Ninova M, Chen YA, Godneeva B, Rogers AK, Luo Y, Fejes Tóth K, Aravin AA. Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing (2020) Mol Cell. 77(3):556-570.e6. doi: 10.1016/j.molcel.2019.11.012.
Ninova M, Godneeva B, Chen YA, Luo Y, Prakash SJ, Jankovics F, Erdélyi M, Aravin AA, Fejes Tóth K. The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation (2020) Mol Cell. 77(3):571-585.e4. doi: 10.1016/j.molcel.2019.09.033.
Yicheng Luo, Elena Fefelova, Maria Ninova, Yung-Chia Ariel Chen, Alexei A. Aravin. Repression of interrupted and intact rDNA by the SUMO pathway in Drosophila melanogaster (2020) Elife 9:e52416. doi: 10.7554/eLife.52416.
Olina A, Kuzmenko A, Ninova M, Aravin AA, Kulbachinskiy A, Esyunina D. Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus (2020). RNA Biol. 17(5):677-688. doi: 10.1080/15476286.2020.1724716.
Lisitskaya L, Petushkov I, Esyunina D, Aravin A, Kulbachinskiy A. Recognition of double-stranded DNA by the Rhodobacter sphaeroides Argonaute protein. (2020) Biochem Biophys Res Commun. 533(4):1484-1489. doi: 10.1016/j.bbrc.2020.10.051.
Kuzmenko A, Yudin D, Ryazansky S, Kulbachinskiy A, Aravin AA. Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea (2019) Nucleic Acids Res. 47(11):5822-5836. doi: 10.1093/nar/gkz379.
Kotov AA, Adashev VE, Godneeva BK, Ninova M, Shatskikh AS, Bazylev SS, Aravin AA, Olenina LV. piRNA silencing contributes to interspecies hybrid sterility and reproductive isolation in Drosophila melanogaster (2019). Nucleic Acids Res. 47(8):4255-4271. doi: 10.1093/nar/gkz130.
Ryazansky S, Kulbachinskiy A, Aravin AA. The Expanded Universe of Prokaryotic Argonaute Proteins (2018) mBio 9(6):e01935-18. doi: 10.1128/mBio.01935-18.
Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ. (2018) Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. Cell Rep. 10;24(2):453-462. doi: 10.1016/j.celrep.2018.06.021.
Ciabrelli F, Comoglio F, Fellous S, Bonev B, Ninova M, Szabo Q, Xuéreb A, Klopp C, Aravin A, Paro R, Bantignies F, Cavalli G. (2017) Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nat Genet. 49(6):876-886. doi: 10.1038/ng.3848.
Y. Chen, E. Stuwe, Y. Luo, M. Ninova, A. Le Thomas, E. Rozhavskaya, S. Li, S. Vempati, J. Laver, D. Patel, C. Smibert, H. Lipshitz, K. Fejes Tóth and A. Aravin (2016) Cutoff suppresses RNA polymerase II termination to ensure expression of piRNA precursors. Molecular Cell. 63(1):97-109. http://dx.doi.org/10.1016/j.molcel.2016.05.010
J. Hur, Y. Luo, S. Moon, M. Ninova, G. Marinov, Y. Chung and A. Aravin (2016) Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila. Genes & Development. 30(7):840-55
A. Webster, S. Li, J. Hur, M. Wachsmuth, J. Bois, E. Perkins, D. Patel and A. Aravin (2015) Aub and Ago3 are recruited to nuage through two mechanisms to form a ping-pong complex assembled by Krimper. Molecular Cell. 59(4):564-75. doi: 10.1016/j.molcel.2015.07.017
S. Manakov, D. Pezic, G. Marinov, W. Pastor, R. Sachidanandam and A. Aravin (2015) MIWI2 and MILI have differential effects on piRNA biogenesis and DNA methylation. Cell Reports. 12(8):1234-1243. doi: 10.1016/j.celrep.2015.07.036.
Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. (2015) The histone chaperone CAF-1 safeguards somatic cell identity. Nature. 528(7581):218-24. doi: 10.1038/nature15749
Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Fejes Tóth K. (2015) Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. Dev Cell. 32(6):765-71. doi: 10.1016/j.devcel.2015.01.013.
A. Le Thomas, G. Marinov and A. Aravin (2014). A Transgenerational Process Defines piRNA Biogenesis in Drosophila virilis. Cell Reports. pii: S2211-1247(14)00676-7.
A. Le Thomas, E. Stuwe, S. Li, J. Du, G. Marinov, N. Rozhkov, YC. Chen, Y. Luo, R. Sachidanandam, K. Fejes Tóth, D. Patel and A. Aravin (2014). Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. Genes & Development 28(15):1667-80.
