Novel histone biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes☆

Abstract 

Covalent histone modifications play crucial roles in chromatin structure and genome stability. We previously reported biotinylation of lysine (K) residues in histones H2A, H3 and H4 by holocarboxylase synthetase and demonstrated that K12-biotinylated histone H4 (H4K12bio) is enriched in repeat regions and participates in gene repression. The biological functions of biotinylation marks other than H4K12bio are poorly understood. Here, novel biotinylation site-specific antibodies against H3K9bio, H3K18bio and H4K8bio were used in chromatin immunoprecipitation studies to obtain first insights into possible biological functions of these marks. Chromatin immunoprecipitation assays were conducted in human primary fibroblasts and Jurkat lymphoblastoma cells, and revealed that H3K9bio, H3K18bio and H4K8bio are enriched in repeat regions such as pericentromeric alpha satellite repeats and long-terminal repeats while being depleted in transcriptionally active promoters in euchromatin. Transcriptional stimulation of the repressed interleukin-2 promoter triggered a rapid depletion of histone biotinylation marks at this locus in Jurkat cells, which was paralleled by an increase in interleukin-2 mRNA. Importantly, the enrichment of H3K9bio, H3K18bio and H4K8bio at genomic loci depended on the concentration of biotin in culture media at nutritionally relevant levels, suggesting a novel mechanism of gene regulation by biotin.

Abbreviations: ADH5, aldehyde dehydrogenase 5, GAPDH, glyceraldehyde3-phosphate dehydrogenase, H3K4bio, K4-biotinylated histone H3, H3K9bio, K9-biotinylated histone H3, H3K18bio, K18-biotinylated histone H3, H3K9me2, K9-dimethylated histone H3, H3K9ac, K9-acetylated histone H3, H4K8bio, K8-biotinylated histone H4, H4K12bio, K12-biotinylated histone H4, HCS, holocarboxylase synthetase, K, lysine, LTR, long terminal repeat, μChIP, micro chromatin immunoprecipitation, PHA, phytohemagglutinin, PMA, phorbol-12-myristate-13-acetate, qRT-PCR, quantitative real-time polymerase chain reaction, SMVT, sodium-dependent multivitamin transporter

Keywords: Biotin, Gene regulation, Heterochromatin, Histones, Human