Aravin, Alexei

Combined from CaltechAUTHORS

• Chen, Peiwei and Pan, Katherine C., et el. (2024) Escalation of genome defense capacity enables control of an expanding meiotic driver; PMCID PMC11195268; 10.1101/2024.06.12.598716
• Godneeva, Baira and Ninova, Maria, et el. (2023) SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes; eLife; Vol. 12; RP89493; PMCID PMC10672805; 10.7554/elife.89493
• Luo, Yicheng and He, Peng, et el. (2023) Maternally inherited siRNAs initiate piRNA cluster formation; Molecular Cell; Vol. 83; No. 21; 3835-3851.e7; PMCID PMC10846595; 10.1016/j.molcel.2023.09.033
• Godneeva, Baira and Fejes Toth, Katalin, et el. (2023) Impact of Germline Depletion of Bonus on Chromatin State in Drosophila Ovaries; Cells; Vol. 12; No. 22; 2629; PMCID PMC10670193; 10.3390/cells12222629
• Venkei, Zsolt G. and Gainetdinov, Ildar, et el. (2023) A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila; Nature Cell Biology; Vol. 25; No. 10; 1495-1505; PMCID PMC10567549; 10.1038/s41556-023-01227-4
• Ninova, Maria and Holmes, Hannah, et el. (2023) Pervasive SUMOylation of heterochromatin and piRNA pathway proteins; Cell Genomics; Vol. 3; No. 7; 100329; PMCID PMC10363806; 10.1016/j.xgen.2023.100329
• Chen, Peiwei and Aravin, Alexei A. (2023) Genetic control of a sex-specific piRNA program; Current Biology; Vol. 33; No. 9; 1825-1835.e3; PMCID PMC10431932; 10.1016/j.cub.2023.03.057
• Esyunina, Daria and Okhtienko, Anastasiia, et el. (2023) Specific targeting of plasmids with Argonaute enables genome editing; Nucleic Acids Research; Vol. 51; No. 8; 4086-4099; PMCID PMC10164558; 10.1093/nar/gkad191
• Olina, Anna and Agapov, Aleksei, et el. (2023) Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli; Microbiology Spectrum; Vol. 11; No. 3; Art. No. 04146-22; PMCID PMC10269773; 10.1128/spectrum.04146-22
• Venkei, Zsolt G. and Gainetdinov, Ildar, et el. (2023) Drosophila Males Use 5′-to-3′ Phased Biogenesis to Make Stellate-silencing piRNAs that Lack Homology to Maternally Deposited piRNA Guides; 10.1101/2022.09.12.507655
• Olina, Anna and Agapov, Aleksei, et el. (2023) Bacterial Argonaute proteins aid cell division in the presence of topoisomerase inhibitors in Escherichia coli; 10.1101/2022.09.13.507849
• Lisitskaya, Lidiya and Kropocheva, Ekaterina, et el. (2023) Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo; 10.1101/2022.09.09.507302
• Chen, Peiwei and Aravin, Alexei A. (2023) Genetic control of a sex-specific piRNA program; 10.1101/2022.10.25.513766
• Ninova, Maria and Lomenick, Brett, et el. (2022) Pervasive SUMOylation of heterochromatin and piRNA pathway proteins; 10.1101/2022.08.15.504007
• Lisitskaya, Lidiya and Shin, Yeonoh, et el. (2022) Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity; Nature Communications; Vol. 13; Art. No. 4624; PMCID PMC9360449; 10.1038/s41467-022-32079-5
• Esyunina, Daria and Okhtienko, Anastasiia, et el. (2022) Specific targeting of plasmids with Argonaute enables genome editing; 10.1101/2022.04.14.488398
• Luo, Yicheng and He, Peng, et el. (2022) Maternally inherited siRNAs initiate piRNA cluster formation; 10.1101/2022.02.08.479612
• Chen, Peiwei and Aravin, Alexei A. (2021) Transposon-taming piRNAs in the germline: Where do they come from?; Molecular Cell; Vol. 81; No. 19; 3884-3885; 10.1016/j.molcel.2021.09.017
• Chen, Peiwei and Luo, Yicheng, et el. (2021) RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility; PLoS Genetics; Vol. 17; No. 9; Art. No. e1009591; PMCID PMC8412364; 10.1371/journal.pgen.1009591
