The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Mikiko C. Siomi - One of the best experts on this subject based on the ideXlab platform.

  • Piwi Interacting RNA in drosophila biogenesis transposon regulation and beyond
    Chemical Reviews, 2017
    Co-Authors: Haruna Yamashiro, Mikiko C. Siomi
    Abstract:

    Piwi-Interacting RNAs (piRNAs) are germline-enriched small RNAs that control transposons to maintain genome integrity. To achieve this, upon being processed from piRNA precursors, most of which are transcripts of intergenic piRNA clusters, piRNAs bind Piwi proteins, germline-specific Argonaute proteins, to form effector complexes. The mechanism of this piRNA-mediated transposon silencing pathway is fundamentally similar to that of siRNA/miRNA-dependent gene silencing in that a small RNA guides its partner Argonaute protein to target gene transcripts for repression via RNA–RNA base pairing. However, the uniqueness of this piRNA pathway has emerged through intensive genetic, biochemical, bioinformatic, and structural investigations. Here, we review the studies that elucidated the piRNA pathway, mainly in Drosophila, by describing both historical and recent progress. Studies in other species that have made important contributions to the field are also described.

  • The Piwi-Interacting RNA Molecular Pathway: Insights From Cultured Silkworm Germline Cells.
    BioEssays : news and reviews in molecular cellular and developmental biology, 2017
    Co-Authors: Kazuhiro Sakakibara, Mikiko C. Siomi
    Abstract:

    The Piwi-Interacting RNA (piRNA) pathway, one of the major eukaryotic small RNA silencing pathways, is a genome surveillance system that silences selfish genes in animal gonads. piRNAs guide Piwi protein to target genes through Watson-Crick RNA-RNA base-parings. Loss of piRNA function causes genome instability, inducing failure in gametogenesis and infertility. Studies using fruit flies and mice as key experimental models have resulted in tremendous progress in understanding the mechanism underlying the piRNA pathway. Recent work using cultured silkworm germline cells has also expanded our knowledge of piRNA biogenesis in particular, since these silkworm cells are the only cells of germline origin that can be cultured. In this review, we describe elucidation of the piRNA pathway using cultured silkworm cells as an experimental model by focusing on recent work in biochemistry and structural biology. Earlier studies that made important contributions to the field are also described.

  • Piwi Interacting RNA its biogenesis and functions
    Annual Review of Biochemistry, 2015
    Co-Authors: Yuka W Iwasaki, Mikiko C. Siomi, Haruhiko Siomi
    Abstract:

    Piwi-Interacting RNAs (piRNAs) are a class of small RNAs that are 24–31 nucleotides in length. They associate with Piwi proteins, which constitute a germline-specific subclade of the Argonaute family, to form effector complexes known as piRNA-induced silencing complexes, which repress transposons via transcriptional or posttranscriptional mechanisms and maintain germline genome integrity. In addition to having a role in transposon silencing, piRNAs in diverse organisms function in the regulation of cellular genes. In some cases, piRNAs have shown transgenerational inheritance to pass on the memory of “self” and “nonself,” suggesting a contribution to various cellular processes over generations. Many piRNA factors have been identified; however, both the molecular mechanisms leading to the production of mature piRNAs and the effector phases of gene silencing are still enigmatic. Here, we summarize the current state of our knowledge on the biogenesis of piRNA, its biological functions, and the underlying mec...

  • respective functions of two distinct siwi complexes assembled during Piwi Interacting RNA biogenesis in bombyx germ cells
    Cell Reports, 2015
    Co-Authors: Kazumichi M. Nishida, Haruhiko Siomi, Yukiko Murota, Yuka W Iwasaki, Akihiro Nagao, Taro Mannen, Yumiko Kato, Mikiko C. Siomi
    Abstract:

