The Histone H3 Lysine 9 Methyltransferase DIM-5 Modifies Chromatin at frequency and Represses Light-Activated Gene Expression

Abstract

The transcriptional program controlling the circadian rhythm requires coordinated regulation of chromatin. Characterization of the chromodomain helicase DNA-binding enzyme CHD1 revealed DNA methylation in the promoter of the central clock gene frequency (frq) in Neurospora crassa. In this report, we show that the DNA methylation at frq is not only dependent on the DNA methyltransferase DIM-2 but also on the H3K9 methyltransferase DIM-5 and HP1. Histone H3 lysine 9 trimethylation (H3K9me3) occurs at frq and is most prominent 30 min after light-activated expression. Strains lacking dim-5 have an increase in light-induced transcription, and more White Collar-2 is found associated with the frq promoter. Consistent with the notion that DNA methylation assists in establishing the proper circadian phase, loss of H3K9 methylation results in a phase advance suggesting it delays the onset of frq expression. The dim-5 deletion strain displays an increase in circadian-regulated conidia formation on race tubes and there is a synthetic genetic interaction between dim-5 and ras-1bd. These results indicate DIM-5 has a regulatory role in muting circadian output. Overall, the data support a model where facultative heterochromatic at frq serves to establish the appropriate phase, mute the light response, and repress circadian output.

Repeat-Induced Point Mutation and Other Genome Defense Mechanisms in Fungi

“…These activities are only present during the sexual stage, as it would be expected from the hypothesized deaminases involved in RIP. Nevertheless, it is important to note that in Neurospora vegetative cells, DIM-2 can also methylate coding, nonrepetitive parts of the genome (88). If cytosine methylation of genic regions also takes place in premeiotic cells, then the proposed two-step mechanism would further require the deamination step to be homology-dependent.…”

The frequency natural antisense transcript first promotes, then represses, frequency gene expression via facultative heterochromatin

“…The molecular mechanism of DNA methylation proceeds in a stepwise fashion mediated by DCDC (DIM-5/ DIM-7/DIM-9-CUL4/DDB1 complex) (25,28,29). Both DIM-5 and HP1 are also required for methylation at frq, suggesting that other DCDC components may also be required (30). However, the dependency of qrf expression and the existence of disiRNAs originating from frq suggest a more complicated mechanism because RNAi is not needed for DNA methylation at relics of repeat-induced point mutations throughout the genome (31).…”

“…m 5 C at frq requires both histone H3K9 methylation (H3K9me) and HP1 (30). DIM-5 adds a monomethyl group, dimethyl group, and trimethyl group to H3K9 and is needed for all known DNA methylation in Neurospora (28,34).…”

Seeing the world differently: variability in the photosensory mechanisms of two model fungi

“…Given that NGF-1 was found to interact with “dark” WC-1/2 heterodimer, a model has been proposed wherein light activation of the WCC/NGF-1 complex leads to conformational changes in WCC (converting it to “light” WCC) which in turn leads to an enhancement of HAT activity of NGF-1 (Brenna et al , 2012). More recently, H3K9me3 DNA methylation by methyltransferase DIM-5 and HP1 has been identified to be a component in the repression of light-induced gene expression (Ruesch et al , 2014), and there is higher light-induced transcription of two genes, frq and vvd , in a dim-5 mutant. WC-2 binding at the pLRE (the LRE of the frq promoter) is enhanced in the absence of H3K9me3 under light conditions (Ruesch et al , 2014).…”

“…More recently, H3K9me3 DNA methylation by methyltransferase DIM-5 and HP1 has been identified to be a component in the repression of light-induced gene expression (Ruesch et al , 2014), and there is higher light-induced transcription of two genes, frq and vvd , in a dim-5 mutant. WC-2 binding at the pLRE (the LRE of the frq promoter) is enhanced in the absence of H3K9me3 under light conditions (Ruesch et al , 2014). Similar but less drastic results were found in a set-1 mutant that lacks another histone lysine methyl transferase (Raduwan et al , 2013).…”