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  1. Article: Didier Trono, doyen des Sciences de la vie à l'EPFL: "nous voulons donner un "twist" à la recherche biomédicale".

    Trono, Didier

    Revue medicale suisse

    2007  Volume 3, Issue 93, Page(s) 3–6

    Title translation Didier Trono, dean of life sciences at the EPFL: "we want to give a twist to biomedical research".
    MeSH term(s) Biomedical Research/standards
    Language French
    Publishing date 2007-01-10
    Publishing country Switzerland
    Document type Interview
    ZDB-ID 2177010-4
    ISSN 1660-9379
    ISSN 1660-9379
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5998: Show issues Location:
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  2. Article: Take a walk on the KRAB side: (Trends in Genetics, 39:11 p:844-857, 2023).

    Rosspopoff, Olga / Trono, Didier

    Trends in genetics : TIG

    2023  Volume 40, Issue 2, Page(s) 203–205

    Language English
    Publishing date 2023-12-30
    Publishing country England
    Document type Published Erratum
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2023.12.007
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    Zs.A 2272: Show issues Location:
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  3. Article: Take a walk on the KRAB side.

    Rosspopoff, Olga / Trono, Didier

    Trends in genetics : TIG

    2023  Volume 39, Issue 11, Page(s) 844–857

    Abstract: Canonical Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) act as major repressors of transposable elements (TEs) via the KRAB-mediated recruitment of the heterochromatin scaffold KRAB-associated protein (KAP)1. KZFP genes emerged ... ...

    Abstract Canonical Krüppel-associated box (KRAB)-containing zinc finger proteins (KZFPs) act as major repressors of transposable elements (TEs) via the KRAB-mediated recruitment of the heterochromatin scaffold KRAB-associated protein (KAP)1. KZFP genes emerged some 420 million years ago in the last common ancestor of coelacanth, lungfish, and tetrapods, and dramatically expanded to give rise to lineage-specific repertoires in contemporary species paralleling their TE load and turnover. However, the KRAB domain displays sequence and function variations that reveal repeated diversions from a linear TE-KZFP trajectory. This Review summarizes current knowledge on the evolution of KZFPs and discusses how ancestral noncanonical KZFPs endowed with variant KRAB, SCAN or DUF3669 domains have been utilized to achieve KAP1-independent functions.
    MeSH term(s) Repressor Proteins/genetics ; Zinc Fingers/genetics ; Transcription Factors/genetics ; DNA Transposable Elements ; Heterochromatin
    Chemical Substances Repressor Proteins ; Transcription Factors ; DNA Transposable Elements ; Heterochromatin
    Language English
    Publishing date 2023-09-14
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2023.08.003
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    Zs.A 2272: Show issues Location:
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  4. Article ; Online: Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants.

    Matsushima, Wayo / Planet, Evarist / Trono, Didier

    Cell genomics

    2024  Volume 4, Issue 2, Page(s) 100497

    Abstract: Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual ...

    Abstract Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual species, which limits its scope to relatively intact TE sequences. Here, we report a novel approach to uncover previously unannotated degenerate TEs (degTEs) by probing multiple ancestral genomes reconstructed from hundreds of species. We applied this method to the human genome and achieved a 10.8% increase in coverage over the most recent annotation. Further, we discovered that degTEs contribute to various cis-regulatory elements and transcription factor binding sites, including those of a known TE-controlling family, the KRAB zinc-finger proteins. We also report unannotated chimeric transcripts between degTEs and human genes expressed in embryos. This study provides a novel methodology and a freely available resource that will facilitate the investigation of TE co-option events on a full scale.
    MeSH term(s) Humans ; DNA Transposable Elements/genetics ; Regulatory Sequences, Nucleic Acid ; Genome, Human/genetics
    Chemical Substances DNA Transposable Elements
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2024.100497
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  5. Article ; Online: New ingredients for old recipes.

    Rosspopoff, Olga / Martins, Filipe / Trono, Didier

    Nature genetics

    2023  Volume 55, Issue 12, Page(s) 2023–2024

    Language English
    Publishing date 2023-11-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-023-01591-9
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    Zs.MG 46: Show issues

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  6. Book: Lentiviral vectors

    Trono, Didier

    with 8 tables

    (Current topics in microbiology and immunology ; 261)

    2002  

    Author's details ed. by Didier Trono
    Series title Current topics in microbiology and immunology ; 261
    Collection
    Keywords Lentiviren ; Virusvektor
    Subject Virusüberträger ; Lentiviridae ; Lentivirinae
    Language English
    Size VIII, 258 S. : Ill., graph. Darst.
    Publisher Springer
    Publishing place Berlin u.a.
    Publishing country Germany
    Document type Book
    HBZ-ID HT013230850
    ISBN 3-540-42190-4 ; 978-3-540-42190-0
    Database Catalogue ZB MED Medicine, Health

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    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Ud II Zs 24 -261- verfügbar in Königswinter Königswinter

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  7. Article ; Online: Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP.

    Ernst, Christina / Duc, Julien / Trono, Didier

    Nucleic acids research

    2023  Volume 51, Issue 13, Page(s) e70

    Abstract: RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically ... ...

