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  1. AU="Yehuda, Yishai"
  2. AU="Lelkaitis, Giedrius"

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  1. Article: Genome-wide determination of mammalian replication timing by dna content measurement

    Yehuda, Yishai / Blumenfeld, Britny / Lehmann, Dan / Simon, Itamar

    Journal of visualized experiments. 2017 Jan. 19, , no. 119

    2017  

    Abstract: Replication of the genome occurs during S phase of the cell cycle in a highly regulated process that ensures the fidelity of DNA duplication. Each genomic region is replicated at a distinct time during S phase through the simultaneous activation of ... ...

    Abstract Replication of the genome occurs during S phase of the cell cycle in a highly regulated process that ensures the fidelity of DNA duplication. Each genomic region is replicated at a distinct time during S phase through the simultaneous activation of multiple origins of replication. Time of replication (ToR) correlates with many genomic and epigenetic features and is linked to mutation rates and cancer. Comprehending the full genomic view of the replication program, in health and disease is a major future goal and challenge. This article describes in detail the "Copy Number Ratio of S/G1 for mapping genomic Time of Replication" method (herein called: CNR-ToR), a simple approach to map the genome wide ToR of mammalian cells. The method is based on the copy number differences between S phase cells and G1 phase cells. The CNR-ToR method is performed in 6 steps: 1. Preparation of cells and staining with propidium iodide (PI); 2. Sorting G1 and S phase cells using fluorescence-activated cell sorting (FACS); 3. DNA purification; 4. Sonication; 5. Library preparation and sequencing; and 6. Bioinformatic analysis. The CNR-ToR method is a fast and easy approach that results in detailed replication maps.
    Keywords DNA ; bioinformatics ; epigenetics ; flow cytometry ; genome ; genomics ; interphase ; mammals ; mutation ; neoplasms ; propidium ; sonication ; staining
    Language English
    Dates of publication 2017-0119
    Size p. e55157.
    Publishing place Journal of Visualized Experiments
    Document type Article
    ZDB-ID 2259946-0
    ISSN 1940-087X
    ISSN 1940-087X
    DOI 10.3791/55157
    Database NAL-Catalogue (AGRICOLA)

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  2. Article ; Online: Genome-wide Determination of Mammalian Replication Timing by DNA Content Measurement.

    Yehuda, Yishai / Blumenfeld, Britny / Lehmann, Dan / Simon, Itamar

    Journal of visualized experiments : JoVE

    2017  , Issue 119

    Abstract: Replication of the genome occurs during S phase of the cell cycle in a highly regulated process that ensures the fidelity of DNA duplication. Each genomic region is replicated at a distinct time during S phase through the simultaneous activation of ... ...

    Abstract Replication of the genome occurs during S phase of the cell cycle in a highly regulated process that ensures the fidelity of DNA duplication. Each genomic region is replicated at a distinct time during S phase through the simultaneous activation of multiple origins of replication. Time of replication (ToR) correlates with many genomic and epigenetic features and is linked to mutation rates and cancer. Comprehending the full genomic view of the replication program, in health and disease is a major future goal and challenge. This article describes in detail the "Copy Number Ratio of S/G1 for mapping genomic Time of Replication" method (herein called: CNR-ToR), a simple approach to map the genome wide ToR of mammalian cells. The method is based on the copy number differences between S phase cells and G1 phase cells. The CNR-ToR method is performed in 6 steps: 1. Preparation of cells and staining with propidium iodide (PI); 2. Sorting G1 and S phase cells using fluorescence-activated cell sorting (FACS); 3. DNA purification; 4. Sonication; 5. Library preparation and sequencing; and 6. Bioinformatic analysis. The CNR-ToR method is a fast and easy approach that results in detailed replication maps.
    MeSH term(s) Animals ; Computational Biology ; DNA/genetics ; DNA Replication Timing ; Flow Cytometry ; G1 Phase ; Genomics ; Humans ; Mice ; Ploidies ; S Phase
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2017-01-19
    Publishing country United States
    Document type Journal Article ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/55157
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Characterization of alternative mRNA splicing in cultured cell populations representing progressive stages of human fetal kidney development.

    Wineberg, Yishay / Kanter, Itamar / Ben-Haim, Nissim / Pode-Shakked, Naomi / Bucris, Efrat / Bar-Lev, Tali Hana / Oriel, Sarit / Reinus, Harel / Yehuda, Yishai / Gershon, Rotem / Shukrun, Rachel / Bar-Lev, Dekel Dov / Urbach, Achia / Dekel, Benjamin / Kalisky, Tomer

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 19548

    Abstract: Nephrons are the functional units of the kidney. During kidney development, cells from the cap mesenchyme-a transient kidney-specific progenitor state-undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various ... ...

