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  1. AU="Francesca Storici"
  2. AU="Coulter-Mackie, Marion"
  3. AU="Mayank Goyal"
  4. AU="Lempke, Olga M"
  5. AU="Khan, Asad Majeed"
  6. AU=Ismail Mohd Iswadi
  7. AU="Jewel Park"
  8. AU="Hunter-Smith, David J"
  9. AU="Requião-Moura, Lúcio Roberto"
  10. AU=DesRochers Teresa M.
  11. AU="Kruschwitz, Sabine"
  12. AU=Sriwijiatalai Won
  13. AU="Bozzaro, Claudia"
  14. AU="Beckendorf, C"
  15. AU="Birge, N W"
  16. AU="Hoang, Oi Pui"
  17. AU="Saradha Baskaran"
  18. AU="Culotta, Lorenza"
  19. AU=Cleaver Ondine
  20. AU="Jordan A. Kreidberg"
  21. AU="Al-Marshoud, Majida"
  22. AU="David S Hui"
  23. AU="Manjappa, Shivaprasad"
  24. AU="Balkan, S"
  25. AU="Chen, Emma"
  26. AU="Delean, Ada"
  27. AU="Gurao, Ankita"
  28. AU="Lang, Zhen"
  29. AU="Mahnaz Mohammadpour"
  30. AU="Britta Grillitsch"
  31. AU=Hoeffner Ellen G
  32. AU="Al Harbi, Shmeylan"
  33. AU=Polevoda Bogdan
  34. AU="Raffaele Galiero"
  35. AU=Hruskova Z
  36. AU="Ayers, J"
  37. AU="Cohen, A D"
  38. AU="Brunetti, Gian Luca"
  39. AU=Andrade Daniel
  40. AU=Hay William W Jr

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  1. Artikel ; Online: Gene Co-Expression Analysis of Human RNASEH2A Reveals Functional Networks Associated with DNA Replication, DNA Damage Response, and Cell Cycle Regulation

    Stefania Marsili / Ailone Tichon / Deepali Kundnani / Francesca Storici

    Biology, Vol 10, Iss 221, p

    2021  Band 221

    Abstract: Ribonuclease (RNase) H2 is a key enzyme for the removal of RNA found in DNA-RNA hybrids, playing a fundamental role in biological processes such as DNA replication, telomere maintenance, and DNA damage repair. RNase H2 is a trimer composed of three ... ...

    Abstract Ribonuclease (RNase) H2 is a key enzyme for the removal of RNA found in DNA-RNA hybrids, playing a fundamental role in biological processes such as DNA replication, telomere maintenance, and DNA damage repair. RNase H2 is a trimer composed of three subunits, RNASEH2A being the catalytic subunit. RNASEH2A expression levels have been shown to be upregulated in transformed and cancer cells. In this study, we used a bioinformatics approach to identify RNASEH2A co-expressed genes in different human tissues to underscore biological processes associated with RNASEH2A expression. Our analysis shows functional networks for RNASEH2A involvement such as DNA replication and DNA damage response and a novel putative functional network of cell cycle regulation. Further bioinformatics investigation showed increased gene expression in different types of actively cycling cells and tissues, particularly in several cancers, supporting a biological role for RNASEH2A but not for the other two subunits of RNase H2 in cell proliferation. Mass spectrometry analysis of RNASEH2A-bound proteins identified players functioning in cell cycle regulation. Additional bioinformatic analysis showed that RNASEH2A correlates with cancer progression and cell cycle related genes in Cancer Cell Line Encyclopedia (CCLE) and The Cancer Genome Atlas (TCGA) Pan Cancer datasets and supported our mass spectrometry findings.
    Schlagwörter RNASEH ; RNASEH2A ; co-expression ; genotype-tissue expression ; cell cycle ; cancer ; Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2021-03-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: To nick or not to nick

    Samantha S Katz / Frederick S Gimble / Francesca Storici

    PLoS ONE, Vol 9, Iss 2, p e

    comparison of I-SceI single- and double-strand break-induced recombination in yeast and human cells.

    2014  Band 88840

    Abstract: Genetic modification of a chromosomal locus to replace an existing dysfunctional allele with a corrected sequence can be accomplished through targeted gene correction using the cell's homologous recombination (HR) machinery. Gene targeting is stimulated ... ...