    SUMMARY Piwi-Interacting RNA (piRNA) biogenesis consists of two sequential steps: primary piRNA processing and the ping-pong cycle that depends on reciprocal Slicer-mediated RNA cleavage by Piwi proteins. However, the molecular functions of the factors involved remain elusive. Here, we show that RNAs cleaved by a Bombyx mori Piwi, Siwi, remain bound to the protein upon cleavage but are released by a DEAD box protein BmVasa. BmVasa copurifies with Siwi but not another Piwi BmAgo3. A lack of BmVasa does not affect primary piRNA processing but abolishes the ping-pong cycle. Siwi also forms a complex with BmSpn-E and BmQin. This complex is physically separable from the Siwi/BmVasa complex. BmSpn-E, unlike BmVasa, is necessary for primary piRNA production. We propose a model for piRNA biogenesis, where the BmSpn-E/BmQin dimer binds Siwi to function in primary piRNA processing, whereas BmVasa, by associating with Siwi, ensures target RNA release upon cleavage to facilitate the ping-pong cycle.

  • dmgtsf1 is necessary for Piwi pirisc mediated transcriptional transposon silencing in the drosophila ovary
    Genes & Development, 2013
    Co-Authors: Hitoshi Ohtani, Haruhiko Siomi, Mikiko C. Siomi, Yuka W Iwasaki, Aoi Shibuya, Kuniaki Saito
    Abstract:

    The Piwi-piRNA (Piwi-Interacting RNA) complex (Piwi-piRISC) in Drosophila ovarian somatic cells represses transposons transcriptionally to maintain genome integrity; however, the underlying mechanisms remain obscure. Here, we reveal that DmGTSF1, a Drosophila homolog of gametocyte-specific factor 1 (GTSF1) (which is required for transposon silencing in mouse testes), is necessary for Piwi-piRISC to repress target transposons and neighboring genes. DmGTSF1 depletion affected neither piRNA biogenesis nor nuclear import of Piwi-piRISC. DmGTSF1 mutations caused derepression of transposons and loss of ovary follicle layers, resulting in female infertility. We suggest that DmGTSF1, a nuclear Piwi interactor, is an integral factor in Piwi-piRISC-mediated transcriptional silencing.

Alper Akay - One of the best experts on this subject based on the ideXlab platform.

  • deps 1 is required for piRNA dependent silencing and Piwi condensate organisation in caenorhabditis elegans
    Nature Communications, 2020
    Co-Authors: Kin Man Suen, Fabian Braukmann, Richard Butler, Dalila Bensaddek, Alper Akay
    Abstract:

    Membraneless organelles are sites for RNA biology including small non-coding RNA (ncRNA) mediated gene silencing. How small ncRNAs utilise phase separated environments for their function is unclear. We investigated how the Piwi-Interacting RNA (piRNA) pathway engages with the membraneless organelle P granule in Caenorhabditis elegans. Proteomic analysis of the Piwi protein PRG-1 reveals an interaction with the constitutive P granule protein DEPS-1. DEPS-1 is not required for piRNA biogenesis but piRNA-dependent silencing: deps-1 mutants fail to produce the secondary endo-siRNAs required for the silencing of piRNA targets. We identify a motif on DEPS-1 which mediates a direct interaction with PRG-1. DEPS-1 and PRG-1 form intertwining clusters to build elongated condensates in vivo which are dependent on the Piwi-Interacting motif of DEPS-1. Additionally, we identify EDG-1 as an interactor of DEPS-1 and PRG-1. Our study reveals how specific protein-protein interactions drive the spatial organisation and piRNA-dependent silencing within membraneless organelles.

Haruhiko Siomi - One of the best experts on this subject based on the ideXlab platform.

  • Piwi Interacting RNA its biogenesis and functions
    Annual Review of Biochemistry, 2015
    Co-Authors: Yuka W Iwasaki, Mikiko C. Siomi, Haruhiko Siomi
    Abstract:

    Piwi-Interacting RNAs (piRNAs) are a class of small RNAs that are 24–31 nucleotides in length. They associate with Piwi proteins, which constitute a germline-specific subclade of the Argonaute family, to form effector complexes known as piRNA-induced silencing complexes, which repress transposons via transcriptional or posttranscriptional mechanisms and maintain germline genome integrity. In addition to having a role in transposon silencing, piRNAs in diverse organisms function in the regulation of cellular genes. In some cases, piRNAs have shown transgenerational inheritance to pass on the memory of “self” and “nonself,” suggesting a contribution to various cellular processes over generations. Many piRNA factors have been identified; however, both the molecular mechanisms leading to the production of mature piRNAs and the effector phases of gene silencing are still enigmatic. Here, we summarize the current state of our knowledge on the biogenesis of piRNA, its biological functions, and the underlying mec...

