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  1. Article ; Online: Cis and trans internucleosomal interactions of H3 and H4 tails in tetranucleosomes.

    Nurse, Nathan P / Yuan, Chongli

    Biopolymers

    2015  Volume 103, Issue 1, Page(s) 33–40

    Abstract: Chromatin structure and the transcriptional state of a gene can be modulated by modifications made on H3 and H4 tails of histones. Elucidating the internucleosomal interactions of these tails is vital to understanding epigenetic regulation. ... ...

    Abstract Chromatin structure and the transcriptional state of a gene can be modulated by modifications made on H3 and H4 tails of histones. Elucidating the internucleosomal interactions of these tails is vital to understanding epigenetic regulation. Differentiation between cis (intra-nucleosomal) and trans (inter-nucleosomal) interactions is often difficult with conventional techniques since H3 and H4 tails are flexible. The distinction, however, is important because these interactions model short- and long-range chromatin interactions respectively and have different bearings in biological processes. Combining FCS and PCH analysis, we can decouple the contribution of histone tails to cis and trans effects. A Mg(2+) gradient was employed to facilitate compaction and oligomerization of tetranucleosomes with H3 and/or H4 tail truncations. H3 tails were found to play a multifunctional role and exhibit the ability to partake in both attractive cis and trans interactions simultaneously. H4 tails partake in attractive cis and repulsive trans interactions at low [Mg(2+)]. These interactions are diminished at higher [Mg(2+)]. Simultaneous H3 and H4 tail truncation inhibited array oligomerization but maintained local array compaction at relatively high [Mg(2+)]. The established experimental approach can be extended to study the detailed molecular interactions mediated by epigenetic modification of flexible histone tails.
    MeSH term(s) Histones/chemistry ; Histones/metabolism ; Nucleic Acid Conformation ; Nucleosomes/chemistry ; Nucleosomes/metabolism ; Protein Binding
    Chemical Substances Histones ; Nucleosomes
    Language English
    Publishing date 2015-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1123-x
    ISSN 1097-0282 ; 0006-3525
    ISSN (online) 1097-0282
    ISSN 0006-3525
    DOI 10.1002/bip.22560
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 77: 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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  2. Article ; Online: Clipping of flexible tails of histones H3 and H4 affects the structure and dynamics of the nucleosome.

    Nurse, Nathan P / Jimenez-Useche, Isabel / Smith, Ian Tad / Yuan, Chongli

    Biophysical journal

    2013  Volume 104, Issue 5, Page(s) 1081–1088

    Abstract: Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to ... ...

    Abstract Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to partake in intranucleosomal interactions by restricting the DNA breathing motion and compacting the nucleosome. The H3 tail effects were mostly independent of the ionic strength and valency of the ions. The H4 tail was shown to not greatly affect the nucleosome conformation, but did slightly influence the relative population of the preferred conformation. The role of the H4 tail varied depending on the valency and ionic strength, suggesting that electrostatic forces play a primary role in H4 tail interactions. Interestingly, despite the H4 tail's lack of influence, when H3 and H4 tails were simultaneously clipped, a more dramatic effect was seen than when only H3 or H4 tails were clipped. The combinatorial effect of H3 and H4 tail truncation suggests a potential mechanism by which various combinations of histone tail modifications can be used to control accessibility of DNA-binding proteins to nucleosomal DNA.
    MeSH term(s) Amino Acid Sequence ; Animals ; DNA/chemistry ; Fluorescence Resonance Energy Transfer ; Histones/chemistry ; Nucleosomes/chemistry ; Osmolar Concentration ; Protein Binding ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Sequence Deletion ; Static Electricity ; Xenopus laevis
    Chemical Substances Histones ; Nucleosomes ; Recombinant Proteins ; DNA (9007-49-2)
    Language English
    Publishing date 2013-03-06
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2013.01.019
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: 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 ; Online: DNA methylation effects on tetra-nucleosome compaction and aggregation.

    Jimenez-Useche, Isabel / Nurse, Nathan P / Tian, Yuqing / Kansara, Bhargav S / Shim, Daphne / Yuan, Chongli

    Biophysical journal

    2014  Volume 107, Issue 7, Page(s) 1629–1636

    Abstract: DNA CpG methylation has been associated with chromatin compaction and gene silencing. Whether DNA methylation directly contributes to chromatin compaction remains an open question. In this study, we used fluorescence fluctuation spectroscopy (FFS) to ... ...