• Huang, Xiawei and Hu, Hongmiao, et el. (2021) Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex; Nature Communications; Vol. 12; Art. No. 4061; 10.1038/s41467-021-24351-x
• Lisitskaya, L. and Esyunina, D., et el. (2021) Analysis of a putative nuclease associated with the Argonaute protein from Rhodobacter sphaeroides; FEBS Open Bio; Vol. 11; No. S1; 238; 10.1002/2211-5463.13205
• Chen, Peiwei and Kotov, Alexei A., et el. (2021) piRNA-mediated gene regulation and adaptation to sex-specific transposon expression in D. melanogaster male germline; Genes and Development; Vol. 35; No. 11-12; 914-935; PMCID PMC8168559; 10.1101/gad.345041.120
• Kropocheva, Ekaterina and Kuzmenko, Anton, et el. (2021) A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis; Nucleic Acids Research; Vol. 49; No. 7; 4054-4065; PMCID PMC8053121; 10.1093/nar/gkab182
• Adashev, Vladimir E. and Kotov, Alexei A., et el. (2021) Stellate Genes and the piRNA Pathway in Speciation and Reproductive Isolation of Drosophila melanogaster; Frontiers in Genetics; Vol. 11; Art. No. 610665; PMCID PMC7874207; 10.3389/fgene.2020.610665
• Lisitskaya, Lidia and Petushkov, Ivan, et el. (2020) Recognition of double-stranded DNA by the Rhodobacter sphaeroides Argonaute protein; Biochemical and Biophysical Research Communications; Vol. 533; No. 4; 1484-1489; 10.1016/j.bbrc.2020.10.051
• Kuzmenko, Anton and Oguienko, Anastasiya, et el. (2020) DNA targeting and interference by a bacterial Argonaute nuclease; Nature; Vol. 587; No. 7835; 632-637; 10.1038/s41586-020-2605-1
• Luo, Yicheng and Fefelova, Elena, et el. (2020) Repression of interrupted and intact rDNA by the SUMO pathway in Drosophila melanogaster; eLife; Vol. 2020; No. 9; Art. No. e52416; PMCID PMC7676866; 10.7554/eLife.52416
• Aravin, Alexei A. (2020) Pachytene piRNAs as beneficial regulators or a defense system gone rogue; Nature Genetics; Vol. 52; No. 7; 644-645; 10.1038/s41588-020-0656-8
• Olina, Anna and Kuzmenko, Anton, et el. (2020) Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus; RNA Biology; Vol. 17; No. 5; 677-688; PMCID PMC7237159; 10.1080/15476286.2020.1724716
• Ninova, Maria and Chen, Yung-Chia Ariel, et el. (2020) Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing; Molecular Cell; Vol. 77; No. 3; 556-570; PMCID PMC7007863; 10.1016/j.molcel.2019.11.012
• Ninova, Maria and Godneeva, Baira, et el. (2020) The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation; Molecular Cell; Vol. 77; No. 3; 571-585; PMCID PMC7007874; 10.1016/j.molcel.2019.09.033
• Ninova, Maria and Fejes Tóth, Katalin, et el. (2019) The control of gene expression and cell identity by H3K9 trimethylation; Development; Vol. 146; No. 19; Art. No. dev181180; PMCID PMC6803365; 10.1242/dev.181180
• Kuzmenko, A. and Yudin, D., et el. (2019) Ago nucleases from Clostridium butyricum and Limnothrix rosea can process DNA substrates at moderate temperatures; FEBS Open Bio; Vol. 9; No. S1; 400; 10.1002/2211-5463.12675
• Yudin, D. and Ryazansky, S., et el. (2019) Insights into genomic DNA sampling by prokaryotic Argonaute proteins; FEBS Open Bio; Vol. 9; No. S1; 62; 10.1002/2211-5463.12675
• Kropocheva, E. and Esyunina, D., et el. (2019) Various modes of nucleic acid processing by mesophilic bacterial Argonaute proteins; FEBS Open Bio; Vol. 9; No. S1; 159; 10.1002/2211-5463.12675
• Olina, A. and Kudinova, A., et el. (2019) Catalytically active Argonaute nuclease from Synechococcus elongatus; FEBS Open Bio; Vol. 9; No. S1; 160; 10.1002/2211-5463.12675
