The histone H3K9M mutation synergizes with H3K14 ubiquitylation to selectively sequester histone H3K9 methyltransferase Clr4 at heterochromatin

Shan, Chun-Min; Kim, Jin-Kwang; Wang, Jiyong; Bao, Kehan; Sun, Yadong; Chen, Huijie; Stirpe, Alessandro; Zhang, Zhiguo; Lü, Chao; Schalch, Thomas; Liti, Gianni; Nagy, Péter L.; Tong, Liang; Qiao, Feng; Jia, Songtao

doi:10.1016/j.celrep.2021.109137

Cited by 11 publications

(10 citation statements)

References 51 publications

(86 reference statements)

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“…The DIM-5 complex has been well characterized in fission yeast. In addition to forming a methyltransferase complex with RiK1, Raf1, Raf2, and Pcu4 subunits ( Oya et al, 2019 ; Shan et al, 2021 ), DIM-5 exists in close association with the Argonaute complex to maintain heterochromatin assembly ( Buker et al, 2007 ). In the B. cinerea genome, the Arb2 subunit of the Argonaute complex was found to be present in the putative H3K14 deacetylase BcHda1 by NCBI B LAST comparison ( Figure 2A ).…”

Section: Resultsmentioning

confidence: 99%

Normal distribution of H3K9me3 occupancy co-mediated by histone methyltransferase BcDIM5 and histone deacetylase BcHda1 maintains stable ABA synthesis in Botrytis cinerea TB-31

Wei,

Shu,

Hou

et al. 2024

Front. Microbiol.

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Abscisic acid (ABA) is a conserved and important “sesquiterpene signaling molecule” widely distributed in different organisms with unique biological functions. ABA coordinates reciprocity and competition between microorganisms and their hosts. In addition, ABA also regulates immune and stress responses in plants and animals. Therefore, ABA has a wide range of applications in agriculture, medicine and related fields. The plant pathogenic ascomycete B. cinerea has been extensively studied as a model strain for ABA production. Nevertheless, there is a relative dearth of research regarding the regulatory mechanism governing ABA biosynthesis in B. cinerea. Here, we discovered that H3K9 methyltransferase BcDIM5 is physically associated with the H3K14 deacetylase BcHda1. Deletion of Bcdim5 and Bchda1 in the high ABA-producing B. cinerea TB-31 led to severe impairment of ABA synthesis. The combined analysis of RNA-seq and ChIP-seq has revealed that the absence of BcDIM5 and BcHda1 has resulted in significant global deficiencies in the normal distribution and level of H3K9me3 modification. In addition, we found that the cause of the decreased ABA production in the ΔBcdim5 and ΔBchda1 mutants was due to cluster gene repression caused by the emergence of hyper-H3K9me3 in the ABA gene cluster. We concluded that the ABA gene cluster is co-regulated by BcDIM5 and BcHda1, which are essential for the normal distribution of the B. cinerea TB-31 ABA gene cluster H3K9me3. This work expands our understanding of the complex regulatory network of ABA biosynthesis and provides a theoretical basis for genetic improvement of high-yielding ABA strains.

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Section: Resultsmentioning

confidence: 99%

Normal distribution of H3K9me3 occupancy co-mediated by histone methyltransferase BcDIM5 and histone deacetylase BcHda1 maintains stable ABA synthesis in Botrytis cinerea TB-31

Wei,

Shu,

Hou

et al. 2024

Front. Microbiol.

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“…For example, RNAi and H3K9me are coupled in fungi and plants ( 52 – 54 ), and DNA methylation can be coupled to H3K9me in fungi, plants, and mammals ( 55 – 58 ). Furthermore, evidence for nucleic acid sequence–independent coupling of histone H3 lysine 27 methylation and histone H2A lysine 119 monoubiquitination can be found in studies of mammals ( 59 ), and critically, mounting evidence for coupling of H3K9me and histone H3 lysine 14 monoubiquitination can be found in studies of native S. pombe heterochromatin ( 60 – 62 ).…”

Section: Discussionmentioning

confidence: 99%

Minimal requirements for the epigenetic inheritance of engineered silent chromatin domains

Yuan,

Moazed

2024

Proc. Natl. Acad. Sci. U.S.A.

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Mechanisms enabling genetically identical cells to differentially regulate gene expression are complex and central to organismal development and evolution. While gene silencing pathways involving DNA sequence–specific recruitment of histone-modifying enzymes are prevalent in nature, examples of sequence-independent heritable gene silencing are scarce. Studies of the fission yeast Schizosaccharomyces pombe indicate that sequence-independent propagation of heterochromatin can occur but requires numerous multisubunit protein complexes and their diverse activities. Such complexity has so far precluded a coherent articulation of the minimal requirements for heritable gene silencing by conventional in vitro reconstitution approaches. Here, we take an unconventional approach to defining these requirements by engineering sequence-independent silent chromatin inheritance in budding yeast Saccharomyces cerevisiae cells. The mechanism conferring memory upon these cells is remarkably simple and requires only two proteins, one that recognizes histone H3 lysine 9 methylation (H3K9me) and catalyzes the deacetylation of histone H4 lysine 16 (H4K16), and another that recognizes deacetylated H4K16 and catalyzes H3K9me. Together, these bilingual “read–write” proteins form an interdependent positive feedback loop that is sufficient for the transmission of DNA sequence–independent silent information over multiple generations.

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“…A similar interaction with H3K14ub has also been documented for SUV39H2 but not for G9a. [54,55] Besides, the Clr4 molecule itself contains many lysine residues that can be ubiquitinated. Without this modification at position K109, K110, K113, or K114, the enzyme can dimethylate but loses the ability to trimethylate H3K9 [56] (Figure 1).…”

Section: The Set Domainmentioning

confidence: 99%

Diversity and functional specialization of H3K9‐specific histone methyltransferases

Koryakov

2023

BioEssays

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Histone modifications play a critical role in the control over activities of the eukaryotic genome; among these chemical alterations, the methylation of lysine K9 in histone H3 (H3K9) is one of the most extensively studied. The number of enzymes capable of methylating H3K9 varies greatly across different organisms: in fission yeast, only one such methyltransferase is present, whereas in mammals, 10 are known. If there are several such enzymes, each of them must have some specific function, and they can interact with one another. Thus arises a complex system of interchangeability, “division of labor,” and contacts with each other and with diverse proteins. Histone methyltransferases specialize in the number of methyl groups that they attach and have different intracellular localizations as well as different distributions on chromosomes. Each also shows distinct binding to different types of sequences and has a specific set of nonhistone substrates.

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The histone H3K9M mutation synergizes with H3K14 ubiquitylation to selectively sequester histone H3K9 methyltransferase Clr4 at heterochromatin

Cited by 11 publications

References 51 publications

Normal distribution of H3K9me3 occupancy co-mediated by histone methyltransferase BcDIM5 and histone deacetylase BcHda1 maintains stable ABA synthesis in Botrytis cinerea TB-31

Normal distribution of H3K9me3 occupancy co-mediated by histone methyltransferase BcDIM5 and histone deacetylase BcHda1 maintains stable ABA synthesis in Botrytis cinerea TB-31

Minimal requirements for the epigenetic inheritance of engineered silent chromatin domains

Diversity and functional specialization of H3K9‐specific histone methyltransferases

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