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  1. Article ; Online: The chromatin - triple helix connection.

    Maldonado, Rodrigo / Längst, Gernot

    Biological chemistry

    2023  Volume 404, Issue 11-12, Page(s) 1037–1049

    Abstract: Mammalian genomes are extensively transcribed, producing a large number of coding and non-coding transcripts. A large fraction of the nuclear RNAs is physically associated with chromatin, functioning in gene activation and silencing, shaping higher-order ...

    Abstract Mammalian genomes are extensively transcribed, producing a large number of coding and non-coding transcripts. A large fraction of the nuclear RNAs is physically associated with chromatin, functioning in gene activation and silencing, shaping higher-order genome organisation, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions. Different mechanisms allow the tethering of these chromatin-associated RNAs (caRNA) to chromosomes, including RNA binding proteins, the RNA polymerases and R-loops. In this review, we focus on the sequence-specific targeting of RNA to DNA by forming triple helical structures and describe its interplay with chromatin. It turns out that nucleosome positioning at triple helix target sites and the nucleosome itself are essential factors in determining the formation and stability of triple helices. The histone H3-tail plays a critical role in triple helix stabilisation, and the role of its epigenetic modifications in this process is discussed.
    MeSH term(s) Animals ; Chromatin/genetics ; Nucleosomes ; Binding Sites/genetics ; Histones/metabolism ; DNA/metabolism ; RNA/genetics ; Mammals/genetics ; Mammals/metabolism
    Chemical Substances Chromatin ; Nucleosomes ; Histones ; DNA (9007-49-2) ; RNA (63231-63-0)
    Language English
    Publishing date 2023-07-31
    Publishing country Germany
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1334659-3
    ISSN 1437-4315 ; 1431-6730 ; 1432-0355
    ISSN (online) 1437-4315
    ISSN 1431-6730 ; 1432-0355
    DOI 10.1515/hsz-2023-0189
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  2. Article ; Online: Nrf2 pre-recruitment at Enhancer 2 is a hallmark of H

    Carrasco-Wong, Ivo / Längst, Gernot / Sobrevia, Luis / Casanello, Paola

    Journal of cellular physiology

    2024  

    Abstract: Maternal obesity (MO) is a significant cause of increased cardiometabolic risk in offspring, who present endothelial dysfunction at birth. Alterations in physiologic and cellular redox status are strongly associated with altered gene regulation in ... ...

    Abstract Maternal obesity (MO) is a significant cause of increased cardiometabolic risk in offspring, who present endothelial dysfunction at birth. Alterations in physiologic and cellular redox status are strongly associated with altered gene regulation in arterial endothelium. However, specific mechanisms by which the pro-oxidant fetal environment in MO could modulate the vascular gene expression and function during the offspring's postnatal life are elusive. We tested if oxidative stress could reprogram the antioxidant-coding gene's response to a pro-oxidant challenge through an epigenetic transcriptional memory (ETM) mechanism. A pro-oxidant double-hit protocol was applied to human umbilical artery endothelial cells (HUAECs) and EA.hy 926 endothelial cell lines. The ETM acquisition in the HMOX1 gene was analyzed by RT-qPCR. HMOX1 mRNA decay was evaluated by Actinomycin-D treatment and RT-qPCR. To assess the chromatin accessibility and the enrichment of NRF2, RNAP2, and phosphorylation at serin-5 of RNAP2, at HMOX1 gene regulatory regions, were used DNase HS-qPCR and ChIP-qPCR assays, respectively. The CpG methylation pattern at the HMOX1 core promoter was analyzed by DNA bisulfite conversion and Sanger sequencing. Data were analyzed using two-way ANOVA, and p < 0.05 was statistically significant. Using a pro-oxidant double-hit protocol, we found that the Heme Oxygenase gene (HMOX1) presents an ETM response associated with changes in the chromatin structure at the promoter and gene regulatory regions. The ETM response was characterized by a paused-RNA Polymerase 2 and NRF2 enrichment at the transcription start site and Enhancer 2 of the HMOX1 gene, respectively. Changes in DNA methylation pattern at the HMOX1 promoter were not a hallmark of this oxidative stress-induced ETM. These data suggest that a pro-oxidant milieu could trigger an ETM at the vascular level, indicating a potential epigenetic mechanism involved in the increased cardiovascular risk in the offspring of women with obesity.
    Language English
    Publishing date 2024-03-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3116-1
    ISSN 1097-4652 ; 0021-9541
    ISSN (online) 1097-4652
    ISSN 0021-9541
    DOI 10.1002/jcp.31243
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  3. Article ; Online: Preparation of Chromatin Templates to Study RNA Polymerase I Transcription In Vitro.

    Längst, Gernot

    Methods in molecular biology (Clifton, N.J.)