• Kuzmenko, Anton and Yudin, Denis, et el. (2019) Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea; Nucleic Acids Research; Vol. 47; No. 11; 5822-5836; PMCID PMC6582412; 10.1093/nar/gkz379
• Kotov, Alexei A. and Adashev, Vladimir E., et el. (2019) piRNA silencing contributes to interspecies hybrid sterility and reproductive isolation in Drosophila melanogaster; Nucleic Acids Research; Vol. 47; No. 8; 4255-4271; PMCID PMC6486647; 10.1093/nar/gkz130
• Lisitskaya, Lidiya and Aravin, Alexei A., et el. (2018) DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins; Nature Communications; Vol. 9; Art. No. 5165; PMCID PMC6279821; 10.1038/s41467-018-07449-7
• Ryazansky, Sergei and Kulbachinskiy, Andrey, et el. (2018) The expanded universe of prokaryotic Argonaute proteins; mBio; Vol. 9; No. 6; Art. No. e01935-18; PMCID PMC6299218; 10.1128/mBio.01935-18
• Liu, Yiwei and Esyunina, Daria, et el. (2018) Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA; Cell Reports; Vol. 24; No. 2; 453-462; PMCID PMC6269105; 10.1016/j.celrep.2018.06.021
• Yudin, D. and Ryazansky, S., et el. (2018) Catalytically active Argonaute proteins from mesophilic bacteria; FEBS Open Bio; Vol. 8; No. S1; Art. No. P.01-071; 10.1002/2211-5463.12453
• Esyunina, D. and Ninova, M., et el. (2018) Highly specific target recognition by an Argonaute protein from Rhodobacter sphaeroides; FEBS Open Bio; Vol. 8; No. S1; Art. No. P.01-076; 10.1002/2211-5463.12453
• Kropocheva, E. and Oguienko, A., et el. (2018) Functional activities of DNA-guided and RNA-guided bacterial Argonaute proteins; FEBS Open Bio; Vol. 8; No. S1; Art. No. P.01-074; 10.1002/2211-5463.12453
• Lisitskaya, L. and Petushkov, I., et el. (2018) Interactions of a bacterial Argonaute protein with DNA targets in vitro; FEBS Open Bio; Vol. 8; No. S1; Art. No. P.18-108; 10.1002/2211-5463.12453
• Olina, A. V. and Kulbachinskiy, A. V., et el. (2018) Argonaute Proteins and Mechanisms of RNA Interference in Eukaryotes and Prokaryotes; Biochemistry (Moscow); Vol. 83; No. 5; 483-497; 10.1134/S0006297918050024
• Huang, Xiawei and Fejes Tóth, Katalin, et el. (2017) piRNA Biogenesis in Drosophila melanogaster; Trends in Genetics; Vol. 33; No. 11; 882-894; PMCID PMC5773129; 10.1016/j.tig.2017.09.002
• Bamezai, S. and Mulaw, M., et el. (2017) PIWIL4 Acts as a piRNA Binding, Epigenetically Active and Growth Regulatory Protein in Human Acute Myeloid Leukemia; Haematologica; Vol. 102; No. S2; Art. No. S429
• Ciabrelli, Filippo and Comoglio, Federico, et el. (2017) Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila; Nature Genetics; Vol. 49; No. 6; 876-886; PMCID PMC5484582; 10.1038/ng.3848
• Chen, Yung-Chia Ariel and Stuwe, Evelyn, et el. (2016) Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors; Molecular Cell; Vol. 63; No. 1; 97-109; PMCID PMC4980073; 10.1016/j.molcel.2016.05.010
• Hur, Junho K. and Luo, Yicheng, et el. (2016) Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila; Genes and Development; Vol. 30; No. 7; 840-855; PMCID PMC4826399; 10.1101/gad.276030.115
• Cheloufi, Sihem and Ninova, Maria, et el. (2015) The histone chaperone CAF-1 safeguards somatic cell identity; Nature; Vol. 528; No. 7581; 218-224; PMCID PMC4866648; 10.1038/nature15749
• Manakov, Sergei A. and Pezic, Dubravka, et el. (2015) MIWI2 and MILI Have Differential Effects on piRNA Biogenesis and DNA Methylation; Cell Reports; Vol. 12; No. 8; 1234-1243; PMCID PMC4554733; 10.1016/j.celrep.2015.07.036
