Transposable elements such as long terminal repeats (LTR) constitute about 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 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, transposition events, and ultimately decreases chromosomal stability. Collectively, this study reveals a novel diet-dependent epigenetic mechanism that could affect cancer risk.

Histone H3 Lys4 (H3K4) is methylated by yeast Set1-COMPASS and its mammalian homolog, the MLL complex. Human JARID1d can demethylate trimethyl-H3K4 (H3K4me3). We identified Drosophila melanogaster little imaginal discs (Lid) as the JARID1d homolog. We report that Lid knockdown using RNA interference results in a specific genome-wide increase in H3K4me3 levels without affecting other patterns of H3 methylation, and results in an altered distribution of the chromo-helicase protein Chd1.

The Rtf1 subunit of the Paf1 complex is required for proper monoubiquitination of histone H2B and methylation of histone H3 on lysines 4 (H3K4) and 79 in yeast Saccharomyces cerevisiae. Using RNAi, we examined the role of Rtf1 in histone methylation and gene expression in Drosophila melanogaster. We show that Drosophila Rtf1 (dRtf1) is required for proper gene expression and development. Furthermore, we show that RNAi-mediated reduction of dRtf1 results in a reduction in histone H3K4 trimethylation levels on bulk histones and chromosomes in vivo, indicating that the histone modification pathway via Rtf1 is conserved among yeast, Drosophila, and human. Recently, it was demonstrated that histone H3K4 methylation mediated via the E3 ligase Bre1 is critical for transcription of Notch target genes in Drosophila. Here we demonstrate that the dRtf1 component of the Paf1 complex functions in Notch signaling.chromatin ͉ elongation ͉ RNA polymerase II ͉ transcription ͉ monoubiquitination I nterplay between transcriptional activators and repressors regulates gene expression by RNA polymerase II (RNA Pol II). In several cases, chromatin structure is implicated in transcriptional activation and repression. Posttranslational methylation of lysines on the N-terminal tails of histones is thought to modulate higher-order chromatin folding and can activate or repress transcription, depending on the residue being methylated, the regulatory protein recruited by the methyl mark, and whether the lysine is mono-, di-, or trimethylated (1).Histone modifications can be interdependent, such that one modification requires another preexisting modification (1). Histone H3 methylation at lysines 4 and 79 is catalyzed by the complex of proteins associated with Set1 (COMPASS) and Dot1p, respectively in Saccharomyces cerevisiae (1-8). Methylation at these residues requires monoubiquitination of histone H2B at lysine 123 by Rad6͞Bre1 (9-11). The Paf1 complex indirectly regulates histone methylation through its regulation of H2B monoubiquitination and interaction of COMPASS with RNA Pol II (12-14).The Paf1 complex in yeast is composed of five subunits, Paf1, Rtf1, Cdc73, Ctr9, and Leo1, and is associated with the elongating form of RNA Pol II (1, 15-18). The Rtf1 component of Paf1 is required for H2B ubiquitination by and for the recruitment of Set1͞COMPASS to elongating RNA Pol II (12, 13). Because Rtf1 is essential for histone monoubiquitination, methylation, and transcriptional control in yeast, we sought the Drosophila homologue dRtf1 to characterize its role in higher eukaryotes. Here we use RNAi to reduce dRtf1 expression levels and examine the in vivo effect of dRtf1 reduction on transcription and development in the fly. We show that RNAi knockdown of dRtf1 causes pupal lethality. To demonstrate a role for dRtf1 in gene expression, we tested the effect of dRtf1 RNAi knockdown on heat shock gene expression and found that Rtf1 knockdown results in a reduction in heat shock (Hsp70) gene expression. Recently, Bray et al. (19) demonstrated th...

Energy restriction increases stress resistance and lifespan in Drosophila melanogaster and other species. The roles of individual nutrients in stress resistance and longevity are largely unknown. The vitamin biotin is a potential candidate for mediating these effects, given its known roles in stress signaling and gene regulation by epigenetic mechanisms, i.e. biotinylation of histones. Here, we tested the hypothesis that prolonged culture of Drosophila on biotin-deficient (BD) medium increases stress resistance and lifespan. Flies were fed a BD diet for multiple generations; controls were fed a biotin-normal diet. In some experiments, a third group of flies was fed a BD diet for 12 generations and then switched to control diets for 2 generations to eliminate potential effects of short-term biotin deficiency. Flies fed a BD diet exhibited a 30% increase in lifespan. This increase was associated with enhanced resistance to the DNA-damaging agent hydroxyurea and heat stress. Also, fertility increased significantly compared with biotin-normal controls. Biotinylation of histones was barely detectable in biotin-deprived flies, suggesting that epigenetic events might have contributed to effects of biotin deprivation.

GGAs are monomeric adaptor proteins implicated in clathrin-mediated vesicular transport between the trans-Golgi network and endosomes, characterized mainly from cell culture analysis of lysosomal sorting. To provide the first demonstration of GGA’s role in vivo, we used Drosophila which has a single GGA and a single lysosomal sorting receptor, LERP. Using RNAi knockdowns, we show that the Drosophila GGA is required for lysosomal sorting. We further identified authentic components of the Drosophila lysosomal sorting system – the sorting receptor LERP, the sorting adaptor GGA and the lysosomal cargo cathepsins B1, D and L – to demonstrate that GGA depletion results in lysosomal dysfunction. Abnormal lysosomal morphology, missorting of lysosomal cathepsins and impaired lysosomal proteolysis demonstrate disturbed LERP-trafficking after GGA depletion. GGA is highly expressed in the mushroom bodies and the pigment cells of the retina and increasing or decreasing the levels of GGA in the eyes leads to retinal defects. Reduced GGA levels also enhance an eye defect caused by overexpression of the autophagy-associated protein Bluecheese (Bchs), implicating GGA in autophagic processes. This shows that Drosophila provides an excellent whole-animal model to gain new insights into the function of GGA in the physiological environment of a multicellular organism.