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  1. Article ; Online: Why Ys are not necessarily toxic.

    Yamashita, Yukiko M

    Nature ecology & evolution

    2023  Volume 7, Issue 8, Page(s) 1177–1178

    Language English
    Publishing date 2023-06-12
    Publishing country England
    Document type Journal Article
    ISSN 2397-334X
    ISSN (online) 2397-334X
    DOI 10.1038/s41559-023-02079-9
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  2. Article ; Online: Asymmetric Stem Cell Division and Germline Immortality.

    Yamashita, Yukiko M

    Annual review of genetics

    2023  Volume 57, Page(s) 181–199

    Abstract: Germ cells are the only cell type that is capable of transmitting genetic information to the next generation, which has enabled the continuation of multicellular life for the last 1.5 billion years. Surprisingly little is known about the mechanisms ... ...

    Abstract Germ cells are the only cell type that is capable of transmitting genetic information to the next generation, which has enabled the continuation of multicellular life for the last 1.5 billion years. Surprisingly little is known about the mechanisms supporting the germline's remarkable ability to continue in this eternal cycle, termed germline immortality. Even unicellular organisms age at a cellular level, demonstrating that cellular aging is inevitable. Extensive studies in yeast have established the framework of how asymmetric cell division and gametogenesis may contribute to the resetting of cellular age. This review examines the mechanisms of germline immortality-how germline cells reset the aging of cells-drawing a parallel between yeast and multicellular organisms.
    MeSH term(s) Asymmetric Cell Division/genetics ; Saccharomyces cerevisiae/genetics ; Germ Cells ; Stem Cells
    Language English
    Publishing date 2023-08-08
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 207928-8
    ISSN 1545-2948 ; 0066-4170 ; 0066-4197
    ISSN (online) 1545-2948
    ISSN 0066-4170 ; 0066-4197
    DOI 10.1146/annurev-genet-022123-040039
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Satellite DNA.

    Yamashita, Yukiko M

    Seminars in cell & developmental biology

    2022  Volume 128, Page(s) 1

    MeSH term(s) Base Sequence ; DNA, Satellite/genetics
    Chemical Substances DNA, Satellite
    Language English
    Publishing date 2022-05-14
    Publishing country England
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2022.05.002
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  4. Article ; Online: Running the gauntlet: challenges to genome integrity in spermiogenesis.

    Kitaoka, Maiko / Yamashita, Yukiko M

    Nucleus (Austin, Tex.)

    2024  Volume 15, Issue 1, Page(s) 2339220

    Abstract: Species' continuity depends on gametogenesis to produce the only cell types that can transmit genetic information across generations. Spermiogenesis, which encompasses post-meiotic, haploid stages of male gametogenesis, is a process that leads to the ... ...

    Abstract Species' continuity depends on gametogenesis to produce the only cell types that can transmit genetic information across generations. Spermiogenesis, which encompasses post-meiotic, haploid stages of male gametogenesis, is a process that leads to the formation of sperm cells well-known for their motility. Spermiogenesis faces three major challenges. First, after two rounds of meiotic divisions, the genome lacks repair templates (no sister chromatids, no homologous chromosomes), making it incredibly vulnerable to any genomic insults over an extended time (typically days-weeks). Second, the sperm genome becomes transcriptionally silent, making it difficult to respond to new perturbations as spermiogenesis progresses. Third, the histone-to-protamine transition, which is essential to package the sperm genome, counterintuitively involves DNA break formation. How spermiogenesis handles these challenges remains poorly understood. In this review, we discuss each challenge and their intersection with the biology of protamines. Finally, we discuss the implication of protamines in the process of evolution.
    MeSH term(s) Male ; Humans ; Semen/metabolism ; Spermatogenesis/genetics ; Histones/metabolism ; Spermatozoa/metabolism ; Protamines/genetics ; Protamines/metabolism
    Chemical Substances Histones ; Protamines
    Language English
    Publishing date 2024-04-09
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2619626-8
    ISSN 1949-1042 ; 1949-1042
    ISSN (online) 1949-1042
    ISSN 1949-1042
    DOI 10.1080/19491034.2024.2339220
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  5. Article ; Online: Analysis of Gene Expression Patterns and RNA Localization by Fluorescence in Situ Hybridization in Whole Mount Drosophila Testes.