  • respective functions of two distinct siwi complexes assembled during Piwi Interacting RNA biogenesis in bombyx germ cells
    Cell Reports, 2015
    Co-Authors: Kazumichi M. Nishida, Haruhiko Siomi, Yukiko Murota, Yuka W Iwasaki, Akihiro Nagao, Taro Mannen, Yumiko Kato, Mikiko C. Siomi
    Abstract:

    SUMMARY Piwi-Interacting RNA (piRNA) biogenesis consists of two sequential steps: primary piRNA processing and the ping-pong cycle that depends on reciprocal Slicer-mediated RNA cleavage by Piwi proteins. However, the molecular functions of the factors involved remain elusive. Here, we show that RNAs cleaved by a Bombyx mori Piwi, Siwi, remain bound to the protein upon cleavage but are released by a DEAD box protein BmVasa. BmVasa copurifies with Siwi but not another Piwi BmAgo3. A lack of BmVasa does not affect primary piRNA processing but abolishes the ping-pong cycle. Siwi also forms a complex with BmSpn-E and BmQin. This complex is physically separable from the Siwi/BmVasa complex. BmSpn-E, unlike BmVasa, is necessary for primary piRNA production. We propose a model for piRNA biogenesis, where the BmSpn-E/BmQin dimer binds Siwi to function in primary piRNA processing, whereas BmVasa, by associating with Siwi, ensures target RNA release upon cleavage to facilitate the ping-pong cycle.

  • dmgtsf1 is necessary for Piwi pirisc mediated transcriptional transposon silencing in the drosophila ovary
    Genes & Development, 2013
    Co-Authors: Hitoshi Ohtani, Haruhiko Siomi, Mikiko C. Siomi, Yuka W Iwasaki, Aoi Shibuya, Kuniaki Saito
    Abstract:

    The Piwi-piRNA (Piwi-Interacting RNA) complex (Piwi-piRISC) in Drosophila ovarian somatic cells represses transposons transcriptionally to maintain genome integrity; however, the underlying mechanisms remain obscure. Here, we reveal that DmGTSF1, a Drosophila homolog of gametocyte-specific factor 1 (GTSF1) (which is required for transposon silencing in mouse testes), is necessary for Piwi-piRISC to repress target transposons and neighboring genes. DmGTSF1 depletion affected neither piRNA biogenesis nor nuclear import of Piwi-piRISC. DmGTSF1 mutations caused derepression of transposons and loss of ovary follicle layers, resulting in female infertility. We suggest that DmGTSF1, a nuclear Piwi interactor, is an integral factor in Piwi-piRISC-mediated transcriptional silencing.

  • Gender-Specific Hierarchy in Nuage Localization of Piwi-Interacting RNA Factors in Drosophila.
    Frontiers in genetics, 2011
    Co-Authors: Akihiro Nagao, Kazumichi M. Nishida, Haruhiko Siomi, Kaoru Sato, Mikiko C. Siomi
    Abstract:

    Piwi-Interacting RNAs (piRNAs) are germline-specific small non-coding RNAs that form piRNA-induced silencing complexes (piRISCs) by associating with Piwi proteins, a subclade of the Argonaute proteins predominantly expressed in the germline. piRISCs protect the integrity of the germline genome from invasive transposable DNA elements by silencing them. Multiple piRNA biogenesis factors have been identified in Drosophila. The majority of piRNA factors are localized in the nuage, electron-dense non-membranous cytoplasmic structures located in the perinuclear regions of germ cells. Thus, piRNA biogenesis is thought to occur in the nuage in germ cells. Immunofluorescence analyses of ovaries from piRNA factor mutants have revealed a localization hierarchy of piRNA factors in female nuage. However, whether this hierarchy is female-specific or can also be applied in male gonads remains undetermined. Here, we show by immunostaining of both ovaries and testes from piRNA factor mutants that the molecular hierarchy of piRNA factors shows gender-specificity, especially for Krimper (Krimp), a Tudor-domain containing protein of unknown function(s): Krimp is dispensable for Piwi protein Aubergine (Aub) nuage localization in ovaries but Krimp and Aub require each other for their proper nuage localization in testes. This suggests that the functional requirement of Krimp in piRNA biogenesis may be different in male and female gonads.

