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  1. Book: Piwi-interacting RNAs

    Siomi, Mikiko C.

    methods and protocols

    (Methods in molecular biology ; 1093 ; Springer protocols)

    2013  

    Author's details ed. by Mikiko C. Siomi
    Series title Methods in molecular biology ; 1093
    Springer protocols
    Collection
    Language English
    Size XI, 249 S. : Ill., graph. Darst.
    Publisher Humana Press
    Publishing place New York u.a.
    Publishing country United States
    Document type Book
    HBZ-ID HT017902472
    ISBN 978-1-62703-693-1 ; 9781627036948 ; 1-62703-693-8 ; 1627036946
    Database Catalogue ZB MED Medicine, Health

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    Shelf markLoan statusLocation
    2013 A 3655 available for loan (reading room) Lesesaal EG

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  2. Article ; Online: The piRNA pathway in Drosophila ovarian germ and somatic cells.

    Sato, Kaoru / Siomi, Mikiko C

    Proceedings of the Japan Academy. Series B, Physical and biological sciences

    2020  Volume 96, Issue 1, Page(s) 32–42

    Abstract: RNA silencing refers to gene silencing pathways mediated by small non-coding RNAs, including microRNAs. Piwi-interacting RNAs (piRNAs) constitute the largest class of small non-coding RNAs in animal gonads, which repress transposons to protect the ... ...

    Abstract RNA silencing refers to gene silencing pathways mediated by small non-coding RNAs, including microRNAs. Piwi-interacting RNAs (piRNAs) constitute the largest class of small non-coding RNAs in animal gonads, which repress transposons to protect the germline genome from the selfish invasion of transposons. Deterioration of the system causes DNA damage, leading to severe defects in gametogenesis and infertility. Studies using Drosophila ovaries show that piRNAs originate from specific genomic loci, termed piRNA clusters, and that in piRNA biogenesis, cluster transcripts are processed into mature piRNAs via three distinct pathways: initiator or responder for ping-pong piRNAs and trailing for phased piRNAs. piRNAs then assemble with PIWI members of the Argonaute family of proteins to form piRNA-induced RNA silencing complexes (piRISCs), the core engine of the piRNA-mediated silencing pathway. Upon piRISC assembly, the PIWI member, Piwi, is translocated to the nucleus and represses transposons co-transcriptionally by inducing local heterochromatin formation at target transposon loci.
    MeSH term(s) Animals ; Argonaute Proteins/genetics ; Drosophila Proteins/genetics ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Developmental ; Gene Silencing ; Germ Cells/metabolism ; Ovary/metabolism ; RNA, Small Interfering/metabolism ; RNA-Induced Silencing Complex/metabolism
    Chemical Substances Argonaute Proteins ; Drosophila Proteins ; RNA, Small Interfering ; RNA-Induced Silencing Complex
    Language English
    Publishing date 2020-01-13
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 161781-3
    ISSN 1349-2896 ; 0386-2208
    ISSN (online) 1349-2896
    ISSN 0386-2208
    DOI 10.2183/pjab.96.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association.

    Yamazaki, Hiroya / Namba, Yurika / Kuriyama, Shogo / Nishida, Kazumichi M / Kajiya, Asako / Siomi, Mikiko C

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 1942

    Abstract: Bombyx Vasa (BmVasa) assembles non-membranous organelle, nuage or Vasa bodies, in germ cells, known as the center for Siwi-dependent transposon silencing and concomitant Ago3-piRISC biogenesis. However, details of the body assembly remain unclear. Here, ... ...

    Abstract Bombyx Vasa (BmVasa) assembles non-membranous organelle, nuage or Vasa bodies, in germ cells, known as the center for Siwi-dependent transposon silencing and concomitant Ago3-piRISC biogenesis. However, details of the body assembly remain unclear. Here, we show that the N-terminal intrinsically disordered region (N-IDR) and RNA helicase domain of BmVasa are responsible for self-association and RNA binding, respectively, but N-IDR is also required for full RNA-binding activity. Both domains are essential for Vasa body assembly in vivo and droplet formation in vitro via phase separation. FAST-iCLIP reveals that BmVasa preferentially binds transposon mRNAs. Loss of Siwi function derepresses transposons but has marginal effects on BmVasa-RNA binding. This study shows that BmVasa assembles nuage by phase separation via its ability to self-associate and bind newly exported transposon mRNAs. This unique property of BmVasa allows transposon mRNAs to be sequestered and enriched in nuage, resulting in effective Siwi-dependent transposon repression and Ago3-piRISC biogenesis.
    MeSH term(s) Animals ; RNA, Small Interfering/metabolism ; Bombyx/genetics ; Bombyx/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Drosophila Proteins/metabolism
    Chemical Substances RNA, Small Interfering ; RNA, Messenger ; Drosophila Proteins
    Language English
    Publishing date 2023-04-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-37634-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association

    Hiroya Yamazaki / Yurika Namba / Shogo Kuriyama / Kazumichi M. Nishida / Asako Kajiya / Mikiko C. Siomi

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 15

    Abstract: Bombyx Vasa assembles Vasa bodies, the site of transposon silencing by Siwi and Ago3-piRISC formation. Here, the authors show Vasa sequesters transposon mRNAs in Vasa bodies via phase separation requiring RNA binding and self-association of Vasa. ...