    Abstract Nephrons are the functional units of the kidney. During kidney development, cells from the cap mesenchyme-a transient kidney-specific progenitor state-undergo a mesenchymal to epithelial transition (MET) and subsequently differentiate into the various epithelial cell types that create the tubular structures of the nephron. Faults in this transition can lead to a pediatric malignancy of the kidney called Wilms' tumor that mimics normal kidney development. While human kidney development has been characterized at the gene expression level, a comprehensive characterization of alternative splicing is lacking. Therefore, in this study, we performed RNA sequencing on cell populations representing early, intermediate, and late developmental stages of the human fetal kidney, as well as three blastemal-predominant Wilms' tumor patient-derived xenografts. Using this newly generated RNAseq data, we identified a set of transcripts that are alternatively spliced between the different developmental stages. Moreover, we found that cells from the earliest developmental stage have a mesenchymal splice-isoform profile that is similar to that of blastemal-predominant Wilms' tumor xenografts. RNA binding motif enrichment analysis suggests that the mRNA binding proteins ESRP1, ESRP2, RBFOX2, and QKI regulate alternative mRNA splicing during human kidney development. These findings illuminate new molecular mechanisms involved in human kidney development and pediatric kidney cancer.
    MeSH term(s) Humans ; Child ; Alternative Splicing ; RNA, Messenger/genetics ; Wilms Tumor/genetics ; Wilms Tumor/pathology ; Kidney Neoplasms/pathology ; Kidney/pathology ; Cells, Cultured ; RNA Splicing Factors/genetics ; Repressor Proteins/genetics
    Chemical Substances RNA, Messenger ; RBFOX2 protein, human ; RNA Splicing Factors ; Repressor Proteins
    Language English
    Publishing date 2022-11-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-24147-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Chromosomal coordination and differential structure of asynchronous replicating regions.

    Blumenfeld, Britny / Masika, Hagit / Farago, Marganit / Yehuda, Yishai / Halaseh, Lamia / Vardi, Oriya / Rapoport, Rachel / Levin-Klein, Rena / Cedar, Howard / Bergman, Yehudit / Simon, Itamar

    Nature communications

    2021  Volume 12, Issue 1, Page(s) 1035

    Abstract: Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations ... ...

    Abstract Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations derived from C57BL6/Castaneous mice, we have mapped the genome-wide AS-RT loci, independently of genetic differences. These regions are characterized by differential chromatin accessibility, mono-allelic expression and include new gene families involved in specifying cell identity. By combining population level mapping with single cell FISH, our data reveal the existence of a novel regulatory program that coordinates a fixed relationship between AS-RT regions on any given chromosome, with some loci set to replicate in a parallel and others set in the anti-parallel orientation. Our results show that AS-RT is a highly regulated epigenetic mark established during early embryogenesis that may be used for facilitating the programming of mono-allelic choice throughout development.
    MeSH term(s) Alleles ; Animals ; Bone Marrow Cells/cytology ; Bone Marrow Cells/metabolism ; Chromatin/chemistry ; Chromatin/metabolism ; Chromatin/ultrastructure ; Clone Cells ; Crosses, Genetic ; DNA Replication Timing ; Embryo, Mammalian ; Embryonic Development/genetics ; Epigenesis, Genetic ; Female ; Genetic Loci ; Genome ; In Situ Hybridization, Fluorescence ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Precursor Cells, B-Lymphoid/cytology ; Precursor Cells, B-Lymphoid/metabolism
    Chemical Substances Chromatin
    Language English
    Publishing date 2021-02-15
    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/s41467-021-21348-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The mutation spectrum in genomic late replication domains shapes mammalian GC content.

    Kenigsberg, Ephraim / Yehuda, Yishai / Marjavaara, Lisette / Keszthelyi, Andrea / Chabes, Andrei / Tanay, Amos / Simon, Itamar

    Nucleic acids research

    2016  Volume 44, Issue 9, Page(s) 4222–4232

    Abstract: Genome sequence compositions and epigenetic organizations are correlated extensively across multiple length scales. Replication dynamics, in particular, is highly correlated with GC content. We combine genome-wide time of replication (ToR) data, ... ...

    Abstract Genome sequence compositions and epigenetic organizations are correlated extensively across multiple length scales. Replication dynamics, in particular, is highly correlated with GC content. We combine genome-wide time of replication (ToR) data, topological domains maps and detailed functional epigenetic annotations to study the correlations between replication timing and GC content at multiple scales. We find that the decrease in genomic GC content at large scale late replicating regions can be explained by mutation bias favoring A/T nucleotide, without selection or biased gene conversion. Quantification of the free dNTP pool during the cell cycle is consistent with a mechanism involving replication-coupled mutation spectrum that favors AT nucleotides at late S-phase. We suggest that mammalian GC content composition is shaped by independent forces, globally modulating mutation bias and locally selecting on functional element. Deconvoluting these forces and analyzing them on their native scales is important for proper characterization of complex genomic correlations.
    MeSH term(s) Base Composition ; Cell Line, Tumor ; Chromatin/genetics ; DNA Replication ; Evolution, Molecular ; Genome, Human ; Humans ; Mutation
    Chemical Substances Chromatin
    Language English
    Publishing date 2016-04-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    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/gkw268
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 1067: Show issues Location:
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  6. Article ; Online: Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development.

