Structural dynamics of protein lysine methylation and demethylation

Cheng, Xiaodong; Zhang, Xing

doi:10.1016/j.mrfmmm.2006.05.041

Cited by 65 publications

(36 citation statements)

References 116 publications

(160 reference statements)

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“…In addition to its role in transcriptional regulation, methylation has also been linked to heterochromatin formation, X-chromosome inactivation, DNA repair, RNA processing, and nucleo-cytoplasmic localization (245,248). Histone methylation is catalyzed by a group of histone methyltransferases (HMTases), and they are primarily classified into either lysine-specific (HMKT) or arginine-specific (PRMT) methyltransferases (245,249).…”

Section: Figmentioning

confidence: 99%

“…3) (249). Many SET domain-containing methyltransferases that target site-specific lysines in histones have been identified and characterized (248).…”

Section: Figmentioning

confidence: 99%

“…S15 in the supplemental material) (TR_62964, TA_291656, and TV_163714; TR_22117, TA_229470, and TV_ 47924) that remove methyl groups from H3K4me3 in yeast, plants, and animals (260)(261)(262). Like their homologs in yeast, N. crassa, animals, and plants, the architecture of Trichoderma JARID-like proteins present a JmjN domain, a JmjC domain, and a C5HC2 domain (249,260,262), but only one presents a PHD and a PLU-1 domain (see Fig. S15).…”

Section: Figmentioning

confidence: 99%

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The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Schmoll

Dattenböck

Carreras-Villaseñor

et al. 2016

Microbiol Mol Biol Rev

165

195

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SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.

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Section: Figmentioning

confidence: 99%

“…3) (249). Many SET domain-containing methyltransferases that target site-specific lysines in histones have been identified and characterized (248).…”

Section: Figmentioning

confidence: 99%

Section: Figmentioning

confidence: 99%

See 1 more Smart Citation

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Schmoll

Dattenböck

Carreras-Villaseñor

et al. 2016

Microbiol Mol Biol Rev

165

195

View full text Add to dashboard Cite

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“…Hypoxia may additionally mediate rapid control of these histone and protein modifiers by directly altering the reaction components of their enzymatic processes. Both amine oxidases and JmjC-domain proteins demethylate by oxidation or hydroxylation, processes directly affected under hypoxia [21]. One potential mechanism driving increased H3K4me3 may be hypoxia-induced inactivation of H3K4me3-specfic histone demethylases, which utilize molecular oxygen during enzymatic removal of methyl groups [22][23][24].…”

Section: Hypoxia-induced Gene-specific Histone Modificationsmentioning

confidence: 99%

Hypoxia induces a novel signature of chromatin modifications and global repression of transcription

Johnson¹,

Denko²,

Barton³

2008

Mutation Research/Fundamental and Molecular Mechanisms of Mutag

236

207

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Tumor cells respond to the harsh hypoxic microenvironment, in part, by transcriptional regulation of specific target genes. We found that hypoxia-mediated activation of selected genes occurs amidst widespread repression of transcription that is neither cell type-specific nor HIF-1-dependent. Despite overall repression, hypoxia induces a pool of histone modifications typically associated with transcriptional activation or repression. Chromatin immunoprecipitation analyses showed that this global mixture of hypoxia-modified histones is sorted in a gene-specific manner to correlate with transcriptional response to hypoxia. Exceptions to this were unexpected increases in H3K4me3 levels, typically associated with transcriptional activation, and decreased H3K27me3 levels, generally a marker of transcriptional silencing, at core promoters of both hypoxia-activated andrepressed genes. These data suggest that a novel signature of chromatin modifications is induced under hypoxic stress, which may play a role in gene regulatory switches active in proliferating tumor cells undergoing cycles of hypoxia and reoxygenation.

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“…They each contain a conserved catalytic subunit, EZH2 in humans or E(Z) in flies, which contains the signature SET domain that provides the methyltransferase active site [17]. Structure determinations of other SET domains have revealed an unusual "thread-theneedle" structure, called a pseudoknot ( [18,19] for reviews). The pseudoknot is formed by juxtaposition of two conserved peptide motifs within the SET domain, with one peptide inserted through the loop created by the other.…”

Section: Molecular Biology Of the Ezh2 Histone Methyltransferasementioning

confidence: 99%

Histone Methylation and Epigenetic Silencing in Breast Cancer

Simon¹,

Lange²

2008

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Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations and Reports (0704-0188), 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302. Respondents should be aware that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. REPORT DATE (DD-MM-YYYY) 01-07-2008 REPORT TYPE Annual DATES COVERED (From -To PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBERUniversity of Minnesota Minneapolis, MN 55455-2070 SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR'S ACRONYM(S) U.S. Army Medical Research and Materiel Command Fort Detrick, Maryland 21702-5012 SPONSOR/MONITOR'S REPORT NUMBER(S) DISTRIBUTION / AVAILABILITY STATEMENTApproved for Public Release; Distribution Unlimited SUPPLEMENTARY NOTES ABSTRACTThe purpose of this research is to investigate the role of a chromatin-modifying enzyme, called EZH2, in breast cancer epigenetics and to develop strategies to identify chemical inhibitors of this enzyme. EZH2 is a histone methyltransferase which modifies lysine-27 of histone H3, an epigenetic mark which is generally linked to gene silencing and is implicated in tumor suppressor silencing during breast cancer progression. Progress on this project includes: 1) Identification of target genes that are directly silenced by EZH2 in breast cancer cells and 2) Mapping of EZH2 binding sites within the chromatin of one such target gene. This mapping defines subregions of regulatory DNA likely to contain response elements that mediate EZH2 silencing. The delimitation and characterization of an EZH2 response element is required in the plan for engineering a breast cancer cell-based bioassay to screen for EZH2 inhibitors. These inhibitors provide important drug compounds to test as part of emerging epigenetic therapies to combat cancer. SUBJECT TERMS IntroductionThis research project is to investigate a chromatin-modifying enzyme, called EZH2, which is implicated in epigenetic modifications that contribute to breast cancer progression (Bracken et al. 2003;Kleer et al. 2003;Raaphorst et al. 2003;Cha et al. 2005;Bachmann et al. 2006;Ding et al. 2006). EZH2 is a histone methyltransferase that modifies histone H3 on lysine-27 (Cao et al. 2002;Kuzmichev et al. 2002), which is a chromatin modification linked to gene silencing . The purposes of this research are to 1) reveal basic mechanisms and conse...

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Structural dynamics of protein lysine methylation and demethylation

Cited by 65 publications

References 116 publications

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Hypoxia induces a novel signature of chromatin modifications and global repression of transcription

Histone Methylation and Epigenetic Silencing in Breast Cancer

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