    Abstract DNA CpG methylation has been associated with chromatin compaction and gene silencing. Whether DNA methylation directly contributes to chromatin compaction remains an open question. In this study, we used fluorescence fluctuation spectroscopy (FFS) to evaluate the compaction and aggregation of tetra-nucleosomes containing specific CpG patterns and methylation levels. The compactness of both unmethylated and methylated tetra-nucleosomes is dependent on DNA sequences. Specifically, methylation of the CpG sites located in the central dyad and the major grooves of DNA seem to have opposite effects on modulating the compactness of tetra-nucleosomes. The interactions among tetra-nucleosomes, however, seem to be enhanced because of DNA methylation independent of sequence contexts. Our finding can shed light on understanding the role of DNA methylation in determining nucleosome positioning pattern and chromatin compactness.
    MeSH term(s) Animals ; Base Sequence ; CpG Islands/genetics ; DNA Methylation/drug effects ; Gene Expression Regulation ; Magnesium/pharmacology ; Models, Molecular ; Nucleic Acid Conformation ; Nucleosomes/chemistry ; Nucleosomes/drug effects ; Nucleosomes/genetics ; Protein Aggregates/drug effects ; Protein Conformation ; Spectrometry, Fluorescence
    Chemical Substances Nucleosomes ; Protein Aggregates ; Magnesium (I38ZP9992A)
    Language English
    Publishing date 2014-10-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2014.05.055
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: 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)
    Zs.MO 2: Show issues

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  4. Article: Clipping of Flexible Tails of Histones H3 and H4 Affects the Structure and Dynamics of the Nucleosome

    Nurse, Nathan P / Jimenez-Useche, Isabel / Smith, Ian Tad / Yuan, Chongli

    Biophysical journal. 2013 Mar. 5, v. 104, no. 5

    2013  

    Abstract: Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to ... ...

    Abstract Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to partake in intranucleosomal interactions by restricting the DNA breathing motion and compacting the nucleosome. The H3 tail effects were mostly independent of the ionic strength and valency of the ions. The H4 tail was shown to not greatly affect the nucleosome conformation, but did slightly influence the relative population of the preferred conformation. The role of the H4 tail varied depending on the valency and ionic strength, suggesting that electrostatic forces play a primary role in H4 tail interactions. Interestingly, despite the H4 tail’s lack of influence, when H3 and H4 tails were simultaneously clipped, a more dramatic effect was seen than when only H3 or H4 tails were clipped. The combinatorial effect of H3 and H4 tail truncation suggests a potential mechanism by which various combinations of histone tail modifications can be used to control accessibility of DNA-binding proteins to nucleosomal DNA.
    Keywords DNA ; DNA-binding proteins ; electrostatic interactions ; energy transfer ; histones ; ionic strength ; ions ; nucleosomes
    Language English
    Dates of publication 2013-0305
    Size p. 1081-1088.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2013.01.019
    Database NAL-Catalogue (AGRICOLA)

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    Z 4' 66/63: Show issues

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  5. Article: Clipping of Flexible Tails of Histones H3 and H4 Affects the Structure and Dynamics of the Nucleosome

    Nurse, Nathan P. / Jimenez-Useche, Isabel / Smith, Ian Tad / Yuan, Chongli

    Biophysical journal

    Volume v. 104,, Issue no. 5

    Abstract: Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to ... ...

    Abstract Förster resonance energy transfer was used to monitor the dynamic conformations of mononucleosomes under different chromatin folding conditions to elucidate the role of the flexible N-terminal regions of H3 and H4 histones. The H3 tail was shown to partake in intranucleosomal interactions by restricting the DNA breathing motion and compacting the nucleosome. The H3 tail effects were mostly independent of the ionic strength and valency of the ions. The H4 tail was shown to not greatly affect the nucleosome conformation, but did slightly influence the relative population of the preferred conformation. The role of the H4 tail varied depending on the valency and ionic strength, suggesting that electrostatic forces play a primary role in H4 tail interactions. Interestingly, despite the H4 tail’s lack of influence, when H3 and H4 tails were simultaneously clipped, a more dramatic effect was seen than when only H3 or H4 tails were clipped. The combinatorial effect of H3 and H4 tail truncation suggests a potential mechanism by which various combinations of histone tail modifications can be used to control accessibility of DNA-binding proteins to nucleosomal DNA.
    Keywords DNA-binding proteins ; electrostatic interactions ; histones ; energy transfer ; DNA ; nucleosomes ; ions ; ionic strength
    Language English
    Document type Article
    ISSN 0006-3495
    Database AGRIS - International Information System for the Agricultural Sciences and Technology

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