Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation

Petal senescence is controlled by a complex regulatory network. Epigenetic regulation like histone modification influences chromatin state and gene expression. However, involvement of histone methylation in regulating petal senescence is still largely unknown. Here, we found that the trimethylation of histone H3 at Lysine 4 (H3K4me3) is increased during the ethylene induced petal senescence in carnation (Dianthus caryophyllus L.). The H3K4me3 levels are positively associated with the expression of transcription factor DcWRKY75, ethylene biosynthetic genes DcACS1 and DcACO1, and senescence associated genes (SAGs) DcSAG12 and DcSAG29. Further, we identified that carnation DcATX1 (ARABIDOPSIS HOMOLOG OF TRITHORAX1) encodes a histone lysine methyltransferase which can methylate H3K4. Knockdown of DcATX1 delays ethylene induced petal senescence in carnation, which is associated with the downregulated expression of DcWRKY75, DcACO1 and DcSAG12. While overexpression of DcATX1 exhibits the opposite effects. DcATX1 promotes the transcription of DcWRKY75, DcACO1 and DcSAG12 by targeting to their promoters to elevate the H3K4me3 levels. Overall, our results demonstrate that DcATX1 is a H3K4 methyltransferase that promotes the expression of DcWRKY75, DcACO1 and DcSAG12 by regulating H3K4me3 levels, thereby accelerating ethylene induced petal senescence in carnation. This study further indicates that epigenetic regulation is important for plant senescence process.

SMYD2 targets RIPK1 and restricts TNF-induced apoptosis and necroptosis to support colon tumor growth

SMYD2 is a histone methyltransferase, which methylates both histone H3K4 as well as a number of non-histone proteins. Dysregulation of SMYD2 has been associated with several diseases including cancer. In the present study, we investigated whether and how SMYD2 might contribute to colorectal cancer. Increased expression levels of SMYD2 were detected in human and murine colon tumor tissues compared to tumor-free tissues. SMYD2 deficiency in colonic tumor cells strongly decreased tumor growth in two independent experimental cancer models. On a molecular level, SMYD2 deficiency sensitized colonic tumor cells to TNF-induced apoptosis and necroptosis without affecting cell proliferation. Moreover, we found that SMYD2 targeted RIPK1 and inhibited the phosphorylation of RIPK1. Finally, in a translational approach, pharmacological inhibition of SMYD2 attenuated colonic tumor growth. Collectively, our data show that SMYD2 is crucial for colon tumor growth and inhibits TNF-induced apoptosis and necroptosis.

Set1-mediated histone H3K4 methylation is required for azole induction of the ergosterol biosynthesis genes and antifungal drug resistance in Candida glabrata.

Candida glabrata is an opportunistic pathogen that has developed the ability to adapt and thrive under azole treated conditions. The common mechanisms that can result in Candida drug resistance are due to mutations or overexpression of the drug efflux pump or the target of azole drugs, Cdr1 and Erg11, respectively. However, the role of epigenetic histone modifications in azole-induced gene expression and drug resistance are poorly understood in C. glabrata. In this study, we show for the first time that Set1 mediates histone H3K4 mono-, di-, and trimethylation in C. glabrata. In addition, loss of SET1 and histone H3K4 methylation results in increased susceptibility to azole drugs in both C. glabrata and S. cerevisiae. Intriguingly, this increase in susceptibility to azole drugs in strains lacking Set1-mediated histone H3K4 methylation is not due to altered transcript levels of CDR1, PDR1 or Cdr1s ability to efflux drugs. Genome-wide transcript analysis revealed that Set1 is necessary for azole-induced expression of 12 genes involved in the late biosynthesis of ergosterol including ERG11 and ERG3. Importantly, chromatin immunoprecipitation analysis showed that histone H3K4 trimethylation was detected on chromatin of actively transcribed ERG genes. Furthermore, H3K4 trimethylation increased upon azole-induced gene expression which was also found to be dependent on the catalytic activity of Set1. Altogether, our findings show that Set1-mediated histone H3K4 methylation governs the intrinsic drug resistant status in C. glabrata via epigenetic control of azole-induced ERG gene expression.

Distinct requirements for the COMPASS core subunits Set1, Swd1, and Swd3 during meiosis in the budding yeast Saccharomyces cerevisiae

Meiosis-specific chromatin structures, guided by histone modifications, are critical mediators of a meiotic transient transcription program and progression through prophase I. Histone H3K4 can be methylated up to three times by the Set1-containing COMPASS complex and each methylation mark corresponds to a different chromatin conformation. The level of H3K4 modification is directed by the activity of additional COMPASS components. In this study, we characterized the role of the COMPASS subunits during meiosis in S. cerevisiae. In vegetative cells, previous studies revealed a role for subunits Swd2, Sdc1, and Bre2 for H3K4me2 while Spp1 supported trimethylation. However, we found that Bre2 and Sdc1 are required for H3K4me3 as yeast prepare to enter meiosis while Spp1 is not. Interestingly, we identified distinct meiotic functions for the core COMPASS complex members that required for all H3K4me, Set1, Swd1, and Swd3. While Set1 and Swd1 are required for progression through early meiosis, Swd3 is critical for late meiosis and spore morphogenesis. Furthermore, the meiotic requirement for Set1 is independent of H3K4 methylation, suggesting the presence of non-histone substrates. Finally, checkpoint suppression analyses indicate that Set1 and Swd1 are required for both homologous recombination and chromosome segregation. These data suggest that COMPASS has important new roles for meiosis that are independent of its well-characterized functions during mitotic divisions.

