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  1. Article ; Online: Staying together after the breakup: tRNA halves in extracellular fluids.

    Kaymak, Ebru / Rando, Oliver J

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

    2023  Volume 120, Issue 8, Page(s) e2300300120

    MeSH term(s) Extracellular Fluid ; RNA, Transfer/genetics
    Chemical Substances RNA, Transfer (9014-25-9)
    Language English
    Publishing date 2023-02-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2300300120
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    Zs.A 1148: Show issues Location:
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  2. Article ; Online: Mammalian Micro-C-XL.

    Krietenstein, Nils / Rando, Oliver J

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

    2022  Volume 2458, Page(s) 321–332

    Abstract: Chromosome Conformation Capture (3C) methods are a family of sequencing-based assays to measure the three-dimensional structure of genomes, with Hi-C as the most prominent method in widespread use. The Micro-C-XL protocol is technical variant that ... ...

    Abstract Chromosome Conformation Capture (3C) methods are a family of sequencing-based assays to measure the three-dimensional structure of genomes, with Hi-C as the most prominent method in widespread use. The Micro-C-XL protocol is technical variant that improves the resolution and signal-to-noise ratio of the Hi-C protocol and therefore offers enhanced detection of chromatin features such as chromosome loops and fine-grained resolution of topologically associated domains. Here we describe a detailed step-by-step protocol for Micro-C-XL in mammalian cells.
    MeSH term(s) Animals ; Chromatin/genetics ; Chromosomes/genetics ; Genome ; Mammals/genetics ; Molecular Conformation
    Chemical Substances Chromatin
    Language English
    Publishing date 2022-03-10
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2140-0_17
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  3. Article ; Online: Soma-to-germline RNA communication.

    Conine, Colin C / Rando, Oliver J

    Nature reviews. Genetics

    2021  Volume 23, Issue 2, Page(s) 73–88

    Abstract: More than a century ago, August Weissman defined a distinction between the germline (responsible for propagating heritable information from generation to generation) and the perishable soma. A central motivation for this distinction was to argue against ... ...

    Abstract More than a century ago, August Weissman defined a distinction between the germline (responsible for propagating heritable information from generation to generation) and the perishable soma. A central motivation for this distinction was to argue against the inheritance of acquired characters, as the germline was partly defined by its protection from external conditions. However, recent decades have seen an explosion of studies documenting the intergenerational and transgenerational effects of environmental conditions, forcing a re-evaluation of how external signals are sensed by, or communicated to, the germline epigenome. Here, motivated by the centrality of small RNAs in paradigms of epigenetic inheritance, we review across species the myriad examples of intercellular RNA trafficking from nurse cells or somatic tissues to developing gametes.
    MeSH term(s) Animals ; Cell Differentiation/genetics ; Cell Proliferation/genetics ; Epigenesis, Genetic/genetics ; Epigenomics ; Gene Expression Regulation/genetics ; Gene-Environment Interaction ; Germ Cells/cytology ; Germ Cells/metabolism ; Humans ; Models, Genetic ; RNA/genetics ; RNA/metabolism ; RNA Transport/genetics
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2021-09-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2035157-4
    ISSN 1471-0064 ; 1471-0056
    ISSN (online) 1471-0064
    ISSN 1471-0056
    DOI 10.1038/s41576-021-00412-1
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  4. Article ; Online: Mesoscale organization of the chromatin fiber.

    Krietenstein, Nils / Rando, Oliver J

    Current opinion in genetics & development

    2020  Volume 61, Page(s) 32–36

    Abstract: The proper organization of the physical genome is essential to facilitate DNA-templated processes from transcription to replication to DNA repair. Genome-wide studies over the past two decades have provided us with a detailed understanding of the ... ...

