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  1. Article ; Online: RNA-binding proteins in cardiovascular biology and disease: the beat goes on.

    Völkers, Mirko / Preiss, Thomas / Hentze, Matthias W

    Nature reviews. Cardiology

    2024  

    Abstract: Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology ... ...

    Abstract Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology largely remains to be uncovered, building on the foundation of a few existing paradigms. The discovery during the past decade of hundreds of additional RNA-binding proteins in mammalian cells and organs, including the heart, is expected to accelerate progress and has raised intriguing possibilities for better understanding the intricacies of cardiac development, metabolism and adaptive alterations. In this Review, we discuss the progress and new concepts on RNA-binding proteins and RNA biology and appraise them in the context of common cardiovascular clinical conditions, from cell and organ-wide perspectives. We also discuss how a better understanding of cardiac RNA-binding proteins can fill crucial knowledge gaps in cardiology and might pave the way to developing better treatments to reduce cardiovascular morbidity and mortality.
    Language English
    Publishing date 2024-01-02
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2490375-9
    ISSN 1759-5010 ; 1759-5002
    ISSN (online) 1759-5010
    ISSN 1759-5002
    DOI 10.1038/s41569-023-00958-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2).

    Noble, Michelle / Chatterjee, Aindrila / Sekaran, Thileepan / Schwarzl, Thomas / Hentze, Matthias W

    RNA (New York, N.Y.)

    2024  

    Abstract: Several enzymes of intermediary metabolism have been identified to bind RNA in 2 cells, with potential consequences for the bound RNAs and/or the enzyme. In this 3 study, we investigate the RNA-binding activity of the mitochondrial enzyme malate 4 ... ...

    Abstract Several enzymes of intermediary metabolism have been identified to bind RNA in 2 cells, with potential consequences for the bound RNAs and/or the enzyme. In this 3 study, we investigate the RNA-binding activity of the mitochondrial enzyme malate 4 dehydrogenase 2 (MDH2), which functions in the tricarboxylic acid (TCA) cycle and 5 the malate-aspartate shuttle. We confirmed in cellulo RNA-binding of MDH2 using 6 orthogonal biochemical assays and performed enhanced crosslinking and 7 immunoprecipitation (eCLIP) to identify the cellular RNAs associated with endogenous 8 MDH2. Surprisingly, MDH2 preferentially binds cytosolic over mitochondrial RNAs, 9 although the latter are abundant in the milieu of the mature protein. Subcellular 10 fractionation followed by RNA-binding assays revealed that MDH2-RNA interactions 11 occur predominantly outside of mitochondria. We also found that a cytosolically-12 retained N-terminal deletion mutant of MDH2 is competent to bind RNA, indicating that 13 mitochondrial targeting is dispensable for MDH2-RNA interactions. MDH2 RNA 14 binding increased when cellular NAD+ levels (MDH2's co-factor) was 15 pharmacologically diminished, suggesting that the metabolic state of cells affects RNA 16 binding. Taken together, our data implicate an as yet unidentified function of MDH2 17 binding RNA in the cytosol.
    Language English
    Publishing date 2024-04-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.079925.123
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Small noncoding RNA interactome capture reveals pervasive, carbon source-dependent tRNA engagement of yeast glycolytic enzymes.

    Asencio, Claudio / Schwarzl, Thomas / Sahadevan, Sudeep / Hentze, Matthias W

    RNA (New York, N.Y.)

    2022  Volume 29, Issue 3, Page(s) 330–345

    Abstract: Small noncoding RNAs fulfill key functions in cellular and organismal biology, typically working in concert with RNA-binding proteins (RBPs). While proteome-wide methodologies have enormously expanded the repertoire of known RBPs, these methods do not ... ...

    Abstract Small noncoding RNAs fulfill key functions in cellular and organismal biology, typically working in concert with RNA-binding proteins (RBPs). While proteome-wide methodologies have enormously expanded the repertoire of known RBPs, these methods do not distinguish RBPs binding to small noncoding RNAs from the rest. To specifically identify this relevant subclass of RBPs, we developed small noncoding RNA interactome capture (snRIC
    MeSH term(s) Glycolysis/genetics ; Proteome/genetics ; RNA/metabolism ; RNA Polymerase III/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism
    Chemical Substances Proteome ; RNA (63231-63-0) ; RNA Polymerase III (EC 2.7.7.6) ; RNA, Transfer (9014-25-9) ; RNA-Binding Proteins ; RNA, Small Untranslated
    Language English
    Publishing date 2022-12-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1241540-6
    ISSN 1469-9001 ; 1355-8382
    ISSN (online) 1469-9001
    ISSN 1355-8382
    DOI 10.1261/rna.079408.122
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Elisa Izaurralde 1959-2018.

