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Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing.

Osumi K, Sato K, Murano K, Siomi H, Siomi MC.

EMBO Rep. 2019 Oct 2:e48296. doi: 10.15252/embr.201948296. [Epub ahead of print]


Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation.

Yamanaka S, Nishihara H, Toh H, Eijy Nagai LA, Hashimoto K, Park SJ, Shibuya A, Suzuki AM, Tanaka Y, Nakai K, Carninci P, Sasaki H, Siomi H.

Dev Cell. 2019 Oct 7;51(1):21-34.e5. doi: 10.1016/j.devcel.2019.07.023. Epub 2019 Aug 29.


Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing.

Murano K, Iwasaki YW, Ishizu H, Mashiko A, Shibuya A, Kondo S, Adachi S, Suzuki S, Saito K, Natsume T, Siomi MC, Siomi H.

EMBO J. 2019 Sep 2;38(17):e102870. doi: 10.15252/embj.2019102870. Epub 2019 Aug 1.


Hepatic Ago2-mediated RNA silencing controls energy metabolism linked to AMPK activation and obesity-associated pathophysiology.

Zhang C, Seo J, Murakami K, Salem ESB, Bernhard E, Borra VJ, Choi K, Yuan CL, Chan CC, Chen X, Huang T, Weirauch MT, Divanovic S, Qi NR, Thomas HE, Mercer CA, Siomi H, Nakamura T.

Nat Commun. 2018 Sep 10;9(1):3658. doi: 10.1038/s41467-018-05870-6.


Piwi Nuclear Localization and Its Regulatory Mechanism in Drosophila Ovarian Somatic Cells.

Yashiro R, Murota Y, Nishida KM, Yamashiro H, Fujii K, Ogai A, Yamanaka S, Negishi L, Siomi H, Siomi MC.

Cell Rep. 2018 Jun 19;23(12):3647-3657. doi: 10.1016/j.celrep.2018.05.051.


Hierarchical roles of mitochondrial Papi and Zucchini in Bombyx germline piRNA biogenesis.

Nishida KM, Sakakibara K, Iwasaki YW, Yamada H, Murakami R, Murota Y, Kawamura T, Kodama T, Siomi H, Siomi MC.

Nature. 2018 Mar 8;555(7695):260-264. doi: 10.1038/nature25788. Epub 2018 Feb 28.


Profiling Open Chromatin Structure in the Ovarian Somatic Cells Using ATAC-seq.

Murano K, Iwasaki YW, Siomi H.

Methods Mol Biol. 2018;1680:165-177. doi: 10.1007/978-1-4939-7339-2_11.


Human PIWI (HIWI) is an azoospermia factor.

Hasuwa H, Ishino K, Siomi H.

Sci China Life Sci. 2018 Mar;61(3):348-350. doi: 10.1007/s11427-017-9149-0. Epub 2017 Aug 10. No abstract available.


Deep sequencing and high-throughput analysis of PIWI-associated small RNAs.

Iwasaki YW, Ishino K, Siomi H.

Methods. 2017 Aug 15;126:66-75. doi: 10.1016/j.ymeth.2017.05.020. Epub 2017 May 24.


Mobile elements control stem cell potency.

Hasuwa H, Siomi H.

Science. 2017 Feb 10;355(6325):581-582. doi: 10.1126/science.aam6589. No abstract available.


Identification of Mouse piRNA Pathway Components Using Anti-MIWI2 Antibodies.

Hirano T, Hasuwa H, Siomi H.

Methods Mol Biol. 2017;1463:205-216.


Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA.

Matsumoto N, Nishimasu H, Sakakibara K, Nishida KM, Hirano T, Ishitani R, Siomi H, Siomi MC, Nureki O.

Cell. 2016 Oct 6;167(2):484-497.e9. doi: 10.1016/j.cell.2016.09.002. Epub 2016 Sep 29.


Loss of l(3)mbt leads to acquisition of the ping-pong cycle in Drosophila ovarian somatic cells.