  • how does the royal family of tudor rule the Piwi Interacting RNA pathway
    Genes & Development, 2010
    Co-Authors: Mikiko C. Siomi, Taro Mannen, Haruhiko Siomi
    Abstract:

    Piwi (P-element-induced wimpy testis) proteins are a subset of the Argonaute proteins and are expressed predominantly in the germlines of a variety of organisms, including Drosophila and mammals. Piwi proteins associate specifically with Piwi-Interacting RNAs (piRNAs), small RNAs that are also expressed predominantly in germlines, and silence transposable DNA elements and other genes showing complementarities to the sequences of associated piRNAs. This mechanism helps to maintain the integrity of the genome and the development of gametes. Piwi proteins have been shown recently to contain symmetrical dimethyl arginines (sDMAs), and this modification is mediated by the methyltransferase PRMT5 (also known as Dart5 or Capsuleen). It was then demonstrated that multiple members of the Tudor (Tud) family of proteins, which are necessary for gametogenesis in both flies and mice, associate with Piwi proteins specifically through sDMAs in various but particular combinations. Although Tud domains in Tud family members are known to be sDMA-binding modules, involvement of the Tudor family at the molecular level in the piRNA pathway has only recently come into focus.

Yuka W Iwasaki - One of the best experts on this subject based on the ideXlab platform.

  • nuclear RNA export factor variant initiates piRNA guided co transcriptional silencing
    The EMBO Journal, 2019
    Co-Authors: Kensaku Murano, Yuka W Iwasaki, Aoi Shibuya, Hirotsugu Ishizu, Akane Mashiko, Shu Kondo, Shungo Adachi, Saori Suzuki, Kuniaki Saito
    Abstract:

    The Piwi-Interacting RNA (piRNA) pathway preserves genomic integrity by repressing transposable elements (TEs) in animal germ cells. Among Piwi-clade proteins in Drosophila, Piwi transcriptionally silences its targets through interactions with cofactors, including Panoramix (Panx) and forms heterochromatin characterized by H3K9me3 and H1. Here, we identified Nxf2, a nuclear RNA export factor (NXF) variant, as a protein that forms complexes with Piwi, Panx, and p15. Panx-Nxf2-P15 complex formation is necessary in the silencing by stabilizing protein levels of Nxf2 and Panx. Notably, ectopic targeting of Nxf2 initiates co-transcriptional repression of the target reporter in a manner independent of H3K9me3 marks or H1. However, continuous silencing requires HP1a and H1. In addition, Nxf2 directly interacts with target TE transcripts in a Piwi-dependent manner. These findings suggest a model in which the Panx-Nxf2-P15 complex enforces the association of Piwi with target transcripts to trigger co-transcriptional repression, prior to heterochromatin formation in the nuclear piRNA pathway. Our results provide an unexpected connection between an NXF variant and small RNA-mediated co-transcriptional silencing.

  • Piwi Interacting RNA its biogenesis and functions
    Annual Review of Biochemistry, 2015
    Co-Authors: Yuka W Iwasaki, Mikiko C. Siomi, Haruhiko Siomi
    Abstract:

    Piwi-Interacting RNAs (piRNAs) are a class of small RNAs that are 24–31 nucleotides in length. They associate with Piwi proteins, which constitute a germline-specific subclade of the Argonaute family, to form effector complexes known as piRNA-induced silencing complexes, which repress transposons via transcriptional or posttranscriptional mechanisms and maintain germline genome integrity. In addition to having a role in transposon silencing, piRNAs in diverse organisms function in the regulation of cellular genes. In some cases, piRNAs have shown transgenerational inheritance to pass on the memory of “self” and “nonself,” suggesting a contribution to various cellular processes over generations. Many piRNA factors have been identified; however, both the molecular mechanisms leading to the production of mature piRNAs and the effector phases of gene silencing are still enigmatic. Here, we summarize the current state of our knowledge on the biogenesis of piRNA, its biological functions, and the underlying mec...