D. Pezic, S. Manakov, R. Sachidanandam and A. Aravin (2014) piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells. Genes & Development. 28(13):1410-28. doi: 10.1101/gad.240895.114
Pastor WA, Stroud H, Nee K, Liu W, Pezic D, Manakov S, Lee SA, Moissiard G, Zamudio N, Bourc'his D, Aravin AA, Clark AT, Jacobsen SE. (2014) MORC1 represses transposable elements in the mouse male germline. Nat Commun. 5:5795.
Molaro A, Falciatori I, Hodges E, Aravin AA, Marran K, Rafii S, McCombie WR, Smith AD, Hannon GJ. (2014) Two waves of de novo methylation during mouse germ cell development. Genes & Development 28(14):1544-9.
I. Olovnikov, K. Chan, R. Sachidanandam, D. Newman, A. Aravin (2013) Bacterial Argonaute samples the transcriptome to identify foreign DNA. Molecular Cell. 51(5):594-605.
A. Le Thomas, A. Rogers, A. Webster, G. Marinov, S. Liao, E. Perkins, J. Hur, A. Aravin, and K. Fejes Tóth (2013) Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes & Development 27 (4)
Muerdter F, Olovnikov I, Molaro A, Rozhkov NV, Czech B, Gordon A, Hannon GJ, Aravin AA. (2012). Production of artificial piRNAs in flies and mice. RNA. 18(1):42-52
Invited reviews and book chapters
Ninova M, Fejes Tóth K, Aravin AA. The control of gene expression and cell identity by H3K9 trimethylation (2019) Development. 20;146(19) doi: 10.1242/dev.181180.
Lisitskaya L, Aravin AA, Kulbachinskiy A. DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins (2018). Nat Commun. 9(1):5165. doi: 10.1038/s41467-018-07449-7.
Olina AV, Kulbachinskiy AV, Aravin AA, Esyunina DM. (2018) Argonaute Proteins and Mechanisms of RNA Interference in Eukaryotes and Prokaryotes. Biochemistry 83(5):483-497. doi: 10.1134/S0006297918050024.
Huang X, Fejes Tóth K, Aravin AA. (2017) piRNA Biogenesis in Drosophila melanogaster. Trends Genet. 33(11):882-894. doi: 10.1016/j.tig.2017.09.002.
Chen YA, Aravin AA. (2015). Non-Coding RNAs in Transcriptional Regulation. Current Molecular Biology Reports. 1(1):10-18.
Stuwe E, K. Fejes Tóth, Aravin AA. (2014) Small but sturdy: small RNAs in cellular memory and epigenetics. Genes & Development. 28(5):423-31.
Le Thomas A, K. Fejes Tóth, Aravin AA. (2014) To be or not to be a piRNA: genomic origin and processing of piRNAs. Genome Biol. Jan 27;15(1):204.
Olovnikov I, Le Thomas A, Aravin AA. A Framework for piRNA Cluster Manipulation. (2014) Methods Mol Biol. 1093:47-58. doi: 10.1007/978-1-62703-694-8_5.
Malone C, Brennecke J, Czech B, Aravin A, Hannon GJ. (2012) Preparation of small RNA libraries for high-throughput sequencing. Cold Spring Harb Protocls (10).
Olovnikov I, Aravin A.A, Fejes Tóth K (2012) Small RNA in the nucleus: the RNA-chromatin ping-pong. Curr Opin Genet Dev. 22(2):164-71.
A. Aravin and D. Chan (2011) piRNAs meet mitochondria. Developmental Cell. 20(3):287-8.
M. Siomi, K. Sato, D. Pezic, A. Aravin (2011) PIWI-interacting small RNAs: the vanguard of genome defence. Nature Reviews Molecular Cell Biology. 12(4):246-58.
Rozhkov NV, Aravin AA, Zelentsova ES, Schostak NG, Sachidanandam R, McCombie WR, Hannon GJ, Evgen'ev MB. (2010) Small RNA-based silencing strategies for transposons in the process of invading Drosophila species. RNA. 16(8):1634-45.
A. Aravin, G. van der Heijden, J. Castaneda, V. Vagin, G. Hannon and A. Bortvin (2009) Compartmentalization of the piRNA pathway in Mouse Fetal Gonocytes. PLoS Genetics 5(12):e1000764
V. Vagin, J. Wohlschlegel, J. Qu, Z. Jonsson, X. Huang, S. Chuma, A. Girard, R. Sachidanandam, G. Hannon, A. Aravin (2009). Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members. Genes & Development 23(15):1749-62
A. Aravin and G. Hannon (2009) Small RNA Silencing Pathways in Germ and Stem Cells. Cold Spring Harbor Symposia on Quantitative Biology, Volume LXXIII. 73:283-90.
