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  1. Book: piRNA

    Parrish, Nicholas F. / Iwasaki, Yuka W.

    methods and protocols

    (Methods in molecular biology ; 2509 ; Springer protocols)

    2022  

    Author's details edited by Nicholas F. Parrish, Yuka W. Iwasaki
    Series title Methods in molecular biology ; 2509
    Springer protocols
    Collection
    Keywords Small interfering RNA.
    Subject code 572.88
    Language English
    Size xii, 397 Seiten, Illustrationen, 26 cm
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT021425101
    ISBN 978-1-0716-2379-4 ; 9781071623800 ; 1-0716-2379-6 ; 107162380X
    Database Catalogue ZB MED Medicine, Health

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    Zs A 7042 -2509- not available for loan Lesesaal EG

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  2. Article ; Online: In preprints: revisiting RNA in PRC2.

    Iwasaki, Yuka W / Koseki, Haruhiko / Ito, Shinsuke

    Development (Cambridge, England)

    2023  Volume 150, Issue 22

    MeSH term(s) RNA/genetics ; RNA/metabolism ; Polycomb Repressive Complex 2/metabolism ; Protein Binding
    Chemical Substances RNA (63231-63-0) ; Polycomb Repressive Complex 2 (EC 2.1.1.43)
    Language English
    Publishing date 2023-11-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 90607-4
    ISSN 1477-9129 ; 0950-1991
    ISSN (online) 1477-9129
    ISSN 0950-1991
    DOI 10.1242/dev.202440
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  3. Article ; Online: Rewiring of chromatin state and gene expression by transposable elements.

    Ohtani, Hitoshi / Iwasaki, Yuka W

    Development, growth & differentiation

    2021  Volume 63, Issue 4-5, Page(s) 262–273

    Abstract: Transposable elements form a major fraction of the genome in various eukaryotic species. Although deleterious effects of transpositions within the genome have been reported, recent findings suggest that transposable elements can function as novel ... ...

    Abstract Transposable elements form a major fraction of the genome in various eukaryotic species. Although deleterious effects of transpositions within the genome have been reported, recent findings suggest that transposable elements can function as novel regulatory elements to fine-tune gene expression. Transposable elements can impact the chromatin state through processes such as heterochromatin formation, enhancer-promoter interactions, and chromatin boundary formation, mainly because of the functions of chromatin-based pathways that regulate the expression of transposable elements via DNA methylation and repressive histone modification. Therefore, transposable elements can rewire the chromatin state and gene expression depending on their insertions. Here, we review the findings that reveal the role of transposable elements as modifiers of the chromatin state and gene expression as well as the molecular mechanisms capable of inducing these changes.
    MeSH term(s) Chromatin/genetics ; DNA Methylation ; DNA Transposable Elements/genetics ; Eukaryota ; Gene Expression
    Chemical Substances Chromatin ; DNA Transposable Elements
    Language English
    Publishing date 2021-06-16
    Publishing country Japan
    Document type Journal Article ; Review
    ZDB-ID 280433-5
    ISSN 1440-169X ; 0012-1592
    ISSN (online) 1440-169X
    ISSN 0012-1592
    DOI 10.1111/dgd.12735
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  4. Article ; Online: PIGB maintains nuclear lamina organization in skeletal muscle of Drosophila.

    Yamamoto-Hino, Miki / Ariura, Masaru / Tanaka, Masahito / Iwasaki, Yuka W / Kawaguchi, Kohei / Shimamoto, Yuta / Goto, Satoshi

    The Journal of cell biology

    2024  Volume 223, Issue 2

    Abstract: The nuclear lamina (NL) plays various roles and participates in nuclear integrity, chromatin organization, and transcriptional regulation. Lamin proteins, the main components of the NL, form a homogeneous meshwork structure under the nuclear envelope. ... ...

