Papers - Shiomi, Haruhiko

Human PIWI (HIWI) is an azoospermia factor

Hasuwa Hidetoshi, Ishino Kyoko, Siomi Haruhiko

Science China Life Sciences    1 - 3 2017.08

ISSN  1674-7305

• Access to Document (DOI)

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

Iwasaki Yuka W., Ishino Kyoko, Siomi Haruhiko

Methods  2017.03

ISSN  1046-2023

　View Summary

<p>Small RNAs are now known to be major regulatory factors of gene expression. Emerging methods based on deep-sequencing have enabled the analysis of small RNA expression in a high-throughput manner, leading to the identification of large numbers of small RNAs in various species. Moreover, profiling small RNA data together with transcriptome data enables transcriptional and post-transcriptional regulation mediated by small RNAs to be hypothesized. Here, we isolated PIWIL1 (MIWI)-associated small RNAs from mouse testes, and performed small RNA-seq analysis. In addition, directional RNA-seq was performed using Piwil1 mutant mouse testes. Using these data, we describe protocols for analyzing small RNA-seq reads to obtain profiles of small RNAs associated with PIWI proteins. We also present bioinformatic protocols for analyzing RNA-seq reads that aim to annotate expression of piRNA clusters and identify genes regulated by piRNAs.</p>

• Access to Document (DOI)

Mobile elements control stem cell potency

Hasuwa Hidetoshi, Siomi Haruhiko

Science 355 ( 6325 ) 581 - 582 2017.02

ISSN  0036-8075

• Access to Document (DOI)

Identification of mouse piRNA pathway components using anti-MIWI2 antibodies

Hirano Takamasa, Hasuwa Hidetoshi, Siomi Haruhiko

  205 - 216 2017

　View Summary

<p>The mouse testis has served as a popular model system to study a wide range of biological processes, including germcell development, meiosis, epigenetic changes of chromatin, transposon silencing, and small RNA-mediated epigenetic modifications. PIWI-interacting RNAs (piRNAs) are a class of small RNAs that are almost exclusively expressed in animal gonads. They repress transposons by forming effector complexes with PIWI proteins to maintain genome integrity of the germline. Here we describe detailed procedures of how to produce monoclonal antibodies against a mouse nuclear PIWI protein, MIWI2, which functions in de novo DNA methylation of target transposon loci. We then describe how to use the antibodies to isolate associated complexes and to detect MIWI2 immunohistochemically.</p>

• Access to Document (DOI)

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

Matsumoto Naoki, Nishimasu Hiroshi, Sakakibara Kazuhiro, Nishida Kazumichi M., Hirano Takamasa, Ishitani Ryuichiro, Siomi Haruhiko, Siomi Mikiko C., Nureki Osamu

Cell 167 ( 2 ) 484 - 497.e9 2016.10

ISSN  0092-8674

　View Summary

<p>PIWI-clade Argonaute proteins associate with PIWI-interacting RNAs (piRNAs) and silence transposable elements in animal gonads. Here, we report the crystal structure of a silkworm PIWI-clade Argonaute, Siwi, bound to the endogenous piRNA, at 2.4 Å resolution. Siwi adopts a bilobed architecture consisting of N-PAZ and MID-PIWI lobes, in which the 5′ and 3′ ends of the bound piRNA are anchored by the MID-PIWI and PAZ domains, respectively. A structural comparison of Siwi with AGO-clade Argonautes reveals notable differences in their nucleic-acid-binding channels, likely reflecting the distinct lengths of their guide RNAs and their mechanistic differences in guide RNA loading and cleavage product release. In addition, the structure reveals that Siwi and prokaryotic, but not eukaryotic, AGO-clade Argonautes share unexpected similarities, such as metal-dependent 5′-phosphate recognition and a potential structural transition during the catalytic-tetrad formation. Overall, this study provides a critical starting point toward a mechanistic understanding of piRNA-mediated transposon silencing.</p>

• Access to Document (DOI)

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

Sumiyoshi Tetsutaro, Sato Kaoru, Yamamoto Hitomi, Iwasaki Yuka W., Siomi Haruhiko, Siomi Mikiko C.

Genes and Development 30 ( 14 ) 1617 - 1622 2016.07

ISSN  0890-9369

　View Summary

<p>In Drosophila germ cells, PIWI-interacting RNAs (piR-NAs) are amplified through a PIWI slicer-dependent feed-forward loop termed the ping-pong cycle, yielding secondary piRNAs. However, the detailed mechanism remains poorly understood, largely because an ex vivo model system amenable to biochemical analyses has not been available. Here, we show that CRISPR-mediated loss of function of lethal (3) malignant brain tumor [l(3)mbt] leads to ectopic activation of the germ-specific pingpong cycle in ovarian somatic cells. Perinuclear foci resembling nuage, the ping-pong center, appeared following l(3)mbt mutation. This activation of the ping-pong machinery in cultured cells will greatly facilitate elucidation of the mechanism underlying secondary piRNA biogenesis in Drosophila.</p>

• Access to Document (DOI)

