The <i>Arabidopsis</i> Histone Methyltransferase SUVR4 Binds Ubiquitin via a Domain with a Four-Helix Bundle Structure

Rahman, Mohummad Aminur; Kristiansen, Per Eugen; Veiseth, Silje Veie; Andersen, Jan Terje; Yap, Kyoko L.; Zhou, Ming‐Ming; Sandlie, Inger; Thorstensen, Tage; Aalen, Reidunn B.

doi:10.1021/bi401436h

Cited by 9 publications

(9 citation statements)

References 53 publications

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“…Because of the large number of histone methyltransferases in many plant genomes (10), the histone methylation process has been extensively investigated (11,12). The effects of histone methylation are variable depending on the position of the modified residue and the number of methyl groups added (13). In general, methylation of histone H3 lysine 4 (H3K4) and H3K36 is associated with transcriptional activation (14), whereas methylation of H3K9, H3K27, and H4K20 is characteristic of repressive epigenetic marks (15).…”

Section: Introductionmentioning

confidence: 99%

Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation

2017

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Cellular dedifferentiation, the transition of differentiated somatic cells to pluripotent stem cells, ensures developmental plasticity and contributes to wound healing in plants. Wounding induces cells to form a mass of unorganized pluripotent cells called callus at the wound site. Explanted cells can also form callus tissues in vitro. Reversible cellular differentiation-dedifferentiation processes in higher eukaryotes are controlled mainly by chromatin modifications. We demonstrate that ARABIDOPSIS TRITHORAX-RELATED 2 (ATXR2), a histone lysine methyltransferase that promotes the accumulation of histone H3 proteins that are trimethylated on lysine 36 (H3K36me3) during callus formation, promotes early stages of cellular dedifferentiation through activation of () genes. The genes of are activated during cellular dedifferentiation to enhance the formation of callus. Leaf explants from mutants exhibited a reduced ability to form callus and a substantial reduction in gene expression. ATXR2 bound to the promoters of genes and was required for the deposition of H3K36me3 at these promoters. ATXR2 was recruited to promoters by the transcription factors AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19. Leaf explants from double mutants were defective in callus formation and showed reduced H3K36me3 accumulation at promoters. Genetic analysis provided further support that ARF7 and ARF19 were required for the ability of ATXR2 to promote the expression of genes. These observations indicate that the ATXR2-ARF-LBD axis is key for the epigenetic regulation of callus formation in.

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Section: Introductionmentioning

confidence: 99%

Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation

2017

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“…SUVR4 participates in the epigenetic defense mechanism by introducing H3K9me3 marks to repress potentially harmful transposon activity [93]. SUVR4 specifically converts H3K9me1 into H3K9me3 at transposons and pseudogenes within the euchromatin [93,94], but SUVR1 and SUVR2 show no detected histone methyltransferase activity in vitro [92,95]. In this study, D.…”

Section: Suvr Subclassmentioning

confidence: 72%

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum

Chen

Qiu

Huang

et al. 2020

Preprint

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Background: Dendrobium catenatum used as a precious Chinese herbal medicine is a kind of epiphytic orchid plant which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown. Results: In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris . We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su(var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually have wide but distinguished expression in different tissues and organs. Finally, environmental stresses examination showed the expression of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 is closely associated with drought-recovery treatment, the expression of DcSUVH5a , DcATXR5a and DcSUVR14a is significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock. Conclusions: This study systematically identifies and classifies SDG genes in orchid plant D. catenatum , indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchid.

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“…SUVR4 participates in the epigenetic defense mechanism by introducing H3K9me3 marks to repress potentially harmful transposon activity [102]. SUVR4 specifically converts H3K9me1 into H3K9me3 at transposons and pseudogenes within the euchromatin; SUVR4 binds to ubiquitin by its N-terminal WIYLD domain, facilitating its conversion from a strict di-methylase into a di-/tri-methylase in vitro [102,103]. SUVR1 and SUVR2 can also interact with ubiquitin via their WIYLD domains [103], but show no detected histone methyltransferase activity in vitro [101,104].…”

Section: Suvr Subclassmentioning

confidence: 99%

“…SUVR4 specifically converts H3K9me1 into H3K9me3 at transposons and pseudogenes within the euchromatin; SUVR4 binds to ubiquitin by its N-terminal WIYLD domain, facilitating its conversion from a strict di-methylase into a di-/tri-methylase in vitro [102,103]. SUVR1 and SUVR2 can also interact with ubiquitin via their WIYLD domains [103], but show no detected histone methyltransferase activity in vitro [101,104]. This finding indicates that SUVR1/2 function in transcriptional silencing is independent of ubiquitin binding and histone methyltransferase activity.…”

Section: Suvr Subclassmentioning

confidence: 99%

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum

Chen

Qiu

Huang

et al. 2019

Preprint

View full text Add to dashboard Cite

Background: Dendrobium catenatum used as a precious Chinese herbal medicine is a kind of epiphytic orchid plant which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown.Results: In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris .We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su(var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNAseq derived expression profiling showed that DcSDG proteins usually have wide but distinguished expression in different tissues and organs. Finally, environmental stresses examination showed the expression of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 is closely associated with drought-recovery treatment, the expression of DcSUVH5a , DcATXR5a and DcSUVR14a is significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock.Conclusions: This study systematically identifies and classifies SDG genes in orchid plant D. catenatum , indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchid.3

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The Arabidopsis Histone Methyltransferase SUVR4 Binds Ubiquitin via a Domain with a Four-Helix Bundle Structure

Cited by 9 publications

References 53 publications

Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation

Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum

Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum

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