    Hentze, Matthias W / Valcárcel, Juan

    Nature structural & molecular biology

    2018  Volume 25, Issue 7, Page(s) 547

    Language English
    Publishing date 2018-08-04
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-018-0081-1
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    Zs.MG 56: Show issues

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  5. Article ; Online: 'High vault-age': non-coding RNA control of autophagy.

    Büscher, Magdalena / Horos, Rastislav / Hentze, Matthias W

    Open biology

    2020  Volume 10, Issue 2, Page(s) 190307

    Abstract: RNA-binding proteins typically change the fate of RNA, such as stability, translation or processing. Conversely, we recently uncovered that the small non-coding vault RNA 1-1 (vtRNA1-1) directly binds to the autophagic receptor p62/SQSTM1 and changes the ...

    Abstract RNA-binding proteins typically change the fate of RNA, such as stability, translation or processing. Conversely, we recently uncovered that the small non-coding vault RNA 1-1 (vtRNA1-1) directly binds to the autophagic receptor p62/SQSTM1 and changes the protein's function. We refer to this process as 'riboregulation'. Here, we discuss this newly uncovered vault RNA function against the background of three decades of vault RNA research. We highlight the vtRNA1-1-p62 interaction as an example of riboregulation of a key cellular process.
    MeSH term(s) Animals ; Autophagy ; Gene Expression Regulation ; Humans ; RNA Stability ; RNA, Untranslated/chemistry ; RNA, Untranslated/genetics ; Sequestosome-1 Protein/metabolism
    Chemical Substances RNA, Untranslated ; Sequestosome-1 Protein
    Language English
    Publishing date 2020-02-19
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2630944-0
    ISSN 2046-2441 ; 2046-2441
    ISSN (online) 2046-2441
    ISSN 2046-2441
    DOI 10.1098/rsob.190307
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq.

    Schwarzl, Thomas / Sahadevan, Sudeep / Lang, Benjamin / Miladi, Milad / Backofen, Rolf / Huber, Wolfgang / Hentze, Matthias W / Tartaglia, Gian Gaetano

    Nucleic acids research

    2023  Volume 52, Issue 1, Page(s) e1

    Abstract: Enhanced crosslinking and immunoprecipitation (eCLIP) sequencing is a method for transcriptome-wide detection of binding sites of RNA-binding proteins (RBPs). However, identified crosslink sites can deviate from experimentally established functional ... ...

    Abstract Enhanced crosslinking and immunoprecipitation (eCLIP) sequencing is a method for transcriptome-wide detection of binding sites of RNA-binding proteins (RBPs). However, identified crosslink sites can deviate from experimentally established functional elements of even well-studied RBPs. Current peak-calling strategies result in low replication and high false positive rates. Here, we present the R/Bioconductor package DEWSeq that makes use of replicate information and size-matched input controls. We benchmarked DEWSeq on 107 RBPs for which both eCLIP data and RNA sequence motifs are available and were able to more than double the number of motif-containing binding regions relative to standard eCLIP processing. The improvement not only relates to the number of binding sites (3.1-fold with known motifs for RBFOX2), but also their subcellular localization (1.9-fold of mitochondrial genes for FASTKD2) and structural targets (2.2-fold increase of stem-loop regions for SLBP. On several orthogonal CLIP-seq datasets, DEWSeq recovers a larger number of motif-containing binding sites (3.3-fold). DEWSeq is a well-documented R/Bioconductor package, scalable to adequate numbers of replicates, and tends to substantially increase the proportion and total number of RBP binding sites containing biologically relevant features.
    MeSH term(s) Binding Sites ; Immunoprecipitation ; Protein Binding ; RNA/chemistry ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Software
    Chemical Substances RNA (63231-63-0) ; RNA-Binding Proteins
    Language English
    Publishing date 2023-11-13
    Publishing country England
    Document type 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/gkad998
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    Zs.A 1067: Show issues Location:
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  7. Article ; Online: Superparamagnetic Iron Oxide Nanoparticles Reprogram the Tumor Microenvironment and Reduce Lung Cancer Regrowth after Crizotinib Treatment.