    Fingerhut, Jaclyn M / Yamashita, Yukiko M

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

    2023  Volume 2666, Page(s) 15–28

    Abstract: Researchers have used RNA in situ hybridization to detect the presence of RNA in cells and tissues for approximately 50 years. The recent development of a method capable of visualizing a single RNA molecule by utilizing tiled fluorescently labeled ... ...

    Abstract Researchers have used RNA in situ hybridization to detect the presence of RNA in cells and tissues for approximately 50 years. The recent development of a method capable of visualizing a single RNA molecule by utilizing tiled fluorescently labeled oligonucleotide probes that together produce a diffraction-limited spot has greatly increased the resolution of this technique, allowing for the precise determination of subcellular RNA localization and relative abundance. Here, we present our method for single molecule RNA fluorescence in situ hybridization (smFISH) in whole mount Drosophila testes and discuss how we have utilized this method to better understand the expression pattern of the highly unusual Y-linked genes.
    MeSH term(s) Animals ; Male ; Drosophila/genetics ; In Situ Hybridization, Fluorescence/methods ; Testis/chemistry ; RNA/genetics ; RNA/analysis ; Gene Expression
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2023-05-11
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3191-1_2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: The implications of satellite DNA instability on cellular function and evolution.

    Flynn, Jullien M / Yamashita, Yukiko M

    Seminars in cell & developmental biology

    2023  Volume 156, Page(s) 152–159

    Abstract: Abundant tandemly repeated satellite DNA is present in most eukaryotic genomes. Previous limitations including a pervasive view that it was uninteresting junk DNA, combined with challenges in studying it, are starting to dissolve - and recent studies ... ...

    Abstract Abundant tandemly repeated satellite DNA is present in most eukaryotic genomes. Previous limitations including a pervasive view that it was uninteresting junk DNA, combined with challenges in studying it, are starting to dissolve - and recent studies have found important functions for satellite DNAs. The observed rapid evolution and implied instability of satellite DNA now has important significance for their functions and maintenance within the genome. In this review, we discuss the processes that lead to satellite DNA copy number instability, and the importance of mechanisms to manage the potential negative effects of instability. Satellite DNA is vulnerable to challenges during replication and repair, since it forms difficult-to-process secondary structures and its homology within tandem arrays can result in various types of recombination. Satellite DNA instability may be managed by DNA or chromatin-binding proteins ensuring proper nuclear localization and repair, or by proteins that process aberrant structures that satellite DNAs tend to form. We also discuss the pattern of satellite DNA mutations from recent mutation accumulation (MA) studies that have tracked changes in satellite DNA for up to 1000 generations with minimal selection. Finally, we highlight examples of satellite evolution from studies that have characterized satellites across millions of years of Drosophila fruit fly evolution, and discuss possible ways that selection might act on the satellite DNA composition.
    MeSH term(s) Animals ; DNA, Satellite/genetics ; Drosophila/genetics ; Mutation ; Evolution, Molecular
    Chemical Substances DNA, Satellite
    Language English
    Publishing date 2023-10-17
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2023.10.005
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  7. Article: Insulin signaling regulates R2 retrotransposon expression to orchestrate transgenerational rDNA copy number maintenance.

    Nelson, Jonathan O / Slicko, Alyssa / Raz, Amelie A / Yamashita, Yukiko M

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Preserving a large number of essential yet highly unstable ribosomal DNA (rDNA) repeats is critical for the germline to perpetuate the genome through generations. Spontaneous rDNA loss must be countered by rDNA copy number (CN) expansion. Germline rDNA ... ...

    Abstract Preserving a large number of essential yet highly unstable ribosomal DNA (rDNA) repeats is critical for the germline to perpetuate the genome through generations. Spontaneous rDNA loss must be countered by rDNA copy number (CN) expansion. Germline rDNA CN expansion is best understood in
    Language English
    Publishing date 2024-02-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.28.582629
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  8. Article ; Online: When the Family Treasure Is a Doormat.

