Binding of PHF1 Tudor to H3K36me3 enhances nucleosome accessibility

Musselman, Catherine A.; Gibson, Matthew D.; Hartwick, Erik W.; North, Justin A.; Gatchalian, Jovylyn; Poirier, Michael G.; Kutateladze, Tatiana G.

doi:10.1038/ncomms3969

Cited by 80 publications

(112 citation statements)

References 33 publications

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“…Similar phenomena were observed for other Royal superfamily modules; for example, compared with the chromodomain alone, the preformed complex of the MSL3 [29] or RBBP1 [28] chromodomain with DNA displayed enhanced binding ability to H4K20me1 or H4K20me3 peptides, respectively. In addition, the Tudor domain of PHF1 concomitantly interacts with both H3K36me3 and DNA of the H3K36me3-modified nucleosome core particle with in- creased binding ability [30]. In the case of the PWWP domain, binding affinity towards either histone peptide or DNA oligonucleotide is very weak, but it exhibits significantly enhanced binding affinity to methylated nucleosomes.…”

Section: Reviewmentioning

confidence: 98%

Structure and function of the nucleosome-binding PWWP domain

Min

2014

Trends in Biochemical Sciences

159

129

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Section: Reviewmentioning

confidence: 98%

Structure and function of the nucleosome-binding PWWP domain

Min

2014

Trends in Biochemical Sciences

159

129

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“…It adds weight to the expectation that we will also find physical coupling of the opposite combination of activities, histone deactivation and repression, which are effectively coordinated in many systems (3,4,6,45). Identification of the H3K36me3 demethylase at FLC will allow its physical association with PRC2 to be investigated.…”

Section: Elf6 and Jumonji Domain-containing Protein 13 Are Partiallymentioning

confidence: 99%

Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC

Yang

Howard

Dean

2016

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

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Establishment and maintenance of gene expression states is central to development and differentiation. Transcriptional and epigenetic mechanisms interconnect in poorly understood ways to determine these states. We explore these mechanisms through dissection of the regulation of Arabidopsis thaliana FLOWERING LOCUS C (FLC). FLC can be present in a transcriptionally active state marked by H3K36me3 or a silent state marked by H3K27me3. Here, we investigate the trans factors modifying these opposing histone states and find a physical coupling in vivo between the H3K36 methyltransferase, SDG8, and the H3K27me3 demethylase, ELF6. Previous modeling has predicted this coupling would exist as it facilitates bistability of opposing histone states. We also find association of SDG8 with the transcription machinery, namely RNA polymerase II and the PAF1 complex. Delivery of the active histone modifications is therefore likely to be through transcription at the locus. SDG8 and ELF6 were found to influence the localization of each other on FLC chromatin, showing the functional importance of the interaction. In addition, both influenced accumulation of the associated H3K27me3 and H3K36me3 histone modifications at FLC. We propose the physical coupling of activation and derepression activities coordinates transcriptional activity and prevents ectopic silencing.epigenetic regulation | histone modifications | histone methyltransferase | histone demethylase | FLOWERING LOCUS C C hromatin-based transcriptional activity is particularly important in multicellular organisms, where cells differentiate into very different developmental states. Transcriptional states are induced by internal developmental signals or triggered by environmental conditions and are then epigenetically maintained through many cell divisions. Considerable evidence suggests that opposing histone modifications mark different transcriptional states (1-6). However, there is still great debate as to how histone-based transcriptional states are initially established and maintained through development (7,8). We used Arabidopsis FLOWERING LOCUS C (FLC) as a model gene to explore histone-based transcriptional regulation and epigenetic memory. Local chromatin states are critical for quantitatively controlling FLC expression (9). Active FLC expression requires functional FRIGIDA (FRI) and a set of histone modifying Trithorax homologs, Complex Proteins Associated with Set1 (COMPASS), RNA polymerase II Associated Factor 1 complex (PAF1C), and SET DOMAIN GROUP 8 (SDG8), the major H3K36 methyltransferase (10-17). Repression of FLC requires either the autonomous pathway, which coordinately influences transcriptional initiation and elongation with associated chromatin modulation, or vernalization, the cold-induced Polycomb silencing (18-21). Both of these involve accumulation of high levels of H3K27me3 at FLC (20-22). A series of FLC antisense transcripts (COOLAIR) contribute to these repression pathways (18,(23)(24)(25)(26) Opposing H3K36me3 and H3K27me3 states are particularly ...

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“…Importantly, the Ioc4–H3K36me3 interaction cannot be detected when tested with methylated peptides alone [50,51], and a similar result is observed for the association of the Pdp1 PWWP domain with H4K20me3-nucleosomes [52]. A recent study of the PHF1 Tudor domain also reveals multivalent contacts with H3K36me3 and nucleosomal DNA [53]. In contrast to the PWWP domain this association is far more driven by interaction with the methylated mark itself [53].…”

Section: Contacts Outside the Methylated Histone Tailmentioning

confidence: 83%

Towards understanding methyllysine readout

Musselman

Khorasanizadeh

Kutateladze

2014

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

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Lysine methylation is the most versatile covalent posttranslational modification (PTM) found in histones and non-histone proteins. Over the past decade a number of methyllysine-specific readers have been discovered and their interactions with histone tails have been structurally and biochemically characterized. More recently innovative experimental approaches have emerged that allow for studying reader interactions in the context of the full nucleosome and nucleosomal arrays. New studies reveal various reader-nucleosome contacts outside the methylated histone tail, thus offering a better model for the association of histone readers to chromatin and broadening our understanding of the functional implications of these interactions. In this review we give a brief overview of the known mechanisms of histone lysine methylation readout, summarize progress recently made in exploring interactions with methylated nucleosomes, and discuss the latest advances in the development of small molecule inhibitors of the methyllysine-specific readers.

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Binding of PHF1 Tudor to H3K36me3 enhances nucleosome accessibility

Cited by 80 publications

References 33 publications

Structure and function of the nucleosome-binding PWWP domain

Structure and function of the nucleosome-binding PWWP domain

Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC

Towards understanding methyllysine readout

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