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. Author manuscript; available in PMC: 2009 Aug 1.
Published in final edited form as: Nutr Rev. 2008 Aug;66(Suppl 1):S46–S48. doi: 10.1111/j.1753-4887.2008.00073.x

Epigenetic regulation of chromatin structure and gene function by biotin

are biotin requirements being met?

Janos Zempleni 1, Yap Ching Chew 1, Yousef I Hassan 1, Subhashinee SK Wijeratne 1
PMCID: PMC2562292  NIHMSID: NIHMS66110  PMID: 18673490

Abstract

Histones H2A, H3, and H4 are modified by covalent binding of the vitamin biotin to distinct lysine residues. Binding of biotin to histones is mediated by holocarboxylase synthetase (HCS) and perhaps biotinidase. Biotinylation of lysine- 12 in histone H4 (K12BioH4) plays roles in gene repression, stability of repeat regions and transposable elements, and regulation of biotin transporter expression in eukaryotes. Decreased biotinylation of histones in biotin-deficient and HCS-deficient human cells and Drosophila melanogaster impairs stress resistance, life span, and biotin homeostasis.

CHROMATIN

Chromatin is comprised of DNA and DNA-binding proteins, i.e., histones and non-histone proteins. Histones play a predominant role in the folding of DNA into chromatin.1 Five major classes of histones have been identified in mammals: H1, H2A, H2B, H3, and H4. Histones consist of a globular domain and a more flexible amino terminus (histone “tail”). DNA and histones form repetitive nucleoprotein units, the nucleosomes.1 Each nucleosome (“nucleosomal core particle”) consists of 146 base pairs of DNA wrapped around an octamer of core histones (one H3-H3-H4-H4 tetramer and two H2A-H2B dimers).

The amino terminal tail of histones protrudes from the nucleosomal surface; covalent modifications of this tail affect the structure of chromatin and form the basis for gene regulation.1-3 Amino acid residues in histone tails are modified by covalent acetylation, methylation, phosphorylation, ubiquitination, and poly(ADP-ribosylation). The various modifications of histones have distinct functions. For example, trimethylation of K4 in histone H3 is associated with transcriptional activation of surrounding DNA, whereas dimethylation of K9 is associated with transcriptional silencing.2,3 Covalent modifications of histones are reversible and may have clinical implications.3

BIOTINYLATION OF HISTONES

Recently, we identified a novel modification of histones by investigating the enzymatic biotinylation of histone-based, synthetic peptides: covalent binding of the vitamin biotin to K9, K13, K125, K127, and K129 in histone H2A;4 K4, K9, and K18 in histone H3;5 and K8 and K12 in histone H4.6 Confirmation of biotinylation sites by mass spectrometry (MS) is currently in progress using histone extracts from human lymphoid (Jurkat) cells.7 Biotinylated histones were detected in primary human cells, transformed cell lines, and in other eukaryotes such as Drosophila melanogaster.8-10 Biotinylation of histones is catalyzed by holocarboxylase synthetase, HCS, and perhaps biotinidase, BTD.11,12 HCS and BTD knockdown studies in Drosophila melanogaster have provided evidence that HCS is more important than BTD for biotinylation of histones.10 Previous studies have also revealed that HCS is a chromosomal protein10 and that chromatin can be immunoprecipitated with an antibody to HCS.9 Our laboratory is in the process of identifying zinc-finger proteins that direct HCS to specific regions in chromatin and tyrosine kinases that regulate the nuclear translocation of HCS (Hassan YI and Zempleni J, unpublished observation). Biotinylation of histones is a reversible process, but the identity of the histone debiotinylase(s) is uncertain.13 It has been proposed that BTD might participate in the hydrolytic debiotinylation of histones,13,14 but other mechanisms, such as histone replacement, might also participate in the removal of biotinylated histones.1-3

BIOLOGICAL FUNCTIONS OF HISTONE BIOTINYLATION

Over the past few years substantial progress has been made towards identifying the biological functions of biotinylated species’ histone H4. First, it was shown that K12BioH4 and perhaps lysine (K)-8 biotinylated histone H4 (K8BioH4) are integral components of repeat regions in (peri)centromeric chromatin and mediate silencing of transcriptionally competent chromatin.15 Second, evidence was provided that K12BioH4 is enriched at transposable elements in the eukaryotic genomes (Chew YC, West J, Zempleni J, unpublished observation). These studies also provided evidence that biotin deficiency is associated with decreased abundance of biotinylated histones at transposable elements, increasing the transcriptional activity of endogenous retroviruses and genomic instability. K-9 biotinylated histone H2A (K9BioH2A) and K-13 biotinylated histone H2A (K13BioH2A) also appear to be enriched at transposable elements. Third, a model has been proposed in which biotin homeostasis in human cells is regulated by enrichment of K12BioH4 at promoters driving the expression of biotin transporters.9 In this model, biotin deficiency is associated with decreased abundance of BioK12H4 at biotin transporter loci, causing de-repression of transporter expression and increased biotin uptake. Administration of pharmacological doses of biotin is associated with increased abundance of BioK12H4 at biotin transporter loci, causing repression of transporter expression and decreased biotin uptake.

HCS AND BIOTIN DEFICIENCY

Decreased biotinylation of histones caused by long-term biotin deficiency or by HCS knockdown is associated with decreased life span and stress resistance, and aberrant gene-expression patterns in Drosophila.10 These effects were caused by decreased biotinylation of histones rather than decreased biotinylation of carboxylases, another substrate for biotinylation by HCS.16 In flies, it takes several generations of feeding a biotin-deficient diet before decreased biotinylation of histones in bulk extracts of histones is evident.17 Short-term biotin deficiency has no apparent effect on histone biotinylation,18 although potential effects in confined regions of the genome (e.g., transposable elements) have not been formally excluded.

What is the dietary relevance of these studies? The majority of the studies described above were conducted in cultures of human cells, using biotin concentrations representative of those seen in biotin-deficient, biotinnormal, and biotin-supplemented humans. Both biotin deficiency and supplementation are prevalent in the North American diet. For example, moderate biotin deficiency has been observed in up to 50% of pregnant women.19,20 About 20% of the US population reports taking biotin supplements,21 producing supraphysiological concentrations of the vitamin in tissues and body fluids.22,23 Biotin deficiency and overdose likely have effects on gene regulation and genome stability that go far beyond the classical coenzymic role of biotin in metabolism.

Acknowledgment

Funding. A contribution was received from the University of Nebraska Agricultural Research Division, supported in part by funds provided through the Hatch Act. Additional support was provided by NIH grants DK 063945 and ES 015206, USDA grant 2006-35200-17138, by NSF EPSCoR grant EPS-0701892, and by NSF MCB 6552870.

Footnotes

Declaration of interest. JZ receives royalties from the sales of antibodies to biotinylated histones, based on a licensing agreement with Upstate, Inc. and is named as a co-inventor on U.S. Patent Application No. 20,060,286,611, which covers products and methods relating to antibodies against biotinylated histones and related proteins and assays related thereto. The other authors have no interests to declare.

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