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  1. Book ; Online ; E-Book: Human retrotransposons in health and disease

    Cristofari, Gael

    2017  

    Author's details Gael Cristofari editor
    Keywords Retroelements / genetics ; Genetic Diseases, Inborn ; Long Interspersed Nucleotide Elements / genetics ; Mutagenesis, Insertional
    Language English
    Size 1 Online-Ressource (x, 330 Seiten), Illustrationen
    Publisher Springer
    Publishing place Cham
    Publishing country Switzerland
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    HBZ-ID HT019391446
    ISBN 978-3-319-48344-3 ; 9783319483436 ; 3-319-48344-7 ; 3319483439
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Snapshots of genetic copy-and-paste machinery in action.

    Cristofari, Gael

    Nature

    2024  Volume 626, Issue 7997, Page(s) 40–42

    Language English
    Publishing date 2024-01-29
    Publishing country England
    Document type News
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-024-00112-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 26: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 9: Show issues
    Zs.MO 244: Show issues

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  3. Article ; Online: Cancer Immunotherapy: How to Exploit Transposable Elements?

    Lanciano, Sophie / Cristofari, Gael

    Clinical chemistry

    2023  Volume 70, Issue 1, Page(s) 17–20

    MeSH term(s) Humans ; DNA Transposable Elements ; Immunotherapy ; Neoplasms/genetics ; Neoplasms/therapy
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2023-08-10
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 80102-1
    ISSN 1530-8561 ; 0009-9147
    ISSN (online) 1530-8561
    ISSN 0009-9147
    DOI 10.1093/clinchem/hvad091
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.171: Show issues Location:
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  4. Article ; Online: Noninvasive and Multicancer Biomarkers: The Promise of LINE-1 Retrotransposons.

    Doucet, Aurelien J / Cristofari, Gael

    Cancer discovery

    2023  Volume 13, Issue 12, Page(s) 2502–2504

    Abstract: Summary: LINE-1 retrotransposons are frequently active in epithelial tumors. In a new study, Taylor, Wu and colleagues now describe that one of the proteins encoded by LINE-1 elements, ORF1p, is detected in the bloodstream of patients with cancer, and ... ...

    Abstract Summary: LINE-1 retrotransposons are frequently active in epithelial tumors. In a new study, Taylor, Wu and colleagues now describe that one of the proteins encoded by LINE-1 elements, ORF1p, is detected in the bloodstream of patients with cancer, and can be used as a noninvasive and multicancer biomarker for diagnosis or treatment monitoring. See related article by Taylor, Wu et al., p. 2532 (7).
    MeSH term(s) Humans ; Retroelements ; Long Interspersed Nucleotide Elements ; Proteins/genetics ; Biomarkers ; Neoplasms/diagnosis ; Neoplasms/genetics
    Chemical Substances Retroelements ; Proteins ; Biomarkers
    Language English
    Publishing date 2023-12-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2625242-9
    ISSN 2159-8290 ; 2159-8274
    ISSN (online) 2159-8290
    ISSN 2159-8274
    DOI 10.1158/2159-8290.CD-23-1063
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6916: Show issues Location:
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  5. Article ; Online: Flip-flop genomics: Charting inversions in the human population.

    Lanciano, Sophie / Cristofari, Gael

    Cell

    2022  Volume 185, Issue 11, Page(s) 1811–1813

    Abstract: Detecting large genomic inversions has long been challenging. In a new study, Porubsky et al. resolve these complex rearrangements in 41 individuals and discover wide regions that undergo recurrent inversions, some of which even toggle back and forth ( ... ...

    Abstract Detecting large genomic inversions has long been challenging. In a new study, Porubsky et al. resolve these complex rearrangements in 41 individuals and discover wide regions that undergo recurrent inversions, some of which even toggle back and forth (Porubsky et al., 2022). Many of these regions are associated with genomic disorders.
    MeSH term(s) Gene Rearrangement ; Genomics ; Humans
    Language English
    Publishing date 2022-05-10
    Publishing country United States
    Document type Journal Article ; 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.2022.05.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1167: Show issues Location:
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    Zs.MG 58: Show issues

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  6. Article ; Online: Nascent RNA m

    Billon, Victor / Cristofari, Gael

    Cell research

    2021  Volume 31, Issue 8, Page(s) 829–831

    MeSH term(s) Genetic Techniques ; RNA/genetics ; Retroelements
    Chemical Substances Retroelements ; RNA (63231-63-0)
    Language English
    Publishing date 2021-06-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 1319303-x
    ISSN 1748-7838 ; 1001-0602
    ISSN (online) 1748-7838
    ISSN 1001-0602
    DOI 10.1038/s41422-021-00518-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 5283: Show issues Location:
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  7. Article ; Online: Genome-Wide Young L1 Methylation Profiling by bs-ATLAS-seq.

    Philippe, Claude / Cristofari, Gael

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

    2022  Volume 2607, Page(s) 127–150

    Abstract: By silencing L1 retrotransposons, DNA methylation protects mammalian genomes from potent endogenous mutagens. However, some loci can escape this repressive mechanism and become active, particularly in carcinomas. Alterations of L1 DNA methylation can ... ...