• Webster, Alexandre and Li, Sisi, et el. (2015) Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper; Molecular Cell; Vol. 59; No. 4; 564-575; PMCID PMC4545750; 10.1016/j.molcel.2015.07.017
• Marinov, Georgi K. and Wang, Jie, et el. (2015) Pitfalls of Mapping High-Throughput Sequencing Data to Repetitive Sequences: Piwi's Genomic Targets Still Not Identified; Developmental Cell; Vol. 32; No. 6; 765-771; PMCID PMC4494788; 10.1016/j.devcel.2015.01.013
• Chen, Yung-Chia Ariel and Aravin, Alexei A. (2015) Non-coding RNAs in Transcriptional Regulation; Current Molecular Biology Reports; Vol. 1; No. 1; 10-18; PMCID PMC4479201; 10.1007/s40610-015-0002-6
• Pastor, William A. and Stroud, Hume, et el. (2014) MORC1 represses transposable elements in the mouse male germline; Nature Communications; Vol. 5; No. 12; Art. No. 5795; PMCID PMC4268658; 10.1038/ncomms6795
• Le Thomas, Adrien and Marinov, Georgi K., et el. (2014) A Transgenerational Process Defines piRNA Biogenesis in Drosophila virilis; Cell Reports; Vol. 8; No. 6; 1617-1623; PMCID PMC5054749; 10.1016/j.celrep.2014.08.013
• Le Thomas, Adrien and Stuwe, Evelyn, et el. (2014) Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing; Genes and Development; Vol. 28; No. 15; 1667-1680; PMCID PMC4117942; 10.1101/gad.245514.114
• Molaro, Antoine and Falciatori, Ilaria, et el. (2014) Two waves of de novo methylation during mouse germ cell development; Genes and Development; Vol. 28; No. 14; 1544-1549; PMCID PMC4102761; 10.1101/gad.244350.114
• Pezic, Dubravka and Manakov, Sergei A., et el. (2014) piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells; Genes and Development; Vol. 28; No. 13; 1410-1418; PMCID PMC4083086; 10.1101/gad.240895.114
• Hur, Junho K. and Olovnikov, Ivan, et el. (2014) Prokaryotic Argonautes defend genomes against invasive DNA; Trends in Biochemical Sciences; Vol. 39; No. 6; 257-259; PMCID PMC4041519; 10.1016/j.tibs.2014.04.006
• Stuwe, Evelyn and Fejes Tóth, Katalin, et el. (2014) Small but sturdy: small RNAs in cellular memory and epigenetics; Genes and Development; Vol. 28; No. 5; 421-431; PMCID PMC3950340; 10.1101/gad.236414.113
• Le Thomas, Adrien and Fejes Tóth, Katalin, et el. (2014) To be or not to be a piRNA: genomic origin and processing of piRNAs; Genome Biology; Vol. 15; No. 1; Art. No. 204; PMCID PMC4053809; 10.1186/gb4154
• Olovnikov, Ivan and Le Thomas, Adrien, et el. (2014) A Framework for piRNA Cluster Manipulation; ISBN 978-1-62703-693-1; PIWI-Interacting RNAs: Methods and Protocols; 47-58; 10.1007/978-1-62703-694-8_5
• Olovnikov, Ivan and Chan, Ken, et el. (2013) Bacterial Argonaute Samples the Transcriptome to Identify Foreign DNA; Molecular Cell; Vol. 51; No. 5; 594-605; PMCID PMC3809076; 10.1016/j.molcel.2013.08.014
• Le Thomas, Adrien and Rogers, Alicia K., et el. (2013) Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state; Genes and Development; Vol. 27; No. 4; 390-399; PMCID PMC3589556; 10.1101/gad.209841.112
• Olenkina, O. M. and Egorova, K. S., et el. (2012) Mapping of cis-regulatory sites in the promoter of testis-specific Stellate genes of Drosophila melanogaster; Biochemistry (Moscow); Vol. 77; No. 11; 1285-1293; 10.1134/s0006297912110077
• Olovnikov, Ivan and Aravin, Alexei A., et el. (2012) Small RNA in the nucleus: the RNA-chromatin ping-pong; Current Opinion in Genetics and Development; Vol. 22; No. 2; 164-171; PMCID PMC3345048; 10.1016/j.gde.2012.01.002
• Muerdter, Felix and Olovnikov, Ivan, et el. (2012) Production of artificial piRNAs in flies and mice; RNA; Vol. 18; No. 1; 42-52; PMCID PMC3261743; 10.1261/rna.029769.111
