Evidence That the Histone Methyltransferase Dot1 Mediates Global Genomic Repair by Methylating Histone H3 on Lysine 79

Abstract

Global genomic repair (GGR) and transcription coupled repair (TCR) are two pathways of nucleotide excision repair (NER) that differ in the damage recognition step. How NER factors, especially GGR factors, access DNA damage in the chromatin of eukaryotic cells has been poorly understood. Dot1, a histone methyltransferase required for methylation of histone H3 lysine 79 (H3K79), has been shown to confer yeast cells with resistance to DNA-damaging agents and play a role in activation of DNA damage checkpoints. Here, we show that Dot1 and H3K79 methylation are required for GGR in both nucleosomal core regions and internucleosomal linker DNA, but play no role in TCR. H3K79 trimethylation contributes to but is not absolutely required for GGR, and lower levels of H3K79 methylation (mono-and dimethylation) also promote GGR. Our results also indicate that the roles of Dot1 and H3K79 methylation in GGR are not achieved by either activating DNA damage checkpoints or regulating the expression of the GGR-specific factor Rad16. Rather, the methylated H3K79 may serve as a docking site for the GGR machinery on the chromatin. Our studies identified a novel GGR-specific NER factor and unveiled the critical link between a covalent histone modification and GGR. Nucleotide excision repair (NER)2 is a highly conserved DNA repair mechanism that removes a wide variety of bulky, helixdistorting lesions that generally obstruct transcription and normal replication, such as UV-induced cyclobutane pyrimidine dimers (CPDs) (1). Transcription-coupled repair (TCR) is a specialized NER pathway that is dedicated to rapid repair in the transcribed strand (TS) of active genes and is believed to be initiated by an RNA polymerase stalled at a lesion in the TS (2). The genome-wide NER, which includes repair in the nontranscribed strand (NTS) of actively transcribed genes, is termed global genomic repair (GGR) to be distinguished from TCR. The two NER pathways share most of the common repair factors and differ only in the damage recognition step (1).In the budding yeast Saccharomyces cerevisiae, Rad7, Rad16, and Elc1 are specifically required for GGR (3, 4). The exact roles of these proteins in GGR are not yet clear. The Rad7-Rad16 complex may act as an ATP-dependent motor that translocates along the DNA in search of damage, and upon encountering a lesion, the complex is stalled, which may remodel and open damaged chromatin, thereby facilitating recruitment of other NER factors (5). Elc1 has been shown to be a component of a ubiquitin ligase that contains Rad7 and Rad16 (6). It has also been suggested that Elc1 is a component of another ubiquitin ligase complex, which contains Ela1, Cul3, and Roc1 but not Rad7 and Rad16 (7). The role of Elc1 in GGR does not seem to be subsidiary to that of Rad7 and Rad16 (3).The molecular basis of chromatin dynamics during NER in eukaryotic cells is still not well understood (8, 9). The basic repeating component of chromatin is the nucleosome, which comprises 146 bp of DNA wrapped around an octomer of the four core hi...

Diverse Roles of RNA Polymerase II-associated Factor 1 Complex in Different Subpathways of Nucleotide Excision Repair

“…We also found that Bre1 and monoubiquitination of H2BK123 facilitates GGR, especially in internucleosomal linker regions (23).…”

“…Also, SWI/SNF, an ATP-dependent chromatin-remodeling complex, has been shown to be recruited to chromatin upon induction of DNA damage by UV (22). A critical piece of evidence indicating the active engagement of chromatin in GGR is the recent discovery that methylation of histone H3 lysine 79 (H3K79), catalyzed by the histone methyltransferase Dot1, is required for GGR but plays no role in TCR in yeast (23). The Lys-79 residues of the two histone H3 molecules contained in a nucleosome are located at the top and bottom surfaces of the nucleosome disk and most likely regulate interactions with exogenous proteins (24).…”

“…The Lys-79 residues of the two histone H3 molecules contained in a nucleosome are located at the top and bottom surfaces of the nucleosome disk and most likely regulate interactions with exogenous proteins (24). It was proposed that the methylated H3K79 may serve as a docking site for the GGR machinery on the chromatin (23).…”

Histone modifications in DNA damage response

“…Dot1L-dependent H3K79 methylation is required for the localization of 53BP1 around damaged DNA and 53BP1 tandem Tudor domain binds to methylated H3K79 directly, resulting in the induction of 53BP1 phosphorylation and checkpoint activation (Giannattasio et al, 2005;Huyen et al, 2004;Wakeman et al, 2012;Wysocki et al, 2005). In addition, H3K79 methylation mediated by Dot1L promotes nucleotide excision repair, and H3K79R mutation increases the binding of histone deacetylase complex to eliminate histone acetylation and reduce DNA lesion accessibility to repair enzymes (Chaudhuri et al, 2009;Tatum and Li, 2011). Moreover, Dot1L and H3K79me3 contribute to favorable sister chromatid exchange during HR and facilitate HR repair (Conde et al, 2009;Rossodivita et al, 2014).…”

Epigenetic regulators as promising therapeutic targets in acute myeloid leukemia

“…DOT1L is known to interact with the phosphorylated C-terminal domain of actively transcribing RNA polymerase II (RNAPII) and through this interaction, DOT1L and subsequent H3K79 methylations are targeted to actively transcribed genes [Kim et al 2012a]. Beside its effects on cell cycle, DOT1L appears to also play a role in DNA repair as methylated H3K79 serves as a docking site for the global genomic repair machinery [Tatum and Li, 2011]. A crucial role for DOT1L during embryonic development has been demonstrated using germline Dot1l knockout mouse models.…”