekland, E.H. and D.P. Bartel. 1996. RNA-catalyzed RNA polymerization using nucleoside triphosphates. Nature 382:373-6.

1995

Ekland, E.H., J.W. Szostak, and D.P. Bartel. 1995. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269:364-370.

Ekland, E.H. and D.P. Bartel. 1995. Secondary structure and sequence optimization of an RNA ligase ribozyme. Nucleic Acids Res. 23:3231-3238.

Williams, K.P. and D.P. Bartel. 1995. PCR product with strands of unequal length. Nucleic Acids Res. 23:4220-1.