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  1. Article ; Online: The dynamic epitranscriptome: A to I editing modulates genetic information.

    Tajaddod, Mansoureh / Jantsch, Michael F / Licht, Konstantin

    Chromosoma

    2015  Volume 125, Issue 1, Page(s) 51–63

    Abstract: Adenosine to inosine editing (A to I editing) is a cotranscriptional process that contributes to transcriptome complexity by deamination of adenosines to inosines. Initially, the impact of A to I editing has been described for coding targets in the ... ...

    Abstract Adenosine to inosine editing (A to I editing) is a cotranscriptional process that contributes to transcriptome complexity by deamination of adenosines to inosines. Initially, the impact of A to I editing has been described for coding targets in the nervous system. Here, A to I editing leads to recoding and changes of single amino acids since inosine is normally interpreted as guanosine by cellular machines. However, more recently, new roles for A to I editing have emerged: Editing was shown to influence splicing and is found massively in Alu elements. Moreover, A to I editing is required to modulate innate immunity. We summarize the multiple ways in which A to I editing generates transcriptome variability and highlight recent findings in the field.
    MeSH term(s) Adenosine/metabolism ; Animals ; Deamination ; Humans ; Immunity, Innate ; Inosine ; Mammals ; RNA Editing ; RNA Splicing ; RNA, Messenger/metabolism ; Transcriptome/genetics
    Chemical Substances RNA, Messenger ; Inosine (5A614L51CT) ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2015-07-07
    Publishing country Austria
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 203083-4
    ISSN 1432-0886 ; 0009-5915
    ISSN (online) 1432-0886
    ISSN 0009-5915
    DOI 10.1007/s00412-015-0526-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.

    Vesely, Cornelia / Tauber, Stefanie / Sedlazeck, Fritz J / Tajaddod, Mansoureh / von Haeseler, Arndt / Jantsch, Michael F

    Nucleic acids research

    2014  Volume 42, Issue 19, Page(s) 12155–12168

    Abstract: Adenosine deaminases that act on RNA (ADARs) deaminate adenosines to inosines in double-stranded RNAs including miRNA precursors. A to I editing is widespread and required for normal life. By comparing deep sequencing data of brain miRNAs from wild-type ... ...

    Abstract Adenosine deaminases that act on RNA (ADARs) deaminate adenosines to inosines in double-stranded RNAs including miRNA precursors. A to I editing is widespread and required for normal life. By comparing deep sequencing data of brain miRNAs from wild-type and ADAR2 deficient mouse strains, we detect editing sites and altered miRNA processing at high sensitivity. We detect 48 novel editing events in miRNAs. Some editing events reach frequencies of up to 80%. About half of all editing events depend on ADAR2 while some miRNAs are preferentially edited by ADAR1. Sixty-four percent of all editing events are located within the seed region of mature miRNAs. For the highly edited miR-3099, we experimentally prove retargeting of the edited miRNA to novel 3' UTRs. We show further that an abundant editing event in miR-497 promotes processing by Drosha of the corresponding pri-miRNA. We also detect reproducible changes in the abundance of specific miRNAs in ADAR2-deficient mice that occur independent of adjacent A to I editing events. This indicates that ADAR2 binding but not editing of miRNA precursors may influence their processing. Correlating with changes in miRNA abundance we find misregulation of putative targets of these miRNAs in the presence or absence of ADAR2.
    MeSH term(s) Adenosine Deaminase/genetics ; Adenosine Deaminase/metabolism ; Animals ; Base Sequence ; Brain/enzymology ; Cell Line ; HEK293 Cells ; Humans ; Mice ; Mice, Knockout ; MicroRNAs/chemistry ; MicroRNAs/metabolism ; RNA Editing ; RNA Processing, Post-Transcriptional ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism
    Chemical Substances MicroRNAs ; RNA-Binding Proteins ; ADAR2 protein, mouse (EC 3.5.4.4) ; Adenosine Deaminase (EC 3.5.4.4)
    Language English
    Publishing date 2014-09-26
    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/gku844
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article: Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity

    Tajaddod, Mansoureh / Tanzer, Andrea / Licht, Konstantin / Wolfinger, Michael T / Badelt, Stefan / Huber, Florian / Pusch, Oliver / Schopoff, Sandy / Janisiw, Michael / Hofacker, Ivo / Jantsch, Michael F

    Genome biology. 2016 Dec., v. 17, no. 1

    2016  

    Abstract: BACKGROUND: Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to ... ...