    Abstract The proper organization of the physical genome is essential to facilitate DNA-templated processes from transcription to replication to DNA repair. Genome-wide studies over the past two decades have provided us with a detailed understanding of the positions and modification states of nucleosomes across the genomes of many organisms, as well as an increasingly mature understanding of chromosome organization at the kilobase to megabase scale. Here, we explore chromatin organization at intermediate scales of ∼2-10 nucleosomes, from early views supporting a secondary structural element known as the 30nm fiber to more recent 'sea of nucleosomes' models.
    MeSH term(s) Animals ; Chromatin/genetics ; Chromatin/ultrastructure ; Chromosomes/genetics ; Chromosomes/ultrastructure ; DNA/genetics ; DNA/ultrastructure ; DNA Replication/genetics ; Genome/genetics ; Humans ; Nucleosomes/genetics ; Nucleosomes/ultrastructure ; Transcription, Genetic/genetics
    Chemical Substances Chromatin ; Nucleosomes ; DNA (9007-49-2)
    Language English
    Publishing date 2020-04-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1077312-5
    ISSN 1879-0380 ; 0959-437X
    ISSN (online) 1879-0380
    ISSN 0959-437X
    DOI 10.1016/j.gde.2020.02.022
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  5. Article ; Online: Intergenerational Transfer of Epigenetic Information in Sperm.

    Rando, Oliver J

    Cold Spring Harbor perspectives in medicine

    2016  Volume 6, Issue 5

    Abstract: The inheritance of information beyond DNA sequence, known as epigenetic inheritance, has been implicated in a multitude of biological processes from control of plant flowering time to cancer in humans. In addition to epigenetic inheritance that occurs in ...

    Abstract The inheritance of information beyond DNA sequence, known as epigenetic inheritance, has been implicated in a multitude of biological processes from control of plant flowering time to cancer in humans. In addition to epigenetic inheritance that occurs in dividing cells of a multicellular organism, it is also increasingly clear that at least some epigenetic information is transmitted via the gametes in a multitude of organisms, including mammals. Here, I review the evidence for epigenetic information carriers in mammalian sperm, and explore the emerging field of intergenerational transfer of environmental information.
    Language English
    Publishing date 2016-05-02
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2157-1422
    ISSN (online) 2157-1422
    DOI 10.1101/cshperspect.a022988
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  6. Article ; Online: Transgenerational Epigenetic Inheritance.

    Bošković, Ana / Rando, Oliver J

    Annual review of genetics

    2018  Volume 52, Page(s) 21–41

    Abstract: Inheritance of genomic DNA underlies the vast majority of biological inheritance, yet it has been clear for decades that additional epigenetic information can be passed on to future generations. Here, we review major model systems for transgenerational ... ...

    Abstract Inheritance of genomic DNA underlies the vast majority of biological inheritance, yet it has been clear for decades that additional epigenetic information can be passed on to future generations. Here, we review major model systems for transgenerational epigenetic inheritance via the germline in multicellular organisms. In addition to surveying examples of epivariation that may arise stochastically or in response to unknown stimuli, we also discuss the induction of heritable epigenetic changes by genetic or environmental perturbations. Mechanistically, we discuss the increasingly well-understood molecular pathways responsible for epigenetic inheritance, with a focus on the unusual features of the germline epigenome.
    MeSH term(s) DNA Methylation/genetics ; Epigenesis, Genetic ; Epigenomics/trends ; Germ Cells/growth & development ; Inheritance Patterns/genetics
    Language English
    Publishing date 2018-08-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    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-120417-031404
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  7. Article ; Online: Corrigendum: Control of noncoding RNA production and histone levels by a 5' tRNA fragment.

    Boskovic, Ana / Bing, Xin Yang / Kaymak, Ebru / Rando, Oliver J

    Genes & development

    2020  Volume 34, Issue 5-6, Page(s) 462

    Language English
    Publishing date 2020-02-29
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 806684-x
    ISSN 1549-5477 ; 0890-9369
    ISSN (online) 1549-5477
    ISSN 0890-9369
    DOI 10.1101/gad.336958.120
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    Zs.A 2292: Show issues Location:
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  8. Article ; Online: Evidence for RNA or protein transport from somatic tissues to the male reproductive tract in mouse.

    Rinaldi, Vera / Messemer, Kathleen / Desevin, Kathleen / Sun, Fengyun / Berry, Bethany C / Kukreja, Shweta / Tapper, Andrew R / Wagers, Amy J / Rando, Oliver J

    eLife

    2023  Volume 12

    Abstract: The development of tools to manipulate the mouse genome, including knockout and transgenic technology, has revolutionized our ability to explore gene function in mammals. Moreover, for genes that are expressed in multiple tissues or at multiple stages of ...

