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  1. AU="Terrone, Sophie"
  2. AU="Esmaily, Hadi"
  3. AU="Al-Ani, Gada"
  4. AU="Denys, Damiaan A J P"
  5. AU="Irigoin, Victoria"
  6. AU="Kim, Joo-Yun"
  7. AU="Albu, Simona Elena"
  8. AU="Monalisa Feliciano Figueiredo"
  9. AU="Zhao, Houhua"
  10. AU="Kern, Bastian Johannes"
  11. AU="Antonio Vitobello"
  12. AU="Paulus Rahardjo"
  13. AU="Geier, Martina"
  14. AU="Kwon, Tae-Hwan"
  15. AU="Christos Barboutis, "
  16. AU="Fayaz, U"
  17. AU="Ba, Yabo"
  18. AU="Stevens, Valerie A"
  19. AU="Kahouli, Sophia"
  20. AU="Sun, Chuanrui"
  21. AU="Carrera, Carlo Giovanni"
  22. AU="Secrieru, Oana Manuela"
  23. AU="Wang, Lanzhong"

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  1. Artikel ; Online: Functions of DEAD box RNA helicases DDX5 and DDX17 in chromatin organization and transcriptional regulation.

    Giraud, Guillaume / Terrone, Sophie / Bourgeois, Cyril F

    BMB reports

    2018  Band 51, Heft 12, Seite(n) 613–622

    Abstract: RNA helicases DDX5 and DDX17 are multitasking proteins that regulate gene expression in different biological contexts through diverse activities. Special attention has long been paid to their function as coregulators of transcription factors, providing ... ...

    Abstract RNA helicases DDX5 and DDX17 are multitasking proteins that regulate gene expression in different biological contexts through diverse activities. Special attention has long been paid to their function as coregulators of transcription factors, providing insight about their functional association with a number of chromatin modifiers and remodelers. However, to date, the variety of described mechanisms has made it difficult to understand precisely how these proteins work at the molecular level, and the contribution of their ATPase domain to these mechanisms remains unclear as well. In light of their association with long noncoding RNAs that are key epigenetic regulators, an emerging view is that DDX5 and DDX17 may act through modulating the activity of various ribonucleoprotein complexes that could ensure their targeting to specific chromatin loci. This review will comprehensively describe the current knowledge on these different mechanisms. We will also discuss the potential roles of DDX5 and DDX17 on the 3D chromatin organization and how these could impact gene expression at the transcriptional and post-transcriptional levels. [BMB Reports 2018; 51(12): 613-622].
    Mesh-Begriff(e) Animals ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; DEAD-box RNA Helicases/chemistry ; DEAD-box RNA Helicases/metabolism ; Humans ; Protein Processing, Post-Translational ; RNA, Untranslated/chemistry ; RNA, Untranslated/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transcription, Genetic
    Chemische Substanzen Chromatin ; RNA, Untranslated ; Transcription Factors ; DDX17 protein, human (EC 3.6.1.-) ; Ddx5 protein, human (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Sprache Englisch
    Erscheinungsdatum 2018-10-08
    Erscheinungsland Korea (South)
    Dokumenttyp Journal Article ; Review
    ZDB-ID 2410389-5
    ISSN 1976-670X ; 1976-6696
    ISSN (online) 1976-670X
    ISSN 1976-6696
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Novel Intronic Mutation in VMA21 Causing Severe Phenotype of X-Linked Myopathy with Excessive Autophagy—Case Report

    Pegat, Antoine / Streichenberger, Nathalie / Lacoste, Nicolas / Hermier, Marc / Menassa, Rita / Coudert, Laurent / Theuriet, Julian / Froissart, Roseline / Terrone, Sophie / Bouhour, Francoise / Michel-Calemard, Laurence / Schaeffer, Laurent / Jacquier, Arnaud

    Genes (Basel). 2022 Nov. 29, v. 13, no. 12

    2022  

    Abstract: X-linked Myopathy with Excessive Autophagy (XMEA) is a rare autophagic vacuolar myopathy caused by mutations in the Vacuolar ATPase assembly factor VMA21 gene; onset usually occurs during childhood and rarely occurs during adulthood. We described a 22- ... ...