    Abstract RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically challenging and require large amounts of starting material. Herein, we present an improved library preparation strategy for crosslinking and immunoprecipitation (CLIP) that is based on tailing and ligation of cDNA molecules (TLC). TLC involves the generation of solid-phase cDNA, followed by ribotailing to significantly enhance the efficiency of subsequent adapter ligation. These modifications result in a streamlined, fully bead-based library preparation strategy, which eliminates time-consuming purification procedures and drastically reduces sample loss. As a result, TLC-CLIP displays unparalleled sensitivity, enabling the profiling of RNA-protein interactions from as few as 1000 cells. To demonstrate the effectiveness of TLC-CLIP, we profiled four endogenous RNA-binding proteins, showcasing its reproducibility and improved precision resulting from a higher occurrence of crosslinking-induced deletions. These deletions serve as an intrinsic quality metric and increase both specificity and nucleotide-resolution.
    MeSH term(s) RNA/chemistry ; DNA, Complementary/genetics ; Reproducibility of Results ; RNA-Binding Proteins/metabolism ; Immunoprecipitation ; High-Throughput Nucleotide Sequencing/methods ; Binding Sites
    Chemical Substances RNA (63231-63-0) ; DNA, Complementary ; RNA-Binding Proteins
    Language English
    Publishing date 2023-06-07
    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/gkad466
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    Zs.A 1067: Show issues Location:
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  8. Article ; Online: A KRABsody for Embryo-Placental Development.

    Trono, Didier

    Developmental cell

    2017  Volume 41, Issue 6, Page(s) 578–580

    Abstract: Many of the hundreds of KRAB zinc finger proteins encoded by human and mouse are involved in taming the transcriptional regulatory potential of transposable elements. Reporting recently in Science, Yang et al. (2017) reveal that one murine family member, ...

    Abstract Many of the hundreds of KRAB zinc finger proteins encoded by human and mouse are involved in taming the transcriptional regulatory potential of transposable elements. Reporting recently in Science, Yang et al. (2017) reveal that one murine family member, ZFP568, controls Igf2 expression for proper embryonic and placental development.
    MeSH term(s) Animals ; Embryonic Development/physiology ; Female ; Gene Expression Regulation/physiology ; Humans ; Placenta/metabolism ; Placentation/physiology ; Pregnancy ; Repressor Proteins/metabolism ; Zinc Fingers/physiology
    Chemical Substances Repressor Proteins
    Language English
    Publishing date 2017-06-19
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2017.06.005
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  9. Article: Switzerland and the Digital Health Revolution.

    Trono, Didier

    Chimia

    2016  Volume 70, Issue 12, Page(s) 851–852

    Abstract: New technologies in life sciences are helping to revolutionize health management with the objective to move towards personalized healthcare. The Swiss Federal government is investing in multidisciplinary, countrywide initiatives such as Health 2030 to ... ...

    Abstract New technologies in life sciences are helping to revolutionize health management with the objective to move towards personalized healthcare. The Swiss Federal government is investing in multidisciplinary, countrywide initiatives such as Health 2030 to meet this challenge.
    MeSH term(s) Biological Science Disciplines ; Delivery of Health Care ; Humans ; Precision Medicine ; Switzerland
    Language English
    Publishing date 2016-12-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1516-7
    ISSN 0009-4293
    ISSN 0009-4293
    DOI 10.2533/chimia.2016.851
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    In stock of ZB MED Bonn / Germany

    Z 4.5: Show issues

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  10. Article ; Online: Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer.

    Lykoskoufis, Nikolaos M R / Planet, Evarist / Ongen, Halit / Trono, Didier / Dermitzakis, Emmanouil T

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 749

    Abstract: Transposable elements (TEs) are prevalent repeats in the human genome, play a significant role in the regulome, and their disruption can contribute to tumorigenesis. However, TE influence on gene expression in cancer remains unclear. Here, we analyze 275 ...

    Abstract Transposable elements (TEs) are prevalent repeats in the human genome, play a significant role in the regulome, and their disruption can contribute to tumorigenesis. However, TE influence on gene expression in cancer remains unclear. Here, we analyze 275 normal colon and 276 colorectal cancer samples from the SYSCOL cohort, discovering 10,231 and 5,199 TE-expression quantitative trait loci (eQTLs) in normal and tumor tissues, respectively, of which 376 are colorectal cancer specific eQTLs, likely due to methylation changes. Tumor-specific TE-eQTLs show greater enrichment of transcription factors, compared to shared TE-eQTLs suggesting specific regulation of their expression in tumor. Bayesian networks reveal 1,766 TEs as mediators of genetic effects, altering the expression of 1,558 genes, including 55 known cancer driver genes and show that tumor-specific TE-eQTLs trigger the driver capability of TEs. These insights expand our knowledge of cancer drivers, deepening our understanding of tumorigenesis and presenting potential avenues for therapeutic interventions.
    MeSH term(s) Humans ; DNA Transposable Elements/genetics ; Bayes Theorem ; Transcription Factors/metabolism ; Carcinogenesis/genetics ; Colorectal Neoplasms/genetics
    Chemical Substances DNA Transposable Elements ; Transcription Factors
    Language English
    Publishing date 2024-01-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42405-0
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