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  1. Article: Long-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project.

    Schloissnig, Siegfried / Pani, Samarendra / Rodriguez-Martin, Bernardo / Ebler, Jana / Hain, Carsten / Tsapalou, Vasiliki / Söylev, Arda / Hüther, Patrick / Ashraf, Hufsah / Prodanov, Timofey / Asparuhova, Mila / Hunt, Sarah / Rausch, Tobias / Marschall, Tobias / Korbel, Jan O

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Structural variants (SVs) contribute significantly to human genetic diversity and ... ...

    Abstract Structural variants (SVs) contribute significantly to human genetic diversity and disease
    Language English
    Publishing date 2024-04-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.04.18.590093
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Combinatorial Action of Temporally Segregated Transcription Factors.

    Charest, Julien / Daniele, Thomas / Wang, Jingkui / Bykov, Aleksandr / Mandlbauer, Ariane / Asparuhova, Mila / Röhsner, Josef / Gutiérrez-Pérez, Paula / Cochella, Luisa

    Developmental cell

    2020  Volume 55, Issue 4, Page(s) 483–499.e7

    Abstract: Combinatorial action of transcription factors (TFs) with partially overlapping expression is a widespread strategy to generate novel gene-expression patterns and, thus, cellular diversity. Known mechanisms underlying combinatorial activity require co- ... ...

    Abstract Combinatorial action of transcription factors (TFs) with partially overlapping expression is a widespread strategy to generate novel gene-expression patterns and, thus, cellular diversity. Known mechanisms underlying combinatorial activity require co-expression of TFs within the same cell. Here, we describe the mechanism by which two TFs that are never co-expressed generate a new, intersectional expression pattern in C. elegans embryos: lineage-specific priming of a gene by a transiently expressed TF generates a unique intersection with a second TF acting on the same gene four cell divisions later; the second TF is expressed in multiple cells but only activates transcription in those where priming occurred. Early induction of active transcription is necessary and sufficient to establish a competent state, maintained by broadly expressed regulators in the absence of the initial trigger. We uncover additional cells diversified through this mechanism. Our findings define a mechanism for combinatorial TF activity with important implications for generation of cell-type diversity.
    MeSH term(s) Animals ; Caenorhabditis elegans/cytology ; Caenorhabditis elegans/embryology ; Caenorhabditis elegans/metabolism ; Caenorhabditis elegans Proteins/metabolism ; Cell Lineage ; Embryo, Nonmammalian/metabolism ; Gene Expression Regulation ; Genetic Loci ; Neurons/metabolism ; Protein Binding ; Time Factors ; Transcription Factors/metabolism ; Transcription, Genetic
    Chemical Substances Caenorhabditis elegans Proteins ; Transcription Factors
    Language English
    Publishing date 2020-09-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2054967-2
    ISSN 1878-1551 ; 1534-5807
    ISSN (online) 1878-1551
    ISSN 1534-5807
    DOI 10.1016/j.devcel.2020.09.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5742: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 76: Show issues

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  3. Article ; Online: Mammalian INO80 chromatin remodeler cooperates with FANCM to mediate DNA interstrand crosslink-induced checkpoint activation and repair.

    Andreev, Veselin / Hristova, Rossitsa / Asparuhova, Mila / Danovski, Georgi / Stoynov, Stoyno / Gospodinov, Anastas

    DNA repair

    2018  Volume 74, Page(s) 38–50

    Abstract: Chromatin regulators play crucial roles in the DNA damage response. While the chromatin changes needed for double-strand break repair and nucleotide excision repair have been intensely studied, the chromatin requirements of interstrand crosslink (ICL) ... ...

    Abstract Chromatin regulators play crucial roles in the DNA damage response. While the chromatin changes needed for double-strand break repair and nucleotide excision repair have been intensely studied, the chromatin requirements of interstrand crosslink (ICL) repair have remained largely unexplored. Here, we studied the effect of silencing the INO80 chromatin remodeler subunits on the cellular response to ICLs. Cells depleted of Ino80 ATPase were more sensitive to mitomycin C (MMC) and defective in FANCD2 chromatin recruitment. Ino80-deficient cells displayed strongly reduced Chk1 phosphorylation after MMC treatment indicating impaired ATR-dependent DNA damage signaling, likely due to the significantly slower RPA foci formation which we observed in these cells. MMC treatment of cells silenced for FANCM - a protein required for ICL-induced checkpoint signaling, Ino80 or both genes simultaneously led to similar decreases in RPA phosphorylation suggesting that the two proteins were involved in the same checkpoint pathway. Co-immunoprecipitation data indicated that Ino80 and FANCM interact physically. Taken together our data demonstrate for the first time that the INO80 chromatin remodeler cooperates with FANCM to mediate ICL-induced checkpoint activation by promoting accumulation of RPA at the lesion sites. This constitutes a novel mechanism by which the INO80 chromatin remodeler participates in the repair of ICLs and genome integrity maintenance.
    MeSH term(s) Cell Cycle Checkpoints ; Chromatin Assembly and Disassembly ; DNA/chemistry ; DNA/genetics ; DNA Damage ; DNA Helicases/deficiency ; DNA Helicases/genetics ; DNA Helicases/metabolism ; DNA Repair ; Gene Knockdown Techniques ; HeLa Cells ; Humans ; Microfilament Proteins/deficiency ; PC-3 Cells ; Protein Binding ; Replication Protein A/genetics
    Chemical Substances ACTR8 protein, human ; Microfilament Proteins ; Replication Protein A ; DNA (9007-49-2) ; FANCM protein, human (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-) ; INO80 protein, human (EC 3.6.4.-)
    Language English
    Publishing date 2018-12-30
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2071608-4
    ISSN 1568-7856 ; 1568-7864
    ISSN (online) 1568-7856
    ISSN 1568-7864
    DOI 10.1016/j.dnarep.2018.12.007
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5555: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: miR-1 sustains muscle physiology by controlling V-ATPase complex assembly.

    Gutiérrez-Pérez, Paula / Santillán, Emilio M / Lendl, Thomas / Wang, Jingkui / Schrempf, Anna / Steinacker, Thomas L / Asparuhova, Mila / Brandstetter, Marlene / Haselbach, David / Cochella, Luisa

    Science advances

    2021  Volume 7, Issue 42, Page(s) eabh1434

    Abstract: Muscle function requires unique structural and metabolic adaptations that can render muscle cells selectively vulnerable, with mutations in some ubiquitously expressed genes causing myopathies but sparing other tissues. We uncovered a muscle cell ... ...

    Abstract Muscle function requires unique structural and metabolic adaptations that can render muscle cells selectively vulnerable, with mutations in some ubiquitously expressed genes causing myopathies but sparing other tissues. We uncovered a muscle cell vulnerability by studying miR-1, a deeply conserved, muscle-specific microRNA whose ablation causes various muscle defects. Using
    Language English
    Publishing date 2021-10-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.abh1434
    Database MEDical Literature Analysis and Retrieval System OnLINE

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