    Abstract BACKGROUND: Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels. RESULTS: Here, we undertake a genome-wide analysis of insertion patterns of human Alus within transcribed portions of the genome. Multiple, nearby insertions of SINEs within one transcript are more abundant in tandem orientation than in inverted orientation. Indeed, analysis of transcriptome-wide expression levels of 15 ENCODE cell lines suggests a cis-repressive effect of inverted Alu elements on gene expression. Using reporter assays, we show that the negative effect of inverted SINEs on gene expression is independent of known sensors of double-stranded RNAs. Instead, transcriptional elongation seems impaired, leading to reduced mRNA levels. CONCLUSIONS: Our study suggests that there is a bias against multiple SINE insertions that can promote intramolecular base pairing within a transcript. Moreover, at a genome-wide level, mRNAs harboring inverted SINEs are less expressed than mRNAs harboring single or tandemly arranged SINEs. Finally, we demonstrate a novel mechanism by which inverted SINEs can impact on gene expression by interfering with RNA polymerase II.
    Keywords DNA-directed RNA polymerase ; Primates ; double-stranded RNA ; evolution ; gene expression ; genome ; humans ; messenger RNA ; transcription (genetics) ; transposons
    Language English
    Dates of publication 2016-12
    Size p. 220.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6906
    ISSN (online) 1474-760X
    ISSN 1465-6906
    DOI 10.1186/s13059-016-1083-0
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

    Tajaddod, Mansoureh / Tanzer, Andrea / Licht, Konstantin / Wolfinger, Michael T / Badelt, Stefan / Huber, Florian / Pusch, Oliver / Schopoff, Sandy / Janisiw, Michael / Hofacker, Ivo / Jantsch, Michael F

    Genome biology

    2016  Volume 17, Issue 1, Page(s) 220

    Abstract: Background: Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to ... ...

    Abstract Background: Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels.
    Results: Here, we undertake a genome-wide analysis of insertion patterns of human Alus within transcribed portions of the genome. Multiple, nearby insertions of SINEs within one transcript are more abundant in tandem orientation than in inverted orientation. Indeed, analysis of transcriptome-wide expression levels of 15 ENCODE cell lines suggests a cis-repressive effect of inverted Alu elements on gene expression. Using reporter assays, we show that the negative effect of inverted SINEs on gene expression is independent of known sensors of double-stranded RNAs. Instead, transcriptional elongation seems impaired, leading to reduced mRNA levels.
    Conclusions: Our study suggests that there is a bias against multiple SINE insertions that can promote intramolecular base pairing within a transcript. Moreover, at a genome-wide level, mRNAs harboring inverted SINEs are less expressed than mRNAs harboring single or tandemly arranged SINEs. Finally, we demonstrate a novel mechanism by which inverted SINEs can impact on gene expression by interfering with RNA polymerase II.
    MeSH term(s) Alu Elements/genetics ; Cell Line ; Evolution, Molecular ; Gene Expression Regulation ; Genome, Human ; Humans ; RNA Polymerase II/genetics ; RNA, Double-Stranded/genetics ; RNA, Messenger/genetics ; Short Interspersed Nucleotide Elements/genetics ; Transcription, Genetic ; Transcriptome/genetics
    Chemical Substances RNA, Double-Stranded ; RNA, Messenger ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2016-10-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1474-760X
    ISSN (online) 1474-760X
    ISSN 1474-760X
    DOI 10.1186/s13059-016-1083-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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