    Abstract Genetic modification of a chromosomal locus to replace an existing dysfunctional allele with a corrected sequence can be accomplished through targeted gene correction using the cell's homologous recombination (HR) machinery. Gene targeting is stimulated by generation of a DNA double-strand break (DSB) at or near the site of correction, but repair of the break via non-homologous end-joining without using the homologous template can lead to deleterious genomic changes such as in/del mutations, or chromosomal rearrangements. By contrast, generation of a DNA single-strand break (SSB), or nick, can stimulate gene correction without the problems of DSB repair because the uncut DNA strand acts as a template to permit healing without alteration of genetic material. Here, we examine the ability of a nicking variant of the I-SceI endonuclease (K223I I-SceI) to stimulate gene targeting in yeast Saccharomyces cerevisiae and in human embryonic kidney (HEK-293) cells. K223I I-SceI is proficient in both yeast and human cells and promotes gene correction up to 12-fold. We show that K223I I-SceI-driven recombination follows a different mechanism than wild-type I-SceI-driven recombination, thus indicating that the initial DNA break that stimulates recombination is not a low-level DSB but a nick. We also demonstrate that K223I I-SceI efficiently elevates gene targeting at loci distant from the break site in yeast cells. These findings establish the capability of the I-SceI nickase to enhance recombination in yeast and human cells, strengthening the notion that nicking enzymes could be effective tools in gene correction strategies for applications in molecular biology, biotechnology, and gene therapy.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 570
    Sprache Englisch
    Erscheinungsdatum 2014-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel: Rad52 Inverse Strand Exchange Drives RNA-Templated DNA Double-Strand Break Repair

    Mazina, Olga M / Alexander V. Mazin / Francesca Storici / Havva Keskin / Kritika Hanamshet

    Molecular cell. 2017 July 06, v. 67, no. 1

    2017  

    Abstract: RNA can serve as a template for DNA double-strand break repair in yeast cells, and Rad52, a member of the homologous recombination pathway, emerged as an important player in this process. However, the exact mechanism of how Rad52 contributes to RNA- ... ...

    Abstract RNA can serve as a template for DNA double-strand break repair in yeast cells, and Rad52, a member of the homologous recombination pathway, emerged as an important player in this process. However, the exact mechanism of how Rad52 contributes to RNA-dependent DSB repair remained unknown. Here, we report an unanticipated activity of yeast and human Rad52: inverse strand exchange, in which Rad52 forms a complex with dsDNA and promotes strand exchange with homologous ssRNA or ssDNA. We show that in eukaryotes, inverse strand exchange between homologous dsDNA and RNA is a distinctive activity of Rad52; neither Rad51 recombinase nor the yeast Rad52 paralog Rad59 has this activity. In accord with our in vitro results, our experiments in budding yeast provide evidence that Rad52 inverse strand exchange plays an important role in RNA-templated DSB repair in vivo.
    Schlagwörter DNA repair ; eukaryotic cells ; homologous recombination ; humans ; RNA ; single-stranded DNA ; yeasts
    Sprache Englisch
    Erscheinungsverlauf 2017-0706
    Umfang p. 19-29.e3.
    Erscheinungsort Elsevier Inc.
    Dokumenttyp Artikel
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2017.05.019
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  4. Artikel ; Online: Real-Time PCR-Coupled CE-SELEX for DNA Aptamer Selection

    Patrick Ruff / Rekha B. Pai / Francesca Storici

    ISRN Molecular Biology, Vol

    2012  Band 2012

    Schlagwörter Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
    Sprache Englisch
    Erscheinungsdatum 2012-01-01T00:00:00Z
    Verlag Hindawi Publishing Corporation
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii

    Waleed M.M. El-Sayed / Alli L. Gombolay / Penghao Xu / Taehwan Yang / Youngkyu Jeon / Sathya Balachander / Gary Newnam / Sijia Tao / Nicole E. Bowen / Tomáš Brůna / Mark Borodovsky / Raymond F. Schinazi / Baek Kim / Yongsheng Chen / Francesca Storici

    iScience, Vol 24, Iss 1, Pp 102005- (2021)

    2021  

    Abstract: Summary: Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map ... ...

    Abstract Summary: Ribonucleoside monophosphates (rNMPs) represent the most common non-standard nucleotides found in the genome of cells. The distribution of rNMPs in DNA has been studied only in limited genomes. Using the ribose-seq protocol and the Ribose-Map bioinformatics toolkit, we reveal the distribution of rNMPs incorporated into the whole genome of a photosynthetic unicellular green alga, Chlamydomonas reinhardtii. We discovered a disproportionate incorporation of adenosine in the mitochondrial and chloroplast DNA, in contrast to the nuclear DNA, relative to the corresponding nucleotide content of these C. reinhardtii organelle genomes. Our results demonstrate that the rNMP content in the DNA of the algal organelles reflects an elevated ATP level present in the algal cells. We reveal specific biases and patterns in rNMP distributions in the algal mitochondrial, chloroplast, and nuclear DNA. Moreover, we identified the C. reinhardtii orthologous genes for all three subunits of the RNase H2 enzyme using GeneMark-EP + gene finder.
    Schlagwörter Molecular Biology ; Genomics ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2021-01-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine

    Sathya Balachander / Alli L. Gombolay / Taehwan Yang / Penghao Xu / Gary Newnam / Havva Keskin / Waleed M. M. El-Sayed / Anton V. Bryksin / Sijia Tao / Nicole E. Bowen / Raymond F. Schinazi / Baek Kim / Kyung Duk Koh / Fredrik O. Vannberg / Francesca Storici

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Band 14

    Abstract: Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and ... ...