    Yamashita, Yukiko M

    Developmental cell

    2020  Volume 52, Issue 1, Page(s) 3–4

    Abstract: Germ cells carry genetic information to the next generation, necessitating special attention to their genome maintenance. Two new studies in this issue of Developmental Cell (Bhargava et al., 2020; Dokshin et al., 2020) reveal an essential function of ... ...

    Abstract Germ cells carry genetic information to the next generation, necessitating special attention to their genome maintenance. Two new studies in this issue of Developmental Cell (Bhargava et al., 2020; Dokshin et al., 2020) reveal an essential function of germ cell-specific protein GCNA in the genome maintenance of germ cells.
    MeSH term(s) Fertility ; Genome ; Germ Cells
    Language English
    Publishing date 2020-01-03
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2019.12.013
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  9. Article ; Online: The regulation and potential functions of intronic satellite DNA.

    Fingerhut, Jaclyn M / Yamashita, Yukiko M

    Seminars in cell & developmental biology

    2022  Volume 128, Page(s) 69–77

    Abstract: Satellite DNAs are arrays of tandem repeats found in the eukaryotic genome. They are mainly found in pericentromeric heterochromatin and have been believed to be mostly inert, leading satellite DNAs to be erroneously regarded as junk. Recent studies have ...

    Abstract Satellite DNAs are arrays of tandem repeats found in the eukaryotic genome. They are mainly found in pericentromeric heterochromatin and have been believed to be mostly inert, leading satellite DNAs to be erroneously regarded as junk. Recent studies have started to elucidate the function of satellite DNA, yet little is known about the peculiar case where satellite DNA is found within the introns of protein coding genes, resulting in incredibly large introns, a phenomenon termed intron gigantism. Studies in Drosophila demonstrated that satellite DNA-containing introns are transcribed with the gene and require specialized mechanisms to overcome the burdens imposed by the extremely long stretches of repetitive DNA. Whether intron gigantism confers any benefit or serves any functional purpose for cells and/or organisms remains elusive. Here we review our current understanding of intron gigantism: where it is found, the challenges it imposes, how it is regulated and what purpose it may serve.
    MeSH term(s) Animals ; DNA, Satellite/genetics ; Drosophila/genetics ; Gigantism/genetics ; Heterochromatin/genetics ; Introns
    Chemical Substances DNA, Satellite ; Heterochromatin
    Language English
    Publishing date 2022-04-22
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1312473-0
    ISSN 1096-3634 ; 1084-9521
    ISSN (online) 1096-3634
    ISSN 1084-9521
    DOI 10.1016/j.semcdb.2022.04.010
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  10. Article ; Online: Derepression of Y-linked multicopy protamine-like genes interferes with sperm nuclear compaction in

    Park, Jun I / Bell, George W / Yamashita, Yukiko M

    Proceedings of the National Academy of Sciences of the United States of America

    2023  Volume 120, Issue 16, Page(s) e2220576120

    Abstract: Across species, sperm maturation involves the dramatic reconfiguration of chromatin into highly compact nuclei that enhance hydrodynamic ability and ensure paternal genomic integrity. This process is mediated by the replacement of histones by sperm ... ...

    Abstract Across species, sperm maturation involves the dramatic reconfiguration of chromatin into highly compact nuclei that enhance hydrodynamic ability and ensure paternal genomic integrity. This process is mediated by the replacement of histones by sperm nuclear basic proteins, also referred to as protamines. In humans, a carefully balanced dosage between two known protamine genes is required for optimal fertility. However, it remains unknown how their proper balance is regulated and how defects in balance may lead to compromised fertility. Here, we show that a nucleolar protein,
    MeSH term(s) Humans ; Animals ; Male ; Drosophila melanogaster/metabolism ; Histones/genetics ; Histones/metabolism ; Protamines/genetics ; Protamines/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Semen/metabolism ; Spermatozoa/metabolism ; Chromatin/metabolism ; Spermatogenesis/genetics ; Drosophila/genetics
    Chemical Substances Histones ; Protamines ; Drosophila Proteins ; Chromatin
    Language English
    Publishing date 2023-04-10
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2220576120
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