    Horvat, Natalie K / Chocarro, Sara / Marques, Oriana / Bauer, Tobias A / Qiu, Ruiyue / Diaz-Jimenez, Alberto / Helm, Barbara / Chen, Yuanyuan / Sawall, Stefan / Sparla, Richard / Su, Lu / Klingmüller, Ursula / Barz, Matthias / Hentze, Matthias W / Sotillo, Rocío / Muckenthaler, Martina U

    ACS nano

    2024  Volume 18, Issue 17, Page(s) 11025–11041

    Abstract: ALK-positive NSCLC patients demonstrate initial responses to ALK tyrosine kinase inhibitor (TKI) treatments, but eventually develop resistance, causing rapid tumor relapse and poor survival rates. Growing evidence suggests that the combination of drug ... ...

    Abstract ALK-positive NSCLC patients demonstrate initial responses to ALK tyrosine kinase inhibitor (TKI) treatments, but eventually develop resistance, causing rapid tumor relapse and poor survival rates. Growing evidence suggests that the combination of drug and immune therapies greatly improves patient survival; however, due to the low immunogenicity of the tumors, ALK-positive patients do not respond to currently available immunotherapies. Tumor-associated macrophages (TAMs) play a crucial role in facilitating lung cancer growth by suppressing tumoricidal immune activation and absorbing chemotherapeutics. However, they can also be programmed toward a pro-inflammatory tumor suppressive phenotype, which represents a highly active area of therapy development. Iron loading of TAMs can achieve such reprogramming correlating with an improved prognosis in lung cancer patients. We previously showed that superparamagnetic iron oxide nanoparticles containing core-cross-linked polymer micelles (SPION-CCPMs) target macrophages and stimulate pro-inflammatory activation. Here, we show that SPION-CCPMs stimulate TAMs to secrete reactive nitrogen species and cytokines that exert tumoricidal activity. We further show that SPION-CCPMs reshape the immunosuppressive
    MeSH term(s) Lung Neoplasms/drug therapy ; Lung Neoplasms/pathology ; Tumor Microenvironment/drug effects ; Animals ; Magnetic Iron Oxide Nanoparticles/chemistry ; Humans ; Mice ; Crizotinib/pharmacology ; Crizotinib/chemistry ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/chemistry ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/chemistry ; Cell Line, Tumor ; Tumor-Associated Macrophages/drug effects ; Tumor-Associated Macrophages/metabolism ; Cell Proliferation/drug effects ; Female
    Chemical Substances Crizotinib (53AH36668S) ; Antineoplastic Agents ; Protein Kinase Inhibitors
    Language English
    Publishing date 2024-04-16
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.3c08335
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Iron-dependent BMP6 Regulation in Liver Sinusoidal Endothelial Cells Is Instructed by Hepatocyte-derived Secretory Signals.

    Colucci, Silvia / Altamura, Sandro / Marques, Oriana / Müdder, Katja / Agarvas, Anand R / Hentze, Matthias W / Muckenthaler, Martina U

    HemaSphere

    2022  Volume 6, Issue 10, Page(s) e773

    Language English
    Publishing date 2022-09-27
    Publishing country United States
    Document type Journal Article
    ISSN 2572-9241
    ISSN (online) 2572-9241
    DOI 10.1097/HS9.0000000000000773
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  9. Article ; Online: ‘High vault-age’

    Magdalena Büscher / Rastislav Horos / Matthias W. Hentze

    Open Biology, Vol 10, Iss

    non-coding RNA control of autophagy

    2020  Volume 2

    Abstract: RNA-binding proteins typically change the fate of RNA, such as stability, translation or processing. Conversely, we recently uncovered that the small non-coding vault RNA 1-1 (vtRNA1-1) directly binds to the autophagic receptor p62/SQSTM1 and changes the ...

    Abstract RNA-binding proteins typically change the fate of RNA, such as stability, translation or processing. Conversely, we recently uncovered that the small non-coding vault RNA 1-1 (vtRNA1-1) directly binds to the autophagic receptor p62/SQSTM1 and changes the protein's function. We refer to this process as ‘riboregulation'. Here, we discuss this newly uncovered vault RNA function against the background of three decades of vault RNA research. We highlight the vtRNA1-1-p62 interaction as an example of riboregulation of a key cellular process.
    Keywords p62 ; riboregulation ; vault rna 1-1 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher The Royal Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Genetics. IRES unplugged.

    Gebauer, Fátima / Hentze, Matthias W

    Science (New York, N.Y.)

    2016  Volume 351, Issue 6270, Page(s) 228

    MeSH term(s) Genome, Human/genetics ; Genome, Viral/genetics ; Humans ; Protein Biosynthesis/genetics ; RNA Caps/genetics
    Chemical Substances RNA Caps
    Language English
    Publishing date 2016-01-15
    Publishing country United States
    Document type Comment ; Journal Article
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.aad8540
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    Zs.MG 77: Show issues

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