    Abstract Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and nuclear DNA show preference for cytosine and guanosine preceded by deoxyadenosine.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2020-05-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Ribonucleotide incorporation in yeast genomic DNA shows preference for cytosine and guanosine preceded by deoxyadenosine

    Sathya Balachander / Alli L. Gombolay / Taehwan Yang / Penghao Xu / Gary Newnam / Havva Keskin / Waleed M. M. El-Sayed / Anton V. Bryksin / Sijia Tao / Nicole E. Bowen / Raymond F. Schinazi / Baek Kim / Kyung Duk Koh / Fredrik O. Vannberg / Francesca Storici

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Band 14

    Abstract: Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and ... ...

    Abstract Ribonucleoside monophosphates are incorporated by DNA polymerases into double-stranded DNA. Here, the authors use ribose-seq and Ribose-Map techniques to reveal that signatures and patterns of ribonucleotide incorporation in yeast mitochondrial and nuclear DNA show preference for cytosine and guanosine preceded by deoxyadenosine.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2020-05-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: AAV recombineering with single strand oligonucleotides.

    Matthew L Hirsch / Francesca Storici / Chengwen Li / Vivian W Choi / R Jude Samulski

    PLoS ONE, Vol 4, Iss 11, p e

    2009  Band 7705

    Abstract: Adeno-associated virus (AAV) transduction initiates a signaling cascade that culminates in a transient DNA damage response. During this time, host DNA repair proteins convert the linear single-strand AAV genomes to double-strand circular monomers and ... ...

    Abstract Adeno-associated virus (AAV) transduction initiates a signaling cascade that culminates in a transient DNA damage response. During this time, host DNA repair proteins convert the linear single-strand AAV genomes to double-strand circular monomers and concatemers in processes stimulated by the AAV inverted terminal repeats (ITRs). As the orientation of AAV genome concatemerization appears unbiased, the likelihood of concatemerization in a desired orientation is low (less than 1 in 6). Using a novel recombineering method, Oligo-Assisted AAV Genome Recombination (OAGR), this work demonstrates the ability to direct concatemerization specifically to a desired orientation in human cells. This was achieved by a single-strand DNA oligonucleotide (oligo) displaying homology to distinct AAV genomes capable of forming an intermolecular bridge for recombination. This DNA repair process results in concatemers with genomic junctions corresponding to the sequence of oligo homology. Furthermore, OAGR was restricted to single-strand, not duplexed, AAV genomes suggestive of replication-dependent recombination. Consistent with this process, OAGR demonstrated oligo polarity biases in all tested configurations except when a portion of the oligo targeted the ITR. This approach, in addition to being useful for the elucidation of intermolecular homologous recombination, may find eventual relevance for AAV mediated large gene therapy.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 612
    Sprache Englisch
    Erscheinungsdatum 2009-11-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel: From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond

    Michelini, Flavia / Ameya P. Jalihal / Brian Luke / Chance Meers / Corey Jones-Weinert / Fabrizio d’Adda di Fagagna / Francesca Rossiello / Francesca Storici / Giuseppe Biamonti / Julio Aguado / Mariusz Nowacki / Nils G. Walter / Piero Carninci / Sofia Francia / Ubaldo Gioia / Zachary T. Neeb

    Chemical reviews. 2018 Mar. 30, v. 118, no. 8

    2018  

    Abstract: Coding for proteins has been considered the main function of RNA since the “central dogma” of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the ... ...

    Abstract Coding for proteins has been considered the main function of RNA since the “central dogma” of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a “smart” phone, which has replaced the older obsolete “cellular” phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied “cellular” RNA to “smart” RNA.
    Schlagwörter DNA damage ; gene expression ; genome ; genomics ; non-coding RNA ; polypeptides ; proteins ; telomeres
    Sprache Englisch
    Erscheinungsverlauf 2018-0330
    Umfang p. 4365-4403.
    Erscheinungsort American Chemical Society
    Dokumenttyp Artikel
    ZDB-ID 207949-5
    ISSN 1520-6890 ; 0009-2665
    ISSN (online) 1520-6890
    ISSN 0009-2665
    DOI 10.1021/acs.chemrev.7b00487
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