J. Brennecke, C. Malone, A. Aravin, R. Sachidanandam, A. Stark , G. Hannon (2008) An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 28;322(5906):1387-92.
A. Aravin, R. Sachidanandam, D. Bourc’his, C. Schaefer, D. Pezic, K. Fejes Tóth, T. Bestor, and G. Hannon (2008) A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Molecular Cell. 31: 785–799.
O. Tam, A. Aravin (co-first authors), P. Stein, A. Girard, E. Murchison, S. Cheloufi, E. Hodges, M. Anger, R. Sachidanandam, R. Schultz, and G. Hannon (2008) Pseudogene-derived siRNAs regulate gene expression in mouse oocytes. Nature. 453(7194):534-8.
A. Aravin and D. Bourc'his (2008). Small RNA guides for de novo DNA methylation in mammalian germ cells. Genes & Development. 22(8):970-5.
A. Aravin, R. Sachidanandam, A. Girard, K. Fejes Tóth, G. Hannon. (2007) Developmentally regulated piRNA clusters implicate Mili in transposon control. Science. 316(5825):744-7
M. Klenov, S. Lavrov, A. Stolyarenko, S. Ryazansky, A. Aravin, T. Tuschl, V. Gvozdev. (2007) Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline. Nucleic Acids Res. 35(16):5430-8.
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 129(7):1401-14.
J. Brennecke, A. Aravin, A. Stark, M. Dus, M. Kellis, R. Sachidanandam and G. Hannon. (2007) Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 129(7):1401-14.
A. Aravin, G. Hannon & J. Brennecke (2007) The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science. 318(5851):761-4.
A. Aravin, D. Gaidatzis, S. Pfeffer, M. Lagos-Quintana, P. Landgraf, N. Iovino, P. Morris, M.J. Brownstein, S. Kuramochi-Miyagawa, T. Nakano, M. Chien, J. J. Russo, J. Ju, R. Sheridan, C. Sander, M. Zavolan and T. Tuschl (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature. 442(7099):203-7.
Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M. (2005) Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 6, 267.
Altuvia, Y., Landgraf, P., Lithwick, G., Elefant, N., Pfeffer, S., Aravin, A., Brownstein, M. J., Tuschl, T., and Margalit, H. (2005). Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 33, 2697-2706.
Aravin, A., and Tuschl, T. (2005). Identification and characterization of small RNAs involved in RNA silencing. FEBS Lett. 579, 5830-5840
John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., and Marks, D. S. (2004). Human MicroRNA targets. PLoS Biol 2, e363. Aravin, A. A., Klenov, M. S., Vagin, V. V., Bantignies, F., Cavalli, G., and Gvozdev, V. A. (2004). Dissection of a natural RNA silencing process in the Drosophila melanogaster germ line. Mol Cell Biol 24, 6742-6750.
Aravin, A. A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J., and Tuschl, T. (2003). The small RNA profile during Drosophila melanogaster development. Developmental Cell 5, 337-350.
Kogan, G. L., Tulin, A. V., Aravin, A. A., Abramov, Y. A., Kalmykova, A. I., Maisonhaute, C., and Gvozdev, V. A. (2003). The GATE retrotransposon in Drosophila melanogaster: mobility in heterochromatin and aspects of its expression in germline tissues. Mol Genet Genomics 269, 234-242.
Aravin, A. A., Naumova, N. M., Tulin, A. V., Vagin, V. V., Rozovsky, Y. M., and Gvozdev, V. A. (2001). Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Current Biology 11, 1017-1027.
Gvozdev, V. A., Kogan, G. L., Tulin, A. A., Aravin, A. A., Naumova, N. M., and Shevelyov, Y. Y. (2000). Paralogous stellate and Su(Ste) repeats: evolution and ability to silence a reporter gene. Genetica 109, 131-140.
Kogan, G. L., Epstein, V. N., Aravin, A. A., and Gvozdev, V. A. (2000). Molecular evolution of two paralogous tandemly repeated heterochromatic gene clusters linked to the X and Y chromosomes of Drosophila melanogaster. Mol Biol Evol 17, 697-702.
Tulin, A. V., Naumova, N. M., Aravin, A. A., and Gvozdev, V. A. (1998). Repeated, protein-encoding heterochromatic genes cause inactivation of a juxtaposed euchromatic gene. FEBS Lett 425, 513-516.
Aravin, A. A., Yurchenko, V., Merzlyak, E. M., and Kolesnikov, A. A. (1998). The mitochondrial ND8 gene from Crithidia oncopelti is not pan-edited. FEBS Lett 431, 457-460