• Siomi, Mikiko C. and Sato, Kaoru, et el. (2011) PIWI-interacting small RNAs: the vanguard of genome defence; Nature Reviews. Molecular Cell Biology; Vol. 12; No. 4; 246-258; 10.1038/nrm3089
• Aravin, Alexei A. and Chan, David C. (2011) piRNAs Meet Mitochondria; Developmental Cell; Vol. 20; No. 3; 287-288; 10.1016/j.devcel.2011.03.003
• Rozhkov, Nikolay V. and Aravin, Alexei A., et el. (2010) Small RNA-based silencing strategies for transposons in the process of invading Drosophila species; RNA; Vol. 16; No. 8; 1634-1645; PMCID PMC2905761; 10.1261/rna.2217810
• Rozhkov, N. V. and Aravin, A. A., et el. (2010) RNA interference system differently responds to the same mobile element in distant Drosophila species; Doklady Biochemistry and Biophysics; Vol. 431; No. 1; 79-81; PMCID PMC2998894; 10.1134/s1607672910020079
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• Aravin, Alexei A. and van der Heijden, Godfried W., et el. (2009) Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice; PLOS Genetics; Vol. 5; No. 12; Art. No. e1000764; PMCID PMC2785470; 10.1371/journal.pgen.1000764
• Vagin, Vasily V. and Wohlschlegel, James, et el. (2009) Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members; Genes and Development; Vol. 23; No. 15; 1749-1762; PMCID PMC2720255; 10.1101/gad.1814809
• Brennecke, Julius and Malone, Colin D., et el. (2008) An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing; Science; Vol. 322; No. 5906; 1387-1392; PMCID PMC2805124; 10.1126/science.1165171
• Aravin, Alexei A. and Sachidanandam, Ravi, et el. (2008) A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice; Molecular Cell; Vol. 31; No. 6; 785-799; PMCID PMC2730041; 10.1016/j.molcel.2008.09.003
• Tam, Oliver H. and Aravin, Alexei A., et el. (2008) Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes; Nature; Vol. 453; No. 7194; 534-538; PMCID PMC2981145; 10.1038/nature06904
• Aravin, Alexei A. and Bourc'his, Déborah (2008) Small RNA guides for de novo DNA methylation in mammalian germ cells; Genes and Development; Vol. 22; No. 8; 970-975; PMCID PMC2732394; 10.1101/gad.1669408
• Olson, A. J. and Brennecke, J., et el. (2008) Analysis of Large-Scale Sequencing of Small RNAs; ISBN 9789812776082; Pacific Symposium on Biocomputing 2008; 126-136; 10.1142/9789812776136_0014
• Aravin, A. A. and Hannon, G. J. (2008) Small RNA Silencing Pathways in Germ and Stem Cells; ISBN 978-087969862-1; Control and regulation of stem cells; 283-290; 10.1101/sqb.2008.73.058
• Aravin, Alexei A. and Hannon, Gregory J., et el. (2007) The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race; Science; Vol. 318; No. 5851; 761-764; 10.1126/science.1146484
• Klenov, Mikhail S. and Lavrov, Sergey A., et el. (2007) Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline; Nucleic Acids Research; Vol. 35; No. 16; 5430-5438; PMCID PMC2018648; 10.1093/nar/gkm576
• Aravin, Alexei A. and Sachidanandam, Ravi, et el. (2007) Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control; Science; Vol. 316; No. 5825; 744-747; 10.1126/science.1142612
• Brennecke, Julius and Aravin, Alexei A., et el. (2007) Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila; Cell; Vol. 128; No. 6; 1089-1103; 10.1016/j.cell.2007.01.043
• Aravin, Alexei A. and Klenov, Mikhail S., et el. (2004) Dissection of a Natural RNA Silencing Process in the Drosophila melanogaster Germ Line; Molecular and Cellular Biology; Vol. 24; No. 15; 6742-6750; PMCID PMC444866; 10.1128/mcb.24.15.6742-6750.2004
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