    2016  Volume 1455, Page(s) 109–119

    Abstract: Cellular DNA is packaged into chromatin, which is the substrate of all DNA-dependent processes in eukaryotes. The regulation of chromatin requires specialized enzyme activities to allow the access of sequence-specific binding proteins and RNA polymerases. ...

    Abstract Cellular DNA is packaged into chromatin, which is the substrate of all DNA-dependent processes in eukaryotes. The regulation of chromatin requires specialized enzyme activities to allow the access of sequence-specific binding proteins and RNA polymerases. In order to dissect chromatin-dependent features of transcription regulation in detail, in vitro systems to generate defined chromatin templates for transcription are required. I present a protocol that allows the assembly of nucleosomes on ribosomal RNA (rRNA) minigenes by salt gradient dialysis and subsequent sucrose gradient centrifugation. This procedure yields high nucleosome occupancy and high dynamic response in subsequent transcriptional analysis. It provides an invaluable tool to study rRNA gene transcription, as transcription on free DNA is clearly different from the more in vivo-like transcription on reconstituted chromatin templates.
    Language English
    Publishing date 2016
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-3792-9_9
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  4. Article ; Online: Analyzing RNA-DNA Triplex Formation in Chromatin.

    Maldonado, Rodrigo / Längst, Gernot

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2161, Page(s) 247–254

    Abstract: A significant fraction of non-coding RNAs (ncRNAs) is associated with chromatin, shown to regulate gene expression and to organize nuclear architecture. Mechanisms of direct and indirect RNA-chromatin interactions have been described, including the ... ...

    Abstract A significant fraction of non-coding RNAs (ncRNAs) is associated with chromatin, shown to regulate gene expression and to organize nuclear architecture. Mechanisms of direct and indirect RNA-chromatin interactions have been described, including the sequence-specific formation of triple helix structures. Triplexes are formed by the sequence-specific binding of RNA to the bases located in the major groove of DNA. We recently showed that triplexes do exist in the context of cellular chromatin and that these structures are stabilized by the histone H3 tail of adjacent nucleosomes. The in vitro characterization of the specificity and binding affinity of triplex sequences next to nucleosomes are essential parameters to identify potential sites of RNA-chromatin interaction in vivo. Here we provide a detailed protocol to determine the influence of nucleosome positioning on triple helix formation. This assay allows the comparative quantification of triplex formation and specificity for triplex targeting sequences relative to the spatial nucleosome position.
    MeSH term(s) Animals ; Cell Line ; Cells, Cultured ; DNA/chemistry ; Electrophoretic Mobility Shift Assay/methods ; Humans ; Nucleosomes/chemistry ; Nucleosomes/metabolism ; Protein Binding ; RNA, Untranslated/chemistry ; RNA, Untranslated/metabolism
    Chemical Substances Nucleosomes ; RNA, Untranslated ; triplex DNA ; DNA (9007-49-2)
    Language English
    Publishing date 2020-07-17
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0680-3_17
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  5. Book ; Online ; Thesis: Gene regulation via nucleosome stability modulation and RNA:DNA triplex formation

    Wernig-Zorc, Sara [Verfasser] / Längst, Gernot [Akademischer Betreuer]

    2023  

    Author's details Sara Wernig-Zorc ; Betreuer: Gernot Längst
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek Regensburg
    Publishing place Regensburg
    Document type Book ; Online ; Thesis
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  6. Article ; Online: Arabidopsis mRNA export factor MOS11: molecular interactions and role in abiotic stress responses.

    Rödel, Amelie / Weig, Ina / Tiedemann, Sophie / Schwartz, Uwe / Längst, Gernot / Moehle, Christoph / Grasser, Marion / Grasser, Klaus D

    The New phytologist

    2024  

    Abstract: Transcription and export (TREX) is a multi-subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic transport of mRNAs. Plant ... ...

    Abstract Transcription and export (TREX) is a multi-subunit complex that links synthesis, processing and export of mRNAs. It interacts with the RNA helicase UAP56 and export factors such as MOS11 and ALYs to facilitate nucleocytosolic transport of mRNAs. Plant MOS11 is a conserved, but sparsely researched RNA-binding export factor, related to yeast Tho1 and mammalian CIP29/SARNP. Using biochemical approaches, the domains of Arabidopsis thaliana MOS11 required for interaction with UAP56 and RNA-binding were identified. Further analyses revealed marked genetic interactions between MOS11 and ALY genes. Cell fractionation in combination with transcript profiling demonstrated that MOS11 is required for export of a subset of mRNAs that are shorter and more GC-rich than MOS11-independent transcripts. The central α-helical domain of MOS11 proved essential for physical interaction with UAP56 and for RNA-binding. MOS11 is involved in the nucleocytosolic transport of mRNAs that are upregulated under stress conditions and accordingly mos11 mutant plants turned out to be sensitive to elevated NaCl concentrations and heat stress. Collectively, our analyses identify functional interaction domains of MOS11. In addition, the results establish that mRNA export is critically involved in the plant response to stress conditions and that MOS11 plays a prominent role at this.
    Language English
    Publishing date 2024-04-22
    Publishing country England
    Document type Journal Article
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.19773
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    Z 868: Show issues