Sumiyoshi T, Sato K, Yamamoto H, Iwasaki YW, Siomi H, Siomi MC.

Genes Dev. 2016 Jul 15;30(14):1617-22. doi: 10.1101/gad.283929.116.


Piwi Modulates Chromatin Accessibility by Regulating Multiple Factors Including Histone H1 to Repress Transposons.

Iwasaki YW, Murano K, Ishizu H, Shibuya A, Iyoda Y, Siomi MC, Siomi H, Saito K.

Mol Cell. 2016 Aug 4;63(3):408-19. doi: 10.1016/j.molcel.2016.06.008. Epub 2016 Jul 14.


Inheritance of a Nuclear PIWI from Pluripotent Stem Cells by Somatic Descendants Ensures Differentiation by Silencing Transposons in Planarian.

Shibata N, Kashima M, Ishiko T, Nishimura O, Rouhana L, Misaki K, Yonemura S, Saito K, Siomi H, Siomi MC, Agata K.

Dev Cell. 2016 May 9;37(3):226-37. doi: 10.1016/j.devcel.2016.04.009.


Tudor-domain containing proteins act to make the piRNA pathways more robust in Drosophila.

Sato K, Iwasaki YW, Siomi H, Siomi MC.

Fly (Austin). 2015;9(2):86-90. doi: 10.1080/19336934.2015.1128599.


Misprocessed tRNA response targets piRNA clusters.

Yamanaka S, Siomi H.

EMBO J. 2015 Dec 14;34(24):2988-9. doi: 10.15252/embj.201593322. Epub 2015 Nov 13. No abstract available.


Sphere-formation culture of testicular germ cells in the common marmoset, a small New World monkey.

Lin ZY, Hikabe O, Suzuki S, Hirano T, Siomi H, Sasaki E, Imamura M, Okano H.

Primates. 2016 Jan;57(1):129-35. doi: 10.1007/s10329-015-0500-4. Epub 2015 Nov 3.


piRNAs derived from ancient viral processed pseudogenes as transgenerational sequence-specific immune memory in mammals.

Parrish NF, Fujino K, Shiromoto Y, Iwasaki YW, Ha H, Xing J, Makino A, Kuramochi-Miyagawa S, Nakano T, Siomi H, Honda T, Tomonaga K.

RNA. 2015 Oct;21(10):1691-703. doi: 10.1261/rna.052092.115. Epub 2015 Aug 17.


Krimper Enforces an Antisense Bias on piRNA Pools by Binding AGO3 in the Drosophila Germline.

Sato K, Iwasaki YW, Shibuya A, Carninci P, Tsuchizawa Y, Ishizu H, Siomi MC, Siomi H.

Mol Cell. 2015 Aug 20;59(4):553-63. doi: 10.1016/j.molcel.2015.06.024. Epub 2015 Jul 23.


Somatic Primary piRNA Biogenesis Driven by cis-Acting RNA Elements and trans-Acting Yb.

Ishizu H, Iwasaki YW, Hirakata S, Ozaki H, Iwasaki W, Siomi H, Siomi MC.

Cell Rep. 2015 Jul 21;12(3):429-40. doi: 10.1016/j.celrep.2015.06.035. Epub 2015 Jul 9.


RNA. Phased piRNAs tackle transposons.

Siomi H, Siomi MC.

Science. 2015 May 15;348(6236):756-7. doi: 10.1126/science.aab3004. No abstract available.


Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom.

Matsumoto N, Sato K, Nishimasu H, Namba Y, Miyakubi K, Dohmae N, Ishitani R, Siomi H, Siomi MC, Nureki O.

Cell Rep. 2015 Apr 21;11(3):366-75. doi: 10.1016/j.celrep.2015.03.030. Epub 2015 Apr 9.


Small RNAs: artificial piRNAs for transcriptional silencing.

Hirano T, Siomi H.

Curr Biol. 2015 Mar 30;25(7):R280-3. doi: 10.1016/j.cub.2015.02.009.


PIWI-Interacting RNA: Its Biogenesis and Functions.

