The Role of Histone H4 Biotinylation in the Structure of Nucleosomes

Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, United States of America.
PLoS ONE (Impact Factor: 3.23). 01/2011; 6(1):e16299. DOI: 10.1371/journal.pone.0016299
Source: PubMed


Post-translational modifications of histones play important roles in regulating nucleosome structure and gene transcription. It has been shown that biotinylation of histone H4 at lysine-12 in histone H4 (K12Bio-H4) is associated with repression of a number of genes. We hypothesized that biotinylation modifies the physical structure of nucleosomes, and that biotin-induced conformational changes contribute to gene silencing associated with histone biotinylation.
To test this hypothesis we used atomic force microscopy to directly analyze structures of nucleosomes formed with biotin-modified and non-modified H4. The analysis of the AFM images revealed a 13% increase in the length of DNA wrapped around the histone core in nucleosomes with biotinylated H4. This statistically significant (p<0.001) difference between native and biotinylated nucleosomes corresponds to adding approximately 20 bp to the classical 147 bp length of nucleosomal DNA.
The increase in nucleosomal DNA length is predicted to stabilize the association of DNA with histones and therefore to prevent nucleosomes from unwrapping. This provides a mechanistic explanation for the gene silencing associated with K12Bio-H4. The proposed single-molecule AFM approach will be instrumental for studying the effects of various epigenetic modifications of nucleosomes, in addition to biotinylation.

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Available from: Janos Zempleni,
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    • "It is estimated that approximately 30 % of histone H4 molecules in telomeric repeats are biotinylated at position K12 (Hassan and Zempleni 2008). A recent study showed that K12 biotinylation in histone H4 alters the structure of the nucleosomes and leads to \15 % increase in the amount of DNA wrapped around nucleosomes (Filenko et al. 2011). Neurotox Res (2015) 27:172–197 179 The enrichment of H4K12bio depends on the concentration of biotin in the cell culture medium (Zempleni et al. 2009). "
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    ABSTRACT: The complexity of the genome is regulated by epigenetic mechanisms, which act on the level of DNA, histones, and nucleosomes. Epigenetic machinery is involved in various biological processes, including embryonic development, cell differentiation, neurogenesis, and adult cell renewal. In the last few years, it has become clear that the number of players identified in the regulation of chromatin structure and function is still increasing. In addition to well-known phenomena, including DNA methylation and histone modification, new, important elements, including nucleosome mobility, histone tail clipping, and regulatory ncRNA molecules, are being discovered. The present paper provides the current state of knowledge about the role of 16 different histone post-translational modifications, nucleosome positioning, and histone tail clipping in the structure and function of chromatin. We also emphasize the significance of cross-talk among chromatin marks and ncRNAs in epigenetic control.
    Neurotoxicity Research 12/2014; 27(2). DOI:10.1007/s12640-014-9508-6 · 3.54 Impact Factor
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    • "Phosphopantetheinylation and biotinylation are two posttranslational modifications, which occur widely in living organisms, especially in metabolic enzymes to regulate their activity, such as aromatic carboxylic acid reductase, non-ribosomal peptide synthetases (NRPSs), polyketide synthases (PKSs) and carboxylases [16], [17], [18]. Biotinylation of histone H4 has been recently found to be involved in the regulation of nucleosome structure and gene transcription [19]. Biotinylation is also regarded as a useful protein tag in a variety of biochemical experiments [20], [21]. "
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    ABSTRACT: The correct folding of a protein is a pre-requirement for its proper posttranslational modification. The Escherichia coli Sec pathway, in which preproteins, in an unfolded, translocation-competent state, are rapidly secreted across the cytoplasmic membrane, is commonly assumed to be unfavorable for their modification in the cytosol. Whether posttranslationally modified recombinant preproteins can be efficiently transported via the Sec pathway, however, remains unclear. ACP and BCCP domain (BCCP87) are carrier proteins that can be converted into active phosphopantetheinylated ACP (holo-ACP) and biotinylated-BCCP (holo-BCCP) by AcpS and BirA, respectively. In the present study, we show that, when ACP or BCCP87 is fused to the C-terminus of secretory protein YebF or MBP, the resulting fusion protein preYebF-ACP, preYebF-BCCP87, preMBP-ACP or preMBP-BCCP87 can be modified and then secreted. Our data demonstrate that posttranslational modification of preYebF-ACP, preYebF-BCCP87 preMBP-ACP and preMBP-BCCP87 can take place in the cytosol prior to translocation, and the Sec machinery accommodates these previously modified fusion proteins. High levels of active holo-ACP and holo-BCCP87 are achieved when AcpS or BirA is co-expressed, especially when sodium azide is used to retard their translocation across the inner membrane. Our results also provide an alternative to achieve a high level of modified recombinant proteins expressed extracellularly.
    PLoS ONE 08/2012; 7(8):e42519. DOI:10.1371/journal.pone.0042519 · 3.23 Impact Factor
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    • "The di- NCP sample was imaged similarly to the mononucleosome sample described earlier [18] [19] [20] [21] [22]. Diluted samples (0.8 nM concentration in 10 mM Tris-HCl, Ph 7.5, and 4 mM MgCl 2 buffer) were deposited on APS mica and after drying, imaged in air at ambient conditions. "
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    ABSTRACT: Dynamics of nucleosomes and their interactions are important for understanding the mechanism of chromatin assembly. Internucleosomal interaction is required for the formation of higher-order chromatin structures. Although H1 histone is critically involved in the process of chromatin assembly, direct internucleosomal interactions contribute to this process as well. To characterize the interactions of nucleosomes within the nucleosome array, we designed a dinucleosome and performed direct AFM imaging. The analysis of the AFM data showed dinucleosomes are very dynamic systems, enabling the nucleosomes to move in a broad range along the DNA template. Di-nucleosomes in close proximity were observed, but their population was low. The use of the zwitterionic detergent, CHAPS, increased the dynamic range of the di-nucleosome, facilitating the formation of tight di-nucleosomes. The role of CHAPS and similar natural products in chromatin structure and dynamics is also discussed.
    01/2012; 2012:650840. DOI:10.1155/2012/650840
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