  • respective functions of two distinct siwi complexes assembled during Piwi Interacting RNA biogenesis in bombyx germ cells
    Cell Reports, 2015
    Co-Authors: Kazumichi M. Nishida, Haruhiko Siomi, Yukiko Murota, Yuka W Iwasaki, Akihiro Nagao, Taro Mannen, Yumiko Kato, Mikiko C. Siomi
    Abstract:

    SUMMARY Piwi-Interacting RNA (piRNA) biogenesis consists of two sequential steps: primary piRNA processing and the ping-pong cycle that depends on reciprocal Slicer-mediated RNA cleavage by Piwi proteins. However, the molecular functions of the factors involved remain elusive. Here, we show that RNAs cleaved by a Bombyx mori Piwi, Siwi, remain bound to the protein upon cleavage but are released by a DEAD box protein BmVasa. BmVasa copurifies with Siwi but not another Piwi BmAgo3. A lack of BmVasa does not affect primary piRNA processing but abolishes the ping-pong cycle. Siwi also forms a complex with BmSpn-E and BmQin. This complex is physically separable from the Siwi/BmVasa complex. BmSpn-E, unlike BmVasa, is necessary for primary piRNA production. We propose a model for piRNA biogenesis, where the BmSpn-E/BmQin dimer binds Siwi to function in primary piRNA processing, whereas BmVasa, by associating with Siwi, ensures target RNA release upon cleavage to facilitate the ping-pong cycle.

  • dmgtsf1 is necessary for Piwi pirisc mediated transcriptional transposon silencing in the drosophila ovary
    Genes & Development, 2013
    Co-Authors: Hitoshi Ohtani, Haruhiko Siomi, Mikiko C. Siomi, Yuka W Iwasaki, Aoi Shibuya, Kuniaki Saito
    Abstract:

    The Piwi-piRNA (Piwi-Interacting RNA) complex (Piwi-piRISC) in Drosophila ovarian somatic cells represses transposons transcriptionally to maintain genome integrity; however, the underlying mechanisms remain obscure. Here, we reveal that DmGTSF1, a Drosophila homolog of gametocyte-specific factor 1 (GTSF1) (which is required for transposon silencing in mouse testes), is necessary for Piwi-piRISC to repress target transposons and neighboring genes. DmGTSF1 depletion affected neither piRNA biogenesis nor nuclear import of Piwi-piRISC. DmGTSF1 mutations caused derepression of transposons and loss of ovary follicle layers, resulting in female infertility. We suggest that DmGTSF1, a nuclear Piwi interactor, is an integral factor in Piwi-piRISC-mediated transcriptional silencing.

Benjamin Czech - One of the best experts on this subject based on the ideXlab platform.

  • Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila.
    eLife, 2021
    Co-Authors: Evelyn L Eastwood, Marzia Munafo, Emma Kneuss, Susanne Bornelöv, Kayla A. Jara, Vasileios Frantzis, Elisar Barbar, Benjamin Czech
    Abstract:

    In animal gonads, the Piwi-Interacting RNA (piRNA) pathway guards genome integrity in part through the co-transcriptional gene silencing of transposon insertions. In Drosophila ovaries, piRNA-loaded Piwi detects nascent transposon transcripts and instructs heterochromatin formation through the Panoramix-induced co-transcriptional silencing (PICTS) complex, containing Panoramix, Nxf2 and Nxt1. Here, we report that the highly conserved dynein light chain LC8/Cut-up (Ctp) is an essential component of the PICTS complex. Loss of Ctp results in transposon de-repression and a reduction in repressive chromatin marks specifically at transposon loci. In turn, Ctp can enforce transcriptional silencing when artificially recruited to RNA and DNA reporters. We show that Ctp drives dimerisation of the PICTS complex through its interaction with conserved motifs within Panoramix. Artificial dimerisation of Panoramix bypasses the necessity for its interaction with Ctp, demonstrating that conscription of a protein from a ubiquitous cellular machinery has fulfilled a fundamental requirement for a transposon silencing complex.