Histone demethylase AMX-1 is necessary for proper sensitivity to interstrand crosslink DNA damage

Histone methylation is dynamically regulated to shape the epigenome and adjust central nuclear processes including transcription, cell cycle control and DNA repair. Lysine-specific histone demethylase 2 (LSD2) has been implicated in multiple types of human cancers. However, its functions remain poorly understood. This study investigated the histone demethylase LSD2 homolog AMX-1 in C. elegans and uncovered a potential link between H3K4me2 modulation and DNA interstrand crosslink (ICL) repair. AMX-1 is a histone demethylase and mainly localizes to embryonic cells, the mitotic gut and sheath cells. Lack of AMX-1 expression resulted in embryonic lethality, a decreased brood size and disorganized premeiotic tip germline nuclei. Expression of AMX-1 and of the histone H3K4 demethylase SPR-5 is reciprocally up-regulated upon lack of each other and the mutants show increased H3K4me2 levels in the germline, indicating that AMX-1 and SPR-5 regulate H3K4me2 demethylation. Loss of AMX-1 function activates the CHK-1 kinase acting downstream of ATR and leads to the accumulation of RAD-51 foci and increased DNA damage-dependent apoptosis in the germline. AMX-1 is required for the proper expression of mismatch repair component MutL/MLH-1 and sensitivity against ICLs. Interestingly, formation of ICLs lead to ubiquitination-dependent subcellular relocalization of AMX-1. Taken together, our data suggest that AMX-1 functions in ICL repair in the germline.

Histone H3K4 Methyltransferases as Targets for Drug-Resistant Cancers

The KMT2 (MLL) family of proteins, including the major histone H3K4 methyltransferase found in mammals, exists as large complexes with common subunit proteins and exhibits enzymatic activity. SMYD, another H3K4 methyltransferase, and SET7/9 proteins catalyze the methylation of several non-histone targets, in addition to histone H3K4 residues. Despite these structural and functional commonalities, H3K4 methyltransferase proteins have specificity for their target genes and play a role in the development of various cancers as well as in drug resistance. In this review, we examine the overall role of histone H3K4 methyltransferase in the development of various cancers and in the progression of drug resistance. Compounds that inhibit protein–protein interactions between KMT2 family proteins and their common subunits or the activity of SMYD and SET7/9 are continuously being developed for the treatment of acute leukemia, triple-negative breast cancer, and castration-resistant prostate cancer. These H3K4 methyltransferase inhibitors, either alone or in combination with other drugs, are expected to play a role in overcoming drug resistance in leukemia and various solid cancers.

Insights into Transcriptional Regulation by Individual H3K4 Methylation Marks in S. Cerevisiae

Set1 is a lysine methyltransferase in S. cerevisiae that catalyzes the mono, di and tri methylation of the fourth lysine on the amino terminal tail of histone H3 (H3K4). Set1-like methyltransferases are evolutionarily conserved, and research has linked their function to developmental gene regulation and several cancers in higher eukaryotes. Set1 is a member of the multiprotein COMPASS complex in S. cerevisiae. The H3K4 methylation activity of COMPASS regulates gene expression and chromosome segregation in vivo. The three distinct methyl marks on histone H3K4 act in discrete ways to regulate transcription. Trimethylation of H3K4 is usually associated with active transcription whereas dimethylation of H3K4 is associated with gene repression. In this study, amino acid substitution mutants of SET1 that encode partial function Set1 proteins capable of H3K4me1, H3K4me1 and H3K4me2, or H3K4me1and H3K4me3 were analyzed to learn more about the roles of individual H3K4 methyl marks in transcription. The findings reveal a previously unappreciated role for H3K4me1 in activation of transcription of the HIS3 gene in S. cerevisiae cultures grown under histidine-starvation conditions. Surprisingly, induction of the HIS3 gene in cultures grown under histidine starvation is not accompanied by significant changes in the profiles of H3K4-methylated nucleosomes at the HIS3 gene in SET1 wild-type strains and set1 partial-function mutants. The data show that H3K4me1 supports induction of HIS3 mRNA to wild-type levels under histidine-starvation conditions and that higher-order H3K4 methylation (H3K4me2 and H3K4me3) is not required.