    Abstract X-linked Myopathy with Excessive Autophagy (XMEA) is a rare autophagic vacuolar myopathy caused by mutations in the Vacuolar ATPase assembly factor VMA21 gene; onset usually occurs during childhood and rarely occurs during adulthood. We described a 22-year-old patient with XMEA, whose onset was declared at 11 through gait disorder. He had severe four-limb proximal weakness and amyotrophy, and his proximal muscle MRC score was between 2 and 3/5 in four limbs; creatine kinase levels were elevated (1385 IU/L), and electroneuromyography and muscle MRI were suggestive of myopathy. Muscle biopsy showed abnormalities typical of autophagic vacuolar myopathy. We detected a hemizygous, unreported, intronic, single-nucleotide substitution c.164-20T>A (NM_001017980.4) in intron 2 of the VMA21 gene. Fibroblasts derived from this patient displayed a reduced level of VMA21 transcripts (at 40% of normal) and protein, suggesting a pathogenicity related to an alteration of the splicing efficiency associated with an intron retention. This patient with XMEA displayed a severe phenotype (rapid weakness of upper and lower limbs) due to a new intronic variant of VMA21, related to an alteration in the splicing efficiency associated with intron retention, suggesting that phenotype severity is closely related to the residual expression of the VMA21 protein.
    Schlagwörter H-transporting ATP synthase ; adulthood ; autophagy ; biopsy ; childhood ; creatine kinase ; fibroblasts ; gait ; introns ; muscles ; muscular diseases ; pathogenicity ; patients ; phenotype ; single nucleotide polymorphism ; vacuoles
    Sprache Englisch
    Erscheinungsverlauf 2022-1129
    Erscheinungsort Multidisciplinary Digital Publishing Institute
    Dokumenttyp Artikel ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes13122245
    Datenquelle NAL Katalog (AGRICOLA)

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  3. Artikel ; Online: Novel Intronic Mutation in

    Pegat, Antoine / Streichenberger, Nathalie / Lacoste, Nicolas / Hermier, Marc / Menassa, Rita / Coudert, Laurent / Theuriet, Julian / Froissart, Roseline / Terrone, Sophie / Bouhour, Francoise / Michel-Calemard, Laurence / Schaeffer, Laurent / Jacquier, Arnaud

    Genes

    2022  Band 13, Heft 12

    Abstract: X-linked Myopathy with Excessive Autophagy (XMEA) is a rare autophagic vacuolar myopathy caused by mutations in the Vacuolar ATPase assembly ... ...

    Abstract X-linked Myopathy with Excessive Autophagy (XMEA) is a rare autophagic vacuolar myopathy caused by mutations in the Vacuolar ATPase assembly factor
    Sprache Englisch
    Erscheinungsdatum 2022-11-29
    Erscheinungsland Switzerland
    Dokumenttyp Case Reports
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes13122245
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: RNA helicase-dependent gene looping impacts messenger RNA processing.

    Terrone, Sophie / Valat, Jessica / Fontrodona, Nicolas / Giraud, Guillaume / Claude, Jean-Baptiste / Combe, Emmanuel / Lapendry, Audrey / Polvèche, Hélène / Ameur, Lamya Ben / Duvermy, Arnaud / Modolo, Laurent / Bernard, Pascal / Mortreux, Franck / Auboeuf, Didier / Bourgeois, Cyril F

    Nucleic acids research

    2022  Band 50, Heft 16, Seite(n) 9226–9246

    Abstract: DDX5 and DDX17 are DEAD-box RNA helicase paralogs which regulate several aspects of gene expression, especially transcription and splicing, through incompletely understood mechanisms. A transcriptome analysis of DDX5/DDX17-depleted human cells confirmed ... ...

    Abstract DDX5 and DDX17 are DEAD-box RNA helicase paralogs which regulate several aspects of gene expression, especially transcription and splicing, through incompletely understood mechanisms. A transcriptome analysis of DDX5/DDX17-depleted human cells confirmed the large impact of these RNA helicases on splicing and revealed a widespread deregulation of 3' end processing. In silico analyses and experiments in cultured cells showed the binding and functional contribution of the genome organizing factor CTCF to chromatin sites at or near a subset of DDX5/DDX17-dependent exons that are characterized by a high GC content and a high density of RNA Polymerase II. We propose the existence of an RNA helicase-dependent relationship between CTCF and the dynamics of transcription across DNA and/or RNA structured regions, that contributes to the processing of internal and terminal exons. Moreover, local DDX5/DDX17-dependent chromatin loops spatially connect RNA helicase-regulated exons with their cognate promoter, and we provide the first direct evidence that de novo gene looping modifies alternative splicing and polyadenylation. Overall our findings uncover the impact of DDX5/DDX17-dependent chromatin folding on pre-messenger RNA processing.
    Mesh-Begriff(e) Humans ; RNA/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; DEAD-box RNA Helicases/metabolism ; Alternative Splicing ; Chromatin/genetics
    Chemische Substanzen RNA (63231-63-0) ; RNA, Messenger ; DEAD-box RNA Helicases (EC 3.6.4.13) ; Chromatin ; Ddx5 protein, human (EC 3.6.1.-)
    Sprache Englisch
    Erscheinungsdatum 2022-08-30
    Erscheinungsland England
    Dokumenttyp Journal Article
    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/gkac717
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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    Verfügbar in ZB MED Köln/Königswinter

    Zs.A 1067: Hefte anzeigen Standort:
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  5. Artikel ; Online: The RNA helicase DDX17 controls the transcriptional activity of REST and the expression of proneural microRNAs in neuronal differentiation.