    Abstract The nuclear lamina (NL) plays various roles and participates in nuclear integrity, chromatin organization, and transcriptional regulation. Lamin proteins, the main components of the NL, form a homogeneous meshwork structure under the nuclear envelope. Lamins are essential, but it is unknown whether their homogeneous distribution is important for nuclear function. Here, we found that PIGB, an enzyme involved in glycosylphosphatidylinositol (GPI) synthesis, is responsible for the homogeneous lamin meshwork in Drosophila. Loss of PIGB resulted in heterogeneous distributions of B-type lamin and lamin-binding proteins in larval muscles. These phenotypes were rescued by expression of PIGB lacking GPI synthesis activity. The PIGB mutant exhibited changes in lamina-associated domains that are large heterochromatic genomic regions in the NL, reduction of nuclear stiffness, and deformation of muscle fibers. These results suggest that PIGB maintains the homogeneous meshwork of the NL, which may be essential for chromatin distribution and nuclear mechanical properties.
    MeSH term(s) Animals ; Drosophila ; Lamin Type B/genetics ; Muscle Fibers, Skeletal/physiology ; Muscle, Skeletal/physiology ; Nuclear Lamina/physiology ; Drosophila Proteins/genetics ; Drosophila Proteins/physiology ; Glycosylphosphatidylinositols/metabolism
    Chemical Substances Lamin Type B ; Drosophila Proteins ; Glycosylphosphatidylinositols
    Language English
    Publishing date 2024-01-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218154-x
    ISSN 1540-8140 ; 0021-9525
    ISSN (online) 1540-8140
    ISSN 0021-9525
    DOI 10.1083/jcb.202301062
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  5. 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
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  6. Article ; Online: Generation of Stable Drosophila Ovarian Somatic Cell Lines Using the piggyBac System.

    Takeuchi, Chikara / Murano, Kensaku / Ishikawa, Mitsuru / Okano, Hideyuki / Iwasaki, Yuka W

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2509, Page(s) 143–153

    Abstract: Transposable elements (TEs) constitute a large proportion of the genome in multiple organisms. Therefore, anti-transposable element machineries are essential to maintain genomic integrity. PIWI-interacting RNAs (piRNAs) are a major force to repress TEs ... ...

    Abstract Transposable elements (TEs) constitute a large proportion of the genome in multiple organisms. Therefore, anti-transposable element machineries are essential to maintain genomic integrity. PIWI-interacting RNAs (piRNAs) are a major force to repress TEs in Drosophila ovaries. Ovarian somatic cells (OSC), in which nuclear piRNA regulation is functional, have been used for research on piRNA pathway as a cell culture system to elucidate the molecular mechanisms underlying the piRNA pathway. Analysis of piRNA pathway using a reporter system to monitor the gene regulation or overexpression of specific genes would be a powerful approach. Here, we present the technical protocol to establish stable cell lines using the piggyBac system, adopted for OSCs. This easy, consistent, and timesaving protocol may accelerate research on the piRNA pathway.
    MeSH term(s) Animals ; Cell Line ; DNA Transposable Elements/genetics ; Drosophila/genetics ; Drosophila/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/genetics ; Female ; Ovary/metabolism ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism
    Chemical Substances DNA Transposable Elements ; Drosophila Proteins ; RNA, Small Interfering
    Language English
    Publishing date 2022-07-07
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2380-0_9
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  7. Article ; Online: Siwi cooperates with Par-1 kinase to resolve the autoinhibitory effect of Papi for Siwi-piRISC biogenesis.

    Yamada, Hiromi / Nishida, Kazumichi M / Iwasaki, Yuka W / Isota, Yosuke / Negishi, Lumi / Siomi, Mikiko C

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 1518

    Abstract: Bombyx Papi acts as a scaffold for Siwi-piRISC biogenesis on the mitochondrial surface. Papi binds first to Siwi via the Tudor domain and subsequently to piRNA precursors loaded onto Siwi via the K-homology (KH) domains. This second action depends on ... ...

    Abstract Bombyx Papi acts as a scaffold for Siwi-piRISC biogenesis on the mitochondrial surface. Papi binds first to Siwi via the Tudor domain and subsequently to piRNA precursors loaded onto Siwi via the K-homology (KH) domains. This second action depends on phosphorylation of Papi. However, the underlying mechanism remains unknown. Here, we show that Siwi targets Par-1 kinase to Papi to phosphorylate Ser547 in the auxiliary domain. This modification enhances the ability of Papi to bind Siwi-bound piRNA precursors via the KH domains. The Papi S547A mutant bound to Siwi, but evaded phosphorylation by Par-1, abrogating Siwi-piRISC biogenesis. A Papi mutant that lacked the Tudor and auxiliary domains escaped coordinated regulation by Siwi and Par-1 and bound RNAs autonomously. Another Papi mutant that lacked the auxiliary domain bound Siwi but did not bind piRNA precursors. A sophisticated mechanism by which Siwi cooperates with Par-1 kinase to promote Siwi-piRISC biogenesis was uncovered.
    MeSH term(s) Animals ; Bombyx/metabolism ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Tudor Domain
    Chemical Substances RNA, Small Interfering
    Language English
    Publishing date 2022-03-21
    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/s41467-022-29193-9
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  8. Article ; Online: Mod(mdg4) variants repress telomeric retrotransposon HeT-A by blocking subtelomeric enhancers.