    Abstract Bombyx Vasa assembles Vasa bodies, the site of transposon silencing by Siwi and Ago3-piRISC formation. Here, the authors show Vasa sequesters transposon mRNAs in Vasa bodies via phase separation requiring RNA binding and self-association of Vasa.
    Keywords Science ; Q
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Assembly and Function of Gonad-Specific Non-Membranous Organelles in

    Hirakata, Shigeki / Siomi, Mikiko C

    Non-coding RNA

    2019  Volume 5, Issue 4

    Abstract: PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that repress transposons in animal germlines. This protects the genome from the invasive DNA elements. piRNA pathway failures lead to DNA damage, gonadal development defects, and infertility. Thus, ...

    Abstract PIWI-interacting RNAs (piRNAs) are small non-coding RNAs that repress transposons in animal germlines. This protects the genome from the invasive DNA elements. piRNA pathway failures lead to DNA damage, gonadal development defects, and infertility. Thus, the piRNA pathway is indispensable for the continuation of animal life. piRNA-mediated transposon silencing occurs in both the nucleus and cytoplasm while piRNA biogenesis is a solely cytoplasmic event. piRNA production requires a number of proteins, the majority of which localize to non-membranous organelles that specifically appear in the gonads. Other piRNA factors are localized on outer mitochondrial membranes. In situ RNA hybridization experiments show that piRNA precursors are compartmentalized into other non-membranous organelles. In this review, we summarize recent findings about the function of these organelles in the
    Language English
    Publishing date 2019-11-06
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2813993-8
    ISSN 2311-553X ; 2311-553X
    ISSN (online) 2311-553X
    ISSN 2311-553X
    DOI 10.3390/ncrna5040052
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: piRNA- and siRNA-mediated transcriptional repression in Drosophila, mice, and yeast: new insights and biodiversity.

    Onishi, Ryo / Yamanaka, Soichiro / Siomi, Mikiko C

    EMBO reports

    2021  Volume 22, Issue 10, Page(s) e53062

    Abstract: The PIWI-interacting RNA (piRNA) pathway acts as a self-defense mechanism against transposons to maintain germline genome integrity. Failures in the piRNA pathway cause DNA damage in the germline genome, disturbing inheritance of "correct" genetic ... ...

    Abstract The PIWI-interacting RNA (piRNA) pathway acts as a self-defense mechanism against transposons to maintain germline genome integrity. Failures in the piRNA pathway cause DNA damage in the germline genome, disturbing inheritance of "correct" genetic information by the next generations and leading to infertility. piRNAs execute transposon repression in two ways: degrading their RNA transcripts and compacting the genomic loci via heterochromatinization. The former event is mechanistically similar to siRNA-mediated RNA cleavage that occurs in the cytoplasm and has been investigated in many species including nematodes, fruit flies, and mammals. The latter event seems to be mechanistically parallel to siRNA-centered kinetochore assembly and subsequent chromosome segregation, which has so far been studied particularly in fission yeast. Despite the interspecies conservations, the overall schemes of the nuclear events show clear biodiversity across species. In this review, we summarize the recent progress regarding piRNA-mediated transcriptional silencing in Drosophila and discuss the biodiversity by comparing it with the equivalent piRNA-mediated system in mice and the siRNA-mediated system in fission yeast.
    MeSH term(s) Animals ; Argonaute Proteins/metabolism ; Biodiversity ; DNA Transposable Elements/genetics ; Drosophila/genetics ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Gene Silencing ; Mice ; RNA, Small Interfering/genetics ; Saccharomyces cerevisiae/metabolism ; Transcription, Genetic
    Chemical Substances Argonaute Proteins ; DNA Transposable Elements ; Drosophila Proteins ; RNA, Small Interfering
    Language English
    Publishing date 2021-08-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2020896-0
    ISSN 1469-3178 ; 1469-221X
    ISSN (online) 1469-3178
    ISSN 1469-221X
    DOI 10.15252/embr.202153062
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 5433: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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  7. Article ; Online: T-hairpin structure found in the RNA element involved in piRNA biogenesis.

    Takase, Naomi / Otsu, Maina / Hirakata, Shigeki / Ishizu, Hirotsugu / Siomi, Mikiko C / Kawai, Gota

    RNA (New York, N.Y.)

    2022  Volume 28, Issue 4, Page(s) 541–550

    Abstract: PIWI-interacting RNAs (piRNAs) repress transposons to protect the germline genome from DNA damage caused by transposon transposition. ... ...