  • dimerisation of the picts complex via lc8 cut up drives co transcriptional transposon silencing in drosophila
    eLife, 2021
    Co-Authors: Evelyn L Eastwood, Marzia Munafo, Emma Kneuss, Susanne Bornelöv, Kayla A. Jara, Vasileios Frantzis, Elisar Barbar, Benjamin Czech
    Abstract:

    In animal gonads, the Piwi-Interacting RNA (piRNA) pathway guards genome integrity in part through the co-transcriptional gene silencing of transposon insertions. In Drosophila ovaries, piRNA-loaded Piwi detects nascent transposon transcripts and instructs heterochromatin formation through the Panoramix-induced co-transcriptional silencing (PICTS) complex, containing Panoramix, Nxf2 and Nxt1. Here, we report that the highly conserved dynein light chain LC8/Cut-up (Ctp) is an essential component of the PICTS complex. Loss of Ctp results in transposon de-repression and a reduction in repressive chromatin marks specifically at transposon loci. In turn, Ctp can enforce transcriptional silencing when artificially recruited to RNA and DNA reporters. We show that Ctp drives dimerisation of the PICTS complex through its interaction with conserved motifs within Panoramix. Artificial dimerisation of Panoramix bypasses the necessity for its interaction with Ctp, demonstrating that conscription of a protein from a ubiquitous cellular machinery has fulfilled a fundamental requirement for a transposon silencing complex.

  • piRNA guided co transcriptional silencing coopts nuclear export factors
    bioRxiv, 2019
    Co-Authors: Martin H Fabry, Ilaria Falciatori, Gregory J Hannon, Filippo Ciabrelli, Marzia Munafo, Evelyn L Eastwood, Emma Kneuss, Federica A Falconio, Benjamin Czech
    Abstract:

    Summary The Piwi-Interacting RNA (piRNA) pathway is a small RNA-based immune system that controls the expression of transposons and maintains genome integrity in animal gonads. In Drosophila, piRNA-guided silencing is achieved, in part, via co-transcriptional repression of transposons by Piwi. This depends on Panoramix (Panx); however, precisely how an RNA binding event silences transcription remains to be determined. Here we show that Nuclear Export Factor 2 (Nxf2) and its cofactor, Nxt1, form a complex with Panx and are required for co-transcriptional silencing of transposons in somatic and germline cells of the ovary. Tethering of Nxf2 or Nxt1 to RNA results in silencing of target loci and the concomitant accumulation of repressive chromatin marks. Nxf2 and Panx proteins are mutually required for proper localization and stability. We mapped the protein domains crucial for the Nxf2/Panx complex formation and show that the amino-terminal portion of Panx is sufficient to induce transcriptional silencing.

  • oncogenic transformation of drosophila somatic cells induces a functional piRNA pathway
    Genes & Development, 2016
    Co-Authors: Delphine Fagegaltier, Ilaria Falciatori, Benjamin Czech, Stephane E Castel, Norbert Perrimon, Amanda Simcox, Gregory J Hannon
    Abstract:

    Germline genes often become re-expressed in soma-derived human cancers as "cancer/testis antigens" (CTAs), and piRNA (Piwi-Interacting RNA) pathway proteins are found among CTAs. However, whether and how the piRNA pathway contributes to oncogenesis in human neoplasms remain poorly understood. We found that oncogenic Ras combined with loss of the Hippo tumor suppressor pathway reactivates a primary piRNA pathway in Drosophila somatic cells coincident with oncogenic transformation. In these cells, Piwi becomes loaded with piRNAs derived from annotated generative loci, which are normally restricted to either the germline or the somatic follicle cells. Negating the pathway leads to increases in the expression of a wide variety of transposons and also altered expression of some protein-coding genes. This correlates with a reduction in the proliferation of the transformed cells in culture, suggesting that, at least in this context, the piRNA pathway may play a functional role in cancer.