    Abstract By silencing L1 retrotransposons, DNA methylation protects mammalian genomes from potent endogenous mutagens. However, some loci can escape this repressive mechanism and become active, particularly in carcinomas. Alterations of L1 DNA methylation can also locally influence gene expression. Comprehensive measurement of L1 DNA methylation at the locus level remains challenging. Here, we present bs-ATLAS-seq, a genome-wide approach to locate full-length L1 elements in the human genome, and assess their methylation levels at single-base and single-locus resolutions. This strategy targets the youngest, and only retrotransposition-competent family, L1HS, but also detects a significant fraction of older elements (L1PA2 to L1PA8). Bs-ATLAS-seq evaluates methylation at the first 15 CpGs of L1 5' UTR, which corresponds to the first half of the sense promoter. It relies on random fragmentation of the genomic DNA, adapter ligation, bisulfite treatment and suppression PCR, and ends by asymmetrical paired-end sequencing. A dedicated pipeline provides the location of L1 elements and their methylation status, including for non-reference loci, as well as their single-molecule DNA profiles.
    MeSH term(s) Humans ; Animals ; Long Interspersed Nucleotide Elements/genetics ; Sequence Analysis, DNA ; DNA Methylation ; Protein Processing, Post-Translational ; Ascomycota ; Mammals
    Language English
    Publishing date 2022-11-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2883-6_8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Flip-flop genomics: Charting inversions in the human population

    Lanciano, Sophie / Cristofari, Gael

    Cell. 2022 May 26, v. 185, no. 11

    2022  

    Abstract: Detecting large genomic inversions has long been challenging. In a new study, Porubsky et al. resolve these complex rearrangements in 41 individuals and discover wide regions that undergo recurrent inversions, some of which even toggle back and forth ( ... ...

    Abstract Detecting large genomic inversions has long been challenging. In a new study, Porubsky et al. resolve these complex rearrangements in 41 individuals and discover wide regions that undergo recurrent inversions, some of which even toggle back and forth (Porubsky et al., 2022). Many of these regions are associated with genomic disorders.
    Keywords cells ; genomics ; human population
    Language English
    Dates of publication 2022-0526
    Size p. 1811-1813.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2022.05.002
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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    Z 93: Show issues

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  9. Article ; Online: Precise and Scarless Insertion of Transposable Elements by Cas9-Mediated Genome Engineering.

    Weber, Vivien Marie / Doucet, Aurélien J / Cristofari, Gael

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

    2022  Volume 2607, Page(s) 329–353

    Abstract: Transposable element insertions can have broad effects on gene expression, ranging from new regulatory functions to pathogenic consequences by transplanting new cis-regulating elements or perturbing existing ones. Genetic manipulation of such DNA ... ...

    Abstract Transposable element insertions can have broad effects on gene expression, ranging from new regulatory functions to pathogenic consequences by transplanting new cis-regulating elements or perturbing existing ones. Genetic manipulation of such DNA sequences can help decipher their mechanism of action. Here, we describe a CRISPR-Cas9-mediated two-step approach to precisely insert transposable elements into into the genome of cultured human cells, without scar or reporter gene. First, a double-selection cassette is inserted into the desired target locus. Once a clone containing a single copy of this cassette has been isolated, a second editing step is performed to exchange the double-selection cassette with a markerless transposable element sequence. More generally, this method can be used for knocking in any large insert without genetic markers.
    MeSH term(s) Humans ; DNA Transposable Elements/genetics ; CRISPR-Cas Systems/genetics ; Cell Line ; Cicatrix ; Genes, Reporter
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2022-11-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2883-6_15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Targeted Nanopore Resequencing and Methylation Analysis of LINE-1 Retrotransposons.

    Sarkar, Arpita / Lanciano, Sophie / Cristofari, Gael

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

    2022  Volume 2607, Page(s) 173–198

    Abstract: Retrotransposition of LINE-1 (L1) elements represents a major source of insertional polymorphisms in mammals, and their mutagenic activity is restricted by silencing mechanisms, such as DNA methylation. Despite a very high level of sequence identity ... ...

    Abstract Retrotransposition of LINE-1 (L1) elements represents a major source of insertional polymorphisms in mammals, and their mutagenic activity is restricted by silencing mechanisms, such as DNA methylation. Despite a very high level of sequence identity between copies, their internal sequence contains small nucleotide polymorphisms (SNPs) that can alter their activity. Such internal SNPs can also appear in different alleles of a given L1 locus. Given their repetitive nature and relatively long size, short-read sequencing approaches have limited access to L1 internal sequence or DNA methylation state. Here, we describe a targeted method to specifically sequence more than a hundred L1-containing loci in parallel and measure their DNA methylation levels using nanopore long-read sequencing. Each targeted locus is sequenced at high coverage (~45X) with unambiguously mapped reads spanning the entire L1 element, as well as its flanking sequences over several kilobases. Our protocol, modified from the nanopore Cas9 targeted sequencing (nCATS) strategy, provides a full and haplotype-resolved L1 sequence and DNA methylation levels. It introduces a streamlined and multiplex approach to synthesize guide RNAs and a quantitative PCR (qPCR)-based quality check during library preparation for cost-effective L1 sequencing. More generally, this method can be applied to any type of transposable elements and organisms.
    MeSH term(s) Animals ; Long Interspersed Nucleotide Elements ; Retroelements/genetics ; Nanopores ; DNA Methylation ; Mutagenesis, Insertional ; Nucleotides ; Mammals
    Chemical Substances Retroelements ; Nucleotides
    Language English
    Publishing date 2022-11-30
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2883-6_10
    Database MEDical Literature Analysis and Retrieval System OnLINE

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