    Abstract PIWI-interacting RNAs (piRNAs) repress transposons to protect the germline genome from DNA damage caused by transposon transposition. In
    MeSH term(s) Animals ; DNA Transposable Elements ; Drosophila/genetics ; Drosophila/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Germ Cells/metabolism ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism
    Chemical Substances DNA Transposable Elements ; Drosophila Proteins ; RNA, Small Interfering
    Language English
    Publishing date 2022-01-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.078967.121
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    Zs.A 4777: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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  8. Article ; Online: Two distinct transcriptional controls triggered by nuclear Piwi-piRISCs in the Drosophila piRNA pathway.

    Sato, Kaoru / Siomi, Mikiko C

    Current opinion in structural biology

    2018  Volume 53, Page(s) 69–76

    Abstract: Transposons occupy a large proportion of eukaryotic genomes. Spontaneous movement of transposons within the genome leads to genomic mutations that are often life threatening. To avoid such outcomes, host species have acquired an elaborate molecular ... ...

    Abstract Transposons occupy a large proportion of eukaryotic genomes. Spontaneous movement of transposons within the genome leads to genomic mutations that are often life threatening. To avoid such outcomes, host species have acquired an elaborate molecular pathway during evolution, in which PIWI proteins and PIWI-interacting RNAs (piRNAs) collaboratively control transposons to maintain germline genome integrity. Studies of PIWI-piRNA-based transposon silencing have uncovered the molecular mechanisms underlying piRNA biogenesis and the silencing mode-of-action in the pathway. Interestingly, the bilateral events require transcriptional controls triggered by nuclear PIWI-piRNA complexes in positive and negative manners, respectively. This review summarizes the mechanisms of PIWI-piRNA-mediated transcriptional controls in Drosophila ovaries.
    MeSH term(s) Animals ; Argonaute Proteins/metabolism ; Cell Nucleus/metabolism ; DNA Transposable Elements/genetics ; Drosophila/genetics ; Drosophila Proteins/metabolism ; Female ; Gene Expression Regulation ; Gene Silencing ; Germ Cells/metabolism ; Ovary/metabolism ; RNA, Small Interfering/metabolism
    Chemical Substances Argonaute Proteins ; DNA Transposable Elements ; Drosophila Proteins ; RNA, Small Interfering ; piwi protein, Drosophila
    Language English
    Publishing date 2018-07-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2018.06.005
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  9. Article ; Online: Japan: prize diversity, not conformity, to boost research.

    Sheng, Guojun / Carninci, Piero / Siomi, Mikiko C / Suda, Toshio / Alev, Cantas

    Nature

    2021  Volume 599, Issue 7884, Page(s) 201

    MeSH term(s) Creativity ; Humans ; Japan ; Motivation ; Nobel Prize ; Research/standards ; Research Personnel/psychology ; Research Personnel/standards
    Language English
    Publishing date 2021-11-09
    Publishing country England
    Document type Letter
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-021-03070-9
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  10. Article ; Online: Maelstrom functions in the production of Siwi-piRISC capable of regulating transposons in

    Namba, Yurika / Iwasaki, Yuka W / Nishida, Kazumichi M / Nishihara, Hidenori / Sumiyoshi, Tetsutaro / Siomi, Mikiko C

    iScience

    2022  Volume 25, Issue 3, Page(s) 103914

    Abstract: PIWI-interacting RNAs (piRNAs) bind to PIWI proteins to assemble the piRISC, which represses germline transposons. Maelstrom (Mael) is necessary for piRISC biogenesis in germ cells, but its function remains unclear. Here, we show that Mael interconnects ... ...

    Abstract PIWI-interacting RNAs (piRNAs) bind to PIWI proteins to assemble the piRISC, which represses germline transposons. Maelstrom (Mael) is necessary for piRISC biogenesis in germ cells, but its function remains unclear. Here, we show that Mael interconnects Spindle-E (Spn-E), a key piRISC biogenesis factor, with unloaded Siwi, one of two silkworm PIWI members. Mael also assembles a subset of nuage, a non-membranous organelle involved in piRISC biogenesis. Loss of Mael abrogated the Spn-E-Siwi interaction and Ago3-piRISC biogenesis, but Siwi-piRISC was produced. Bioinformatic analysis showed that Siwi-bound piRNAs in Mael-lacking cells were rich in transposon-targeting piRNAs as in normal cells but were biased toward transposons that are marginally controlled by Siwi-piRISC. This explains the impairment in Ago3-piRISC production because transposon mRNAs cleaved by Siwi are the origin of Ago3-loaded piRNAs. We argue that Mael plays a role in the production of primary Siwi-piRISC capable of regulating transposon expression in germ cells.
    Language English
    Publishing date 2022-02-11
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2022.103914
    Database MEDical Literature Analysis and Retrieval System OnLINE

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