    Wineberg, Yishay / Bar-Lev, Tali Hana / Futorian, Anna / Ben-Haim, Nissim / Armon, Leah / Ickowicz, Debby / Oriel, Sarit / Bucris, Efrat / Yehuda, Yishai / Pode-Shakked, Naomi / Gilad, Shlomit / Benjamin, Sima / Hohenstein, Peter / Dekel, Benjamin / Urbach, Achia / Kalisky, Tomer

    Journal of the American Society of Nephrology : JASN

    2020  Volume 31, Issue 10, Page(s) 2278–2291

    Abstract: Background: During mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, Drop-seq single-cell RNA sequencing technology ... ...

    Abstract Background: During mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, Drop-seq single-cell RNA sequencing technology for measuring gene expression from thousands of individual cells identified the different cell types in the developing kidney. However, that analysis did not include the additional layer of heterogeneity that alternative mRNA splicing creates.
    Methods: Full transcript length single-cell RNA sequencing characterized the transcriptomes of 544 individual cells from mouse embryonic kidneys.
    Results: Gene expression levels measured with full transcript length single-cell RNA sequencing identified each cell type. Further analysis comprehensively characterized splice isoform switching during the transition between mesenchymal and epithelial cellular states, which is a key transitional process in kidney development. The study also identified several putative splicing regulators, including the genes
    Conclusions: Discovery of the sets of genes that are alternatively spliced as the fetal kidney mesenchyme differentiates into tubular epithelium will improve our understanding of the molecular mechanisms that drive kidney development.
    MeSH term(s) Animals ; Cell Culture Techniques ; Kidney/embryology ; Mesoderm/embryology ; Mice ; Organogenesis/genetics ; RNA Isoforms ; Sequence Analysis, RNA ; Urothelium/embryology
    Chemical Substances RNA Isoforms
    Language English
    Publishing date 2020-07-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1085942-1
    ISSN 1533-3450 ; 1046-6673
    ISSN (online) 1533-3450
    ISSN 1046-6673
    DOI 10.1681/ASN.2019080770
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3344: Show issues Location:
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  7. Article ; Online: Germline DNA replication timing shapes mammalian genome composition.

    Yehuda, Yishai / Blumenfeld, Britny / Mayorek, Nina / Makedonski, Kirill / Vardi, Oriya / Cohen-Daniel, Leonor / Mansour, Yousef / Baror-Sebban, Shulamit / Masika, Hagit / Farago, Marganit / Berger, Michael / Carmi, Shai / Buganim, Yosef / Koren, Amnon / Simon, Itamar

    Nucleic acids research

    2018  Volume 46, Issue 16, Page(s) 8299–8310

    Abstract: Mammalian DNA replication is a highly organized and regulated process. Large, Mb-sized regions are replicated at defined times along S-phase. Replication Timing (RT) is thought to play a role in shaping the mammalian genome by affecting mutation rates. ... ...

    Abstract Mammalian DNA replication is a highly organized and regulated process. Large, Mb-sized regions are replicated at defined times along S-phase. Replication Timing (RT) is thought to play a role in shaping the mammalian genome by affecting mutation rates. Previous analyses relied on somatic RT profiles. However, only germline mutations are passed on to offspring and affect genomic composition. Therefore, germ cell RT information is necessary to evaluate the influences of RT on the mammalian genome. We adapted the RT mapping technique for limited amounts of cells, and measured RT from two stages in the mouse germline - primordial germ cells (PGCs) and spermatogonial stem cells (SSCs). RT in germline cells exhibited stronger correlations to both mutation rate and recombination hotspots density than those of RT in somatic tissues, emphasizing the importance of using correct tissues-of-origin for RT profiling. Germline RT maps exhibited stronger correlations to additional genetic features including GC-content, transposable elements (SINEs and LINEs), and gene density. GC content stratification and multiple regression analysis revealed independent contributions of RT to SINE, gene, mutation, and recombination hotspot densities. Together, our results establish a central role for RT in shaping multiple levels of mammalian genome composition.
    MeSH term(s) Animals ; Base Composition/genetics ; Cell Line, Tumor ; Cells, Cultured ; DNA Replication/genetics ; DNA Replication Timing/genetics ; DNA Transposable Elements/genetics ; Female ; Genome/genetics ; Germ Cells/cytology ; Germ Cells/metabolism ; Germ-Line Mutation ; Male ; Mammals/genetics ; Mice, 129 Strain ; Mice, Inbred C57BL ; Mice, Inbred DBA ; Mice, Inbred NOD ; Mice, SCID ; Mice, Transgenic ; Short Interspersed Nucleotide Elements/genetics ; Stem Cells/cytology ; Stem Cells/metabolism
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2018-08-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    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/gky610
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
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