    Abstract The development of tools to manipulate the mouse genome, including knockout and transgenic technology, has revolutionized our ability to explore gene function in mammals. Moreover, for genes that are expressed in multiple tissues or at multiple stages of development, the use of tissue-specific expression of the Cre recombinase allows gene function to be perturbed in specific cell types and/or at specific times. However, it is well known that putative tissue-specific promoters often drive unanticipated 'off-target' expression. In our efforts to explore the biology of the male reproductive tract, we unexpectedly found that expression of Cre in the central nervous system resulted in recombination in the epididymis, a tissue where sperm mature for ~1-2 weeks following the completion of testicular development. Remarkably, we not only observed reporter expression in the epididymis when Cre expression was driven from neuron-specific transgenes, but also when Cre expression in the brain was induced from an AAV vector carrying a Cre expression construct. A surprisingly wide range of Cre drivers - including six different neuronal promoters as well as the adipose-specific
    MeSH term(s) Mice ; Male ; Animals ; Mice, Transgenic ; RNA/metabolism ; Semen/metabolism ; Integrases/genetics ; Integrases/metabolism ; Promoter Regions, Genetic ; Protein Transport ; Mammals/genetics
    Chemical Substances RNA (63231-63-0) ; Integrases (EC 2.7.7.-)
    Language English
    Publishing date 2023-03-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.77733
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  9. Article ; Online: Metabolic Inputs into the Epigenome.

    Sharma, Upasna / Rando, Oliver J

    Cell metabolism

    2017  Volume 25, Issue 3, Page(s) 544–558

    Abstract: A number of molecular pathways play key roles in transmitting information in addition to the genomic sequence-epigenetic information-from one generation to the next. However, so-called epigenetic marks also impact an enormous variety of physiological ... ...

    Abstract A number of molecular pathways play key roles in transmitting information in addition to the genomic sequence-epigenetic information-from one generation to the next. However, so-called epigenetic marks also impact an enormous variety of physiological processes, even under circumstances that do not result in heritable consequences. Perhaps inevitably, the epigenetic regulatory machinery is highly responsive to metabolic cues, as, for example, central metabolites are the substrates for the enzymes that catalyze the deposition of covalent modifications on histones, DNA, and RNA. Interestingly, in addition to the effects that metabolites exert over biological regulation in somatic cells, over the past decade multiple studies have shown that ancestral nutrition can alter the metabolic phenotype of offspring, raising the question of how metabolism regulates the epigenome of germ cells. Here, we review the widespread links between metabolism and epigenetic modifications, both in somatic cells and in the germline.
    MeSH term(s) Animals ; Chromatin/metabolism ; DNA Methylation/genetics ; Epigenomics ; Germ Cells/metabolism ; Humans ; Metabolism/genetics ; MicroRNAs/genetics ; MicroRNAs/metabolism
    Chemical Substances Chromatin ; MicroRNAs
    Language English
    Publishing date 2017-03-08
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural
    ZDB-ID 2176834-1
    ISSN 1932-7420 ; 1550-4131
    ISSN (online) 1932-7420
    ISSN 1550-4131
    DOI 10.1016/j.cmet.2017.02.003
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  10. Article ; Online: Daddy issues: paternal effects on phenotype.

    Rando, Oliver J

    Cell

    2012  Volume 151, Issue 4, Page(s) 702–708

    Abstract: The once popular and then heretical idea that ancestral environment can affect the phenotype of future generations is coming back into vogue due to advances in the field of epigenetic inheritance. How paternal environmental conditions influence the ... ...

    Abstract The once popular and then heretical idea that ancestral environment can affect the phenotype of future generations is coming back into vogue due to advances in the field of epigenetic inheritance. How paternal environmental conditions influence the phenotype of progeny is now a tractable question, and researchers are exploring potential mechanisms underlying such effects.
    MeSH term(s) Animals ; Epigenesis, Genetic ; Female ; Gene Expression Regulation ; Gene-Environment Interaction ; Humans ; Male ; Phenotype ; Plants/genetics
    Language English
    Publishing date 2012-11-08
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2012.10.020
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