Biotinylation of histones represses transposable elements in human and mouse cells and cell lines and in Drosophila melanogaster

Abstract

Transposable elements such as long terminal repeats (LTR) constitute approximately 45% of the human genome; transposition events impair genome stability. Fifty-four promoter-active retrotransposons have been identified in humans. Epigenetic mechanisms are important for transcriptional repression of retrotransposons, preventing transposition events, and abnormal regulation of genes. Here, we demonstrate that the covalent binding of the vitamin biotin to lysine-12 in histone H4 (H4K12bio) and lysine-9 in histone H2A (H2AK9bio), mediated by holocarboxylase synthetase (HCS), is an epigenetic mechanism to repress retrotransposon transcription in human and mouse cell lines and in primary cells from a human supplementation study. Abundance of H4K12bio and H2AK9bio at intact retrotransposons and a solitary LTR depended on biotin supply and HCS activity and was inversely linked with the abundance of LTR transcripts. Knockdown of HCS in Drosophila melanogaster enhances retrotransposition in the germline. Importantly, we demonstrated that depletion of H4K12bio and H2AK9bio in biotin-deficient cells correlates with increased production of viral particles and transposition events and ultimately decreases chromosomal stability. Collectively, this study reveals a novel diet-dependent epigenetic mechanism that could affect cancer risk.

FIGURE 1

Structures of LTR. In intact LTR, the viral genes gag, pol, and env are flanked by 2 repeat regions, 5′-LTR and 3′-LTR. The expression of viral genes is regulated by regions in the 5′-LTR. In solitary LTR, the viral genes have been deleted by recombination events between LTR. Solitary LTR may affect the expression of host genes bi-directionally (arrows). LTR contain the following regions: 1) the U3, a noncoding region of 200–1200 bp; U3 in the 5′-LTR contains the promoter elements responsible for transcription of both viral genes and host genes; 2) R region, a short (18–250 bp) repeat sequence; and 3) U5, a noncoding region of 75–250 bp where reverse transcription of the transposon originates.

FIGURE 2

Biotin supplementation leads to enrichment of H4K12bio and H3K9me2 at LTR in human T lymphoma Jurkat cells. (A) Solitary LTR (LTR22); (B) intact retrotransposon LTR (LTR15). The relative enrichment of genomic sequences was expressed as the ratio of antibody-precipitated DNA to an equal amount of input DNA. Relative enrichment was normalized to nucleosomal density at LTR loci by chromatin precipitated with anti-H3-C. Values are means ± SD, n = 3. Means for each variable without a common letter differ, P < 0.05.

FIGURE 3

Biotin supplementation leads to a reduction in LTR transcription in Jurkat cells. Mammalian LTR transcripts originating in the U5 region and at the R/U5 boundary were quantified by quantitative real-time-PCR. Values are means ± SD, n = 3. Means for each variable without a common letter differ, P < 0.05.

FIGURE 4

Production of viral (MMTV) particles in murine mammary carcinoma Mm5MT cells depends on biotin status in cell culture media. Values are means ± SD, n = 3. Means for each variable without a common letter differ, P < 0.05. Inserts depict representative examples from 1 gel.