Iwasaki YW, Siomi MC, Siomi H.

Annu Rev Biochem. 2015;84:405-33. doi: 10.1146/annurev-biochem-060614-034258. Epub 2015 Mar 5. Review.


Gene expression ontogeny of spermatogenesis in the marmoset uncovers primate characteristics during testicular development.

Lin ZY, Hirano T, Shibata S, Seki NM, Kitajima R, Sedohara A, Siomi MC, Sasaki E, Siomi H, Imamura M, Okano H.

Dev Biol. 2015 Apr 1;400(1):43-58. doi: 10.1016/j.ydbio.2015.01.014. Epub 2015 Jan 23.


Respective functions of two distinct Siwi complexes assembled during PIWI-interacting RNA biogenesis in Bombyx germ cells.

Nishida KM, Iwasaki YW, Murota Y, Nagao A, Mannen T, Kato Y, Siomi H, Siomi MC.

Cell Rep. 2015 Jan 13;10(2):193-203. doi: 10.1016/j.celrep.2014.12.013. Epub 2014 Dec 31.


miRNA regulatory ecosystem in early development.

Iwasaki YW, Siomi H.

Mol Cell. 2014 Dec 4;56(5):615-6. doi: 10.1016/j.molcel.2014.11.010.


piRNA clusters and open chromatin structure.

Yamanaka S, Siomi MC, Siomi H.

Mob DNA. 2014 Aug 1;5:22. doi: 10.1186/1759-8753-5-22. eCollection 2014. Review.


Yb integrates piRNA intermediates and processing factors into perinuclear bodies to enhance piRISC assembly.

Murota Y, Ishizu H, Nakagawa S, Iwasaki YW, Shibata S, Kamatani MK, Saito K, Okano H, Siomi H, Siomi MC.

Cell Rep. 2014 Jul 10;8(1):103-13. doi: 10.1016/j.celrep.2014.05.043. Epub 2014 Jun 19.


Small RNA profiling and characterization of piRNA clusters in the adult testes of the common marmoset, a model primate.

Hirano T, Iwasaki YW, Lin ZY, Imamura M, Seki NM, Sasaki E, Saito K, Okano H, Siomi MC, Siomi H.

RNA. 2014 Aug;20(8):1223-37. doi: 10.1261/rna.045310.114. Epub 2014 Jun 9.


It's time to exploit your favorite quirky organism with new technologies.

Siomi H.

EMBO Rep. 2014 Jun;15(6):620-1. doi: 10.15252/embr.201438955. Epub 2014 May 12. No abstract available.


diRNA-Ago2-RAD51 complexes at double-strand break sites.

Yamanaka S, Siomi H.

Cell Res. 2014 May;24(5):511-2. doi: 10.1038/cr.2014.45. Epub 2014 Apr 11.


DmGTSF1 is necessary for Piwi-piRISC-mediated transcriptional transposon silencing in the Drosophila ovary.

Ohtani H, Iwasaki YW, Shibuya A, Siomi H, Siomi MC, Saito K.

Genes Dev. 2013 Aug 1;27(15):1656-61. doi: 10.1101/gad.221515.113.


Purification of dFMR1-containing complexes using tandem affinity purification.

Miyoshi K, Ogino A, Siomi MC, Siomi H.

Methods Mol Biol. 2013;1010:111-21. doi: 10.1007/978-1-62703-411-1_8.


Roles of R2D2, a cytoplasmic D2 body component, in the endogenous siRNA pathway in Drosophila.

Nishida KM, Miyoshi K, Ogino A, Miyoshi T, Siomi H, Siomi MC.

Mol Cell. 2013 Feb 21;49(4):680-91. doi: 10.1016/j.molcel.2012.12.024. Epub 2013 Jan 31.


Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines.

Ishizu H, Siomi H, Siomi MC.

Genes Dev. 2012 Nov 1;26(21):2361-73. doi: 10.1101/gad.203786.112. Review.


Structure and function of Zucchini endoribonuclease in piRNA biogenesis.

