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  • 1.
    Clima, Rosanna
    et al.
    University of Bari, Italy ; University of Bologna, Italy.
    Preste, Roberto
    University of Bari, Italy.
    Calabrese, Claudia
    European Bioinformatics Institute (EMBL-EBI), UK.
    Diroma, Maria Angela
    University of Bari, Italy.
    Santorsola, Mariangela
    University of Bari, Italy.
    Scioscia, Gaetano
    IBM Italia SpA, Italy ; MBLab Bari, Italy.
    Simone, Domenico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Shen, Lishuang
    Children's Hospital Los Angeles, USA.
    Gasparre, Giuseppe
    University of Bologna, Italy.
    Attimonelli, Marcella
    University of Bari, Italy.
    HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor2017In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no D1, p. D698-D706Article in journal (Refereed)
    Abstract [en]

    The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.

  • 2.
    Zoabi, Muhammad
    et al.
    Technion, Israel.
    Nadar-Ponniah, Prathamesh T.
    Technion, Israel.
    Khoury-Haddad, Hanan
    Technion, Israel.
    Ušaj, Marko
    Technion, Israel.
    Budowski-Tal, Inbal
    Technion, Israel.
    Haran, Tali
    Technion, Israel.
    Henn, Arnon
    Technion, Israel.
    Mandel-Gutfreund, Yael
    Technion, Israel.
    Ayoub, Nabieh
    Technion, Israel.
    RNA-dependent chromatin localization of KDM4D lysine demethylase promotes H3K9me3 demethylation2014In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 42, no 21, p. 13026-13038Article in journal (Refereed)
    Abstract [en]

    The JmjC-containing lysine demethylase, KDM4D, demethylates di-and tri-methylation of histone H3 on lysine 9 (H3K9me3). How KDM4D is recruited to chromatin and recognizes its histone substrates remains unknown. Here, we show that KDM4D binds RNA independently of its demethylase activity. We mapped two non-canonical RNA binding domains: the first is within the N-terminal spanning amino acids 115 to 236, and the second is within the C-terminal spanning amino acids 348 to 523 of KDM4D. We also demonstrate that RNA interactions with KDM4D N-terminal region are critical for its association with chromatin and subsequently for demethylating H3K9me3 in cells. This study implicates, for the first time, RNA molecules in regulating the levels of H3K9 methylation by affecting KDM4D association with chromatin.

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