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

Shibata, Norito, Kashima, Makoto, Ishiko, Taisuke, Nishimura, Osamu, Rouhana, Labib, Misaki, Kazuyo, Yonemura, Shigenobu, Saito, Kuniaki, Siomi, Haruhiko, Siomi, Mikiko C., Agata, Kiyokazu

DEVELOPMENTAL CELL 37 ( 3 ) 226 - 237 2016.05

Research paper (scientific journal), Joint Work,  ISSN  1534-5807

• Access to Document (DOI)

Misprocessed tRNA response targets piRNA clusters

Yamanaka, Soichiro, Siomi, Haruhiko

EMBO JOURNAL 34 ( 24 ) 2988 - 2989 2015.12

Research paper (scientific journal), Joint Work,  ISSN  0261-4189

• Access to Document (DOI)

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

Parrish, Nicholas F., Fujino, Kan, Shiromoto, Yusuke, Iwasaki, Yuka W., Ha, Hongseok, Xing, Jinchuan, Makino, Akiko, Kuramochi-Miyagawa, Satomi, Nakano, Toru, Siomi, Haruhiko, Honda, Tomoyuki, Tomonaga, Keizo

RNA 21 ( 10 ) 1691 - 1703 2015.10

Research paper (scientific journal), Joint Work,  ISSN  1355-8382

• Access to Document (DOI)

Krimper enforces an antisense bias on piRNA pools by binding AGO3 in the Drosophila germline.

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

Molecular cell (Cell Press)  59   553 - 563 2015.07

Research paper (scientific journal), Accepted

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

Ishizu, Hirotsugu, Iwasaki, Yuka W., Hirakata, Shigeki, Ozaki, Haruka, Iwasaki, Wataru, Siomi, Haruhiko, Siomi, Mikiko C.

CELL REPORTS 12 ( 3 ) 429 - 440 2015.07

Research paper (scientific journal),  ISSN  2211-1247

• Access to Document (DOI)

Phased piRNAs tackle transposons

Siomi, Haruhiko, Siomi, Mikiko C.

SCIENCE 348 ( 6236 ) 756 - 757 2015.05

Research paper (scientific journal),  ISSN  0036-8075

• Access to Document (DOI)

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

Matsumoto, Naoki, Sato, Kaoru, Nishimasu, Hiroshi, Namba, Yurika, Miyakubi, Kana, Dohmae, Naoshi, Ishitani, Ryuichiro, Siomi, Haruhiko, Siomi, Mikiko C., Nureki, Osamu

Cell Reports 11 ( 3 ) 366 - 375 2015.04

Research paper (scientific journal),  ISSN  2211-1247

• Access to Document (DOI)

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

Lin, Zachary Yu-Ching, Hirano, Takamasa, Shibata, Shinsuke, Seki, Naomi M., Kitajima, Ryunosuke, Sedohara, Ayako, Siomi, Mikiko C., Sasaki, Erika, Siomi, Haruhiko, Imamura, Masanori, Okano, Hideyuki

DEVELOPMENTAL BIOLOGY 400 ( 1 ) 43 - 58 2015.04

Research paper (scientific journal),  ISSN  0012-1606

• Access to Document (DOI)

Small RNAs: Artificial piRNAs for Transcriptional Silencing

Hirano, Takamasa, Siomi, Haruhiko

CURRENT BIOLOGY 25 ( 7 ) R280 - R283 2015.03

Research paper (scientific journal),  ISSN  0960-9822

• Access to Document (DOI)

Respective Functions of Two Distinct Siwi Complexes Assembled during PIWI-Interacting RNA Biogenesis in Bombyx Germ Cells

Nishida, Kazumichi M., Iwasaki, Yuka W., Murota, Yukiko, Nagao, Akihiro, Mannen, Taro, Kato, Yumiko, Siomi, Haruhiko, Siomi, Mikiko C.

CELL REPORTS 10 ( 2 ) 193 - 203 2015.01

Research paper (scientific journal),  ISSN  2211-1247

• Access to Document (DOI)

PIWI-Interacting RNA: Its Biogenesis and Functions

Iwasaki, Yuka W., Siomi, Mikiko C., Siomi, Haruhiko

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 84 84   405 - 433 2015

Research paper (scientific journal),  ISSN  0066-4154

• Access to Document (DOI)

miRNA Regulatory Ecosystem in Early Development

Iwasaki, Yuka W., Siomi, Haruhiko

MOLECULAR CELL 56 ( 5 ) 615 - 616 2014.12

Research paper (scientific journal),  ISSN  1097-2765

• Access to Document (DOI)

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

Hirano, Takamasa, Iwasaki, Yuka W., Lin, Zachary Yu-Ching, Imamura, Masanori, Seki, Naomi M., Sasaki, Erika, Saito, Kuniaki, Okano, Hideyuki, Siomi, Mikiko C., Siomi, Haruhiko

RNA 20 ( 8 ) 1223 - 1237 2014.08

Research paper (scientific journal),  ISSN  1355-8382

• Access to Document (DOI)

piRNA clusters and open chromatin structure

Yamanaka, Soichiro, Siomi, Mikiko C., Siomi, Haruhiko

MOBILE DNA 5   1282 - 1291 2014.08

Research paper (scientific journal),  ISSN  1759-8753

• Access to Document (DOI)