Nishimasu H, Ishizu H, Saito K, Fukuhara S, Kamatani MK, Bonnefond L, Matsumoto N, Nishizawa T, Nakanaga K, Aoki J, Ishitani R, Siomi H, Siomi MC, Nureki O.

Nature. 2012 Nov 8;491(7423):284-7. doi: 10.1038/nature11509. Epub 2012 Oct 14.


Gender-Specific Hierarchy in Nuage Localization of PIWI-Interacting RNA Factors in Drosophila.

Nagao A, Sato K, Nishida KM, Siomi H, Siomi MC.

Front Genet. 2011 Aug 30;2:55. doi: 10.3389/fgene.2011.00055. eCollection 2011.


Maelstrom coordinates microtubule organization during Drosophila oogenesis through interaction with components of the MTOC.

Sato K, Nishida KM, Shibuya A, Siomi MC, Siomi H.

Genes Dev. 2011 Nov 15;25(22):2361-73. doi: 10.1101/gad.174110.111.


Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila.

Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, Lo Sardo F, Saxena A, Miyoshi K, Siomi H, Siomi MC, Carninci P, Gilmour DS, Corona DF, Orlando V.

Nature. 2011 Nov 6;480(7377):391-5. doi: 10.1038/nature10492.


Gatekeepers for Piwi-piRNA complexes to enter the nucleus.

Ishizu H, Nagao A, Siomi H.

Curr Opin Genet Dev. 2011 Aug;21(4):484-90. doi: 10.1016/j.gde.2011.05.001. Epub 2011 Jul 18. Review.


Stress signaling etches heritable marks on chromatin.

Siomi H, Siomi MC.

Cell. 2011 Jun 24;145(7):1005-7. doi: 10.1016/j.cell.2011.06.009.


Biochemical analyzes of endogenous argonaute complexes immunopurified with anti-Argonaute monoclonal antibodies.

Miyoshi K, Okada TN, Siomi H, Siomi MC.

Methods Mol Biol. 2011;725:29-43. doi: 10.1007/978-1-61779-046-1_3.


Natural variation of the amino-terminal glutamine-rich domain in Drosophila argonaute2 is not associated with developmental defects.

Hain D, Bettencourt BR, Okamura K, Csorba T, Meyer W, Jin Z, Biggerstaff J, Siomi H, Hutvagner G, Lai EC, Welte M, Müller HA.

PLoS One. 2010 Dec 17;5(12):e15264. doi: 10.1371/journal.pone.0015264.


Biogenesis pathways of piRNAs loaded onto AGO3 in the Drosophila testis.

Nagao A, Mituyama T, Huang H, Chen D, Siomi MC, Siomi H.

RNA. 2010 Dec;16(12):2503-15. doi: 10.1261/rna.2270710. Epub 2010 Oct 27.


Roles for the Yb body components Armitage and Yb in primary piRNA biogenesis in Drosophila.

Saito K, Ishizu H, Komai M, Kotani H, Kawamura Y, Nishida KM, Siomi H, Siomi MC.

Genes Dev. 2010 Nov 15;24(22):2493-8. doi: 10.1101/gad.1989510. Epub 2010 Oct 21.


A direct role for Hsp90 in pre-RISC formation in Drosophila.

Miyoshi T, Takeuchi A, Siomi H, Siomi MC.

Nat Struct Mol Biol. 2010 Aug;17(8):1024-6. doi: 10.1038/nsmb.1875. Epub 2010 Jul 18. Erratum in: Nat Struct Mol Biol. 2011 Apr;18(4):516.


Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production.

Miyoshi K, Miyoshi T, Siomi H.

Mol Genet Genomics. 2010 Aug;284(2):95-103. doi: 10.1007/s00438-010-0556-1. Epub 2010 Jul 2. Review.


Posttranscriptional regulation of microRNA biogenesis in animals.

Siomi H, Siomi MC.

Mol Cell. 2010 May 14;38(3):323-32. doi: 10.1016/j.molcel.2010.03.013. Review.

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