    Takeuchi, Chikara / Yokoshi, Moe / Kondo, Shu / Shibuya, Aoi / Saito, Kuniaki / Fukaya, Takashi / Siomi, Haruhiko / Iwasaki, Yuka W

    Nucleic acids research

    2022  Volume 50, Issue 20, Page(s) 11580–11599

    Abstract: Telomeres in Drosophila are composed of sequential non-LTR retrotransposons HeT-A, TART and TAHRE. Although they are repressed by the PIWI-piRNA pathway or heterochromatin in the germline, the regulation of these retrotransposons in somatic cells is ... ...

    Abstract Telomeres in Drosophila are composed of sequential non-LTR retrotransposons HeT-A, TART and TAHRE. Although they are repressed by the PIWI-piRNA pathway or heterochromatin in the germline, the regulation of these retrotransposons in somatic cells is poorly understood. In this study, we demonstrated that specific splice variants of Mod(mdg4) repress HeT-A by blocking subtelomeric enhancers in ovarian somatic cells. Among the variants, we found that the Mod(mdg4)-N variant represses HeT-A expression the most efficiently. Subtelomeric sequences bound by Mod(mdg4)-N block enhancer activity within subtelomeric TAS-R repeats. This enhancer-blocking activity is increased by the tandem association of Mod(mdg4)-N to repetitive subtelomeric sequences. In addition, the association of Mod(mdg4)-N couples with the recruitment of RNA polymerase II to the subtelomeres, which reinforces its enhancer-blocking function. Our findings provide novel insights into how telomeric retrotransposons are regulated by the specific variants of insulator proteins associated with subtelomeric sequences.
    Language English
    Publishing date 2022-11-14
    Publishing country England
    Document type Journal Article
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac1034
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  9. Article ; Online: miRNA regulatory ecosystem in early development.

    Iwasaki, Yuka W / Siomi, Haruhiko

    Molecular cell

    2014  Volume 56, Issue 5, Page(s) 615–616

    Abstract: MicroRNAs (miRNAs) reshape spatiotemporal gene expression by both modulating the levels of actively transcribed genes and accelerating the clearance of previously transcribed messages, thereby promoting the transition from a preceding stage to subsequent ...

    Abstract MicroRNAs (miRNAs) reshape spatiotemporal gene expression by both modulating the levels of actively transcribed genes and accelerating the clearance of previously transcribed messages, thereby promoting the transition from a preceding stage to subsequent processes during development. Lee et al. (2014) now demonstrate that maternal miRNAs are adenylated by Wispy, which leads to clearing of maternal miRNAs during early embryogenesis.
    MeSH term(s) Animals ; Argonaute Proteins/metabolism ; Drosophila Proteins/metabolism ; Drosophila melanogaster/embryology ; Drosophila melanogaster/growth & development ; MicroRNAs/metabolism ; Poly A/genetics ; Polynucleotide Adenylyltransferase/metabolism
    Chemical Substances AGO1 protein, Drosophila ; Argonaute Proteins ; Drosophila Proteins ; MicroRNAs ; Poly A (24937-83-5) ; Polynucleotide Adenylyltransferase (EC 2.7.7.19) ; wisp protein, Drosophila (EC 2.7.7.19)
    Language English
    Publishing date 2014-11-13
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2014.11.010
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  10. Article ; Online: Profiling Open Chromatin Structure in the Ovarian Somatic Cells Using ATAC-seq.

    Murano, Kensaku / Iwasaki, Yuka W / Siomi, Haruhiko

    Methods in molecular biology (Clifton, N.J.)

    2017  Volume 1680, Page(s) 165–177

    Abstract: The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was recently established as a method to profile open chromatin, which overcomes the sample size limitations of the alternative methods DNase/MNase-seq. To investigate the role of ... ...

    Abstract The assay for transposase-accessible chromatin using sequencing (ATAC-seq) was recently established as a method to profile open chromatin, which overcomes the sample size limitations of the alternative methods DNase/MNase-seq. To investigate the role of Piwi in heterochromatin formation around transposable element loci, we have used ATAC-seq to examine chromatin accessibility at target transposable elements in a Drosophila cultured cell line, ovarian somatic cells (OSCs). In this chapter, we describe our method to profile open chromatin structure in OSCs using ATAC-seq.
    MeSH term(s) Animals ; Chromatin/genetics ; Chromatin Assembly and Disassembly ; Computational Biology/methods ; DNA Transposable Elements ; Drosophila ; Female ; Gene Library ; High-Throughput Nucleotide Sequencing ; Ovary/cytology ; RNA, Small Untranslated ; Sequence Analysis, DNA/methods
    Chemical Substances Chromatin ; DNA Transposable Elements ; RNA, Small Untranslated
    Language English
    Publishing date 2017-10-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-7339-2_11
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