    Lambert, Marie-Pierre / Terrone, Sophie / Giraud, Guillaume / Benoit-Pilven, Clara / Cluet, David / Combaret, Valérie / Mortreux, Franck / Auboeuf, Didier / Bourgeois, Cyril F

    Nucleic acids research

    2018  Band 46, Heft 15, Seite(n) 7686–7700

    Abstract: The Repressor Element 1-silencing transcription factor (REST) represses a number of neuronal genes in non-neuronal cells or in undifferentiated neural progenitors. Here, we report that the DEAD box RNA helicase DDX17 controls important REST-related ... ...

    Abstract The Repressor Element 1-silencing transcription factor (REST) represses a number of neuronal genes in non-neuronal cells or in undifferentiated neural progenitors. Here, we report that the DEAD box RNA helicase DDX17 controls important REST-related processes that are critical during the early phases of neuronal differentiation. First, DDX17 associates with REST, promotes its binding to the promoter of a subset of REST-targeted genes and co-regulates REST transcriptional repression activity. During neuronal differentiation, we observed a downregulation of DDX17 along with that of the REST complex that contributes to the activation of neuronal genes. Second, DDX17 and its paralog DDX5 regulate the expression of several proneural microRNAs that are known to target the REST complex during neurogenesis, including miR-26a/b that are also direct regulators of DDX17 expression. In this context, we propose a new mechanism by which RNA helicases can control the biogenesis of intronic miRNAs. We show that the processing of the miR-26a2 precursor is dependent on RNA helicases, owing to an intronic regulatory region that negatively impacts on both miRNA processing and splicing of its host intron. Our work places DDX17 in the heart of a pathway involving REST and miRNAs that allows neuronal gene repression.
    Mesh-Begriff(e) Cell Line, Tumor ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; Gene Expression Profiling ; Humans ; MCF-7 Cells ; MicroRNAs/genetics ; Neural Stem Cells/metabolism ; Neurogenesis/genetics ; Neurons/metabolism ; Repressor Proteins/genetics ; Repressor Proteins/metabolism
    Chemische Substanzen MicroRNAs ; RE1-silencing transcription factor ; Repressor Proteins ; DDX17 protein, human (EC 3.6.1.-) ; Ddx5 protein, human (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Sprache Englisch
    Erscheinungsdatum 2018-06-21
    Erscheinungsland England
    Dokumenttyp 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/gky545
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data.

    Benoit-Pilven, Clara / Marchet, Camille / Chautard, Emilie / Lima, Leandro / Lambert, Marie-Pierre / Sacomoto, Gustavo / Rey, Amandine / Cologne, Audric / Terrone, Sophie / Dulaurier, Louis / Claude, Jean-Baptiste / Bourgeois, Cyril F / Auboeuf, Didier / Lacroix, Vincent

    Scientific reports

    2018  Band 8, Heft 1, Seite(n) 4307

    Abstract: Genome-wide analyses estimate that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most methods start by mapping ... ...

    Abstract Genome-wide analyses estimate that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most methods start by mapping the reads to an annotated reference genome, but some start by a de novo assembly of the reads. In this paper, we present a systematic comparison of a mapping-first approach (FARLINE) and an assembly-first approach (KISSPLICE). We applied these methods to two independent RNAseq datasets and found that the predictions of the two pipelines overlapped (70% of exon skipping events were common), but with noticeable differences. The assembly-first approach allowed to find more novel variants, including novel unannotated exons and splice sites. It also predicted AS in recently duplicated genes. The mapping-first approach allowed to find more lowly expressed splicing variants, and splice variants overlapping repeats. This work demonstrates that annotating AS with a single approach leads to missing out a large number of candidates, many of which are differentially regulated across conditions and can be validated experimentally. We therefore advocate for the combined use of both mapping-first and assembly-first approaches for the annotation and differential analysis of AS from RNAseq datasets.
    Mesh-Begriff(e) Alternative Splicing ; Humans ; RNA Splice Sites ; Sequence Analysis, RNA/methods ; Sequence Analysis, RNA/standards ; Software
    Chemische Substanzen RNA Splice Sites
    Sprache Englisch
    Erscheinungsdatum 2018-03-09
    Erscheinungsland England
    Dokumenttyp Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-018-21770-7
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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