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  7. Book ; Online ; Thesis: Genome wide tracking of RNA polymerase II and associated factors during transcript elongation in Arabidopsis thaliana

    Obermeyer, Simon [Verfasser] / Grasser, Klaus [Akademischer Betreuer] / Längst, Gernot [Akademischer Betreuer]

    2023  

    Author's details Simon Obermeyer ; Klaus Grasser, Gernot Längst
    Keywords Naturwissenschaften ; Science
    Subject code sg500
    Language English
    Publisher Universitätsbibliothek Regensburg
    Publishing place Regensburg
    Document type Book ; Online ; Thesis
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  8. Book ; Online ; Thesis: Characterization of stable cell lines, inducibly co-expressing CHD3/4 with PU.1

    Siegel, Michael F. [Verfasser] / Längst, Gernot [Akademischer Betreuer]

    2022  

    Author's details Michael F. Siegel ; Betreuer: Gernot Längst
    Keywords Biowissenschaften, Biologie ; Life Science, Biology
    Subject code sg570
    Language English
    Publisher Universitätsbibliothek Regensburg
    Publishing place Regensburg
    Document type Book ; Online ; Thesis
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  9. Article ; Online: Peculiarities of

    Watzlowik, Maria Theresia / Das, Sujaan / Meissner, Markus / Längst, Gernot

    International journal of molecular sciences

    2021  Volume 22, Issue 10

    Abstract: The highly complex life cycle of the human malaria parasite, ...

    Abstract The highly complex life cycle of the human malaria parasite,
    MeSH term(s) Animals ; Chromatin Assembly and Disassembly ; Epigenesis, Genetic ; Gene Expression Regulation ; Humans ; Life Cycle Stages ; Malaria, Falciparum/parasitology ; Plasmodium falciparum/genetics ; Transcription, Genetic
    Language English
    Publishing date 2021-05-13
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms22105168
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  10. Article ; Online: Characterization of the nuclear import of the human CHD4-NuRD complex.

    Hoffmeister, Helen / Holzinger, Simon / Dürr, Marie-Sofie / Bruckmann, Astrid / Schindler, Susanne / Gröbner-Ferreira, Regina / Depping, Reinhard / Längst, Gernot

    Journal of cell science

    2023  Volume 136, Issue 7

    Abstract: Chromatin remodeling enzymes form large multiprotein complexes that play central roles in regulating access to the genome. Here, we characterize the nuclear import of the human CHD4 protein. We show that CHD4 enters the nucleus by means of several ... ...

    Abstract Chromatin remodeling enzymes form large multiprotein complexes that play central roles in regulating access to the genome. Here, we characterize the nuclear import of the human CHD4 protein. We show that CHD4 enters the nucleus by means of several importin-α proteins (1, 5, 6 and 7), but independently of importin β1. Importin α1 directly interacts with a monopartite 'KRKR'-motif in the N-terminus of CHD4 (amino acids 304-307). However, alanine mutagenesis of this motif only leads to an ∼50% reduction in nuclear localization of CHD4, implying that there are additional import mechanisms. Interestingly, we could show that CHD4 was already associated with the nucleosome remodeling deacetylase (NuRD) core subunits, such as MTA2, HDAC1 and RbAp46 (also known as RBBP7), in the cytoplasm, suggesting an assembly of the NuRD core complex before nuclear import. We propose that, in addition to the importin-α-dependent nuclear localization signal, CHD4 is dragged into the nucleus by a 'piggyback' mechanism using the import signals of the associated NuRD subunits.
    MeSH term(s) Humans ; Mi-2 Nucleosome Remodeling and Deacetylase Complex/genetics ; Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism ; Nucleosomes/metabolism ; alpha Karyopherins/metabolism ; Active Transport, Cell Nucleus ; Cell Nucleus/metabolism ; Histone Deacetylases/metabolism ; Repressor Proteins/metabolism
    Chemical Substances Mi-2 Nucleosome Remodeling and Deacetylase Complex (EC 3.5.1.98) ; Nucleosomes ; alpha Karyopherins ; CHD4 protein, human ; MTA2 protein, human (EC 3.5.1.-) ; Histone Deacetylases (EC 3.5.1.98) ; Repressor Proteins
    Language English
    Publishing date 2023-04-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    DOI 10.1242/jcs.260724
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