Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette

Li, Sisi; Yang, Zhenlin; Du, Xuan; Li, Rui; Wilkinson, Alex W.; Gozani, Or; Jacobsen, Steven E.; Patel, Dinshaw J.; Du, Jiamu

doi:10.1016/j.str.2016.01.004

Cited by 19 publications

(13 citation statements)

References 31 publications

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“…Both readers create the binding site and surround the same region of the peptide. The extensive set of hydrogen bonds formed between BAH–PHD and the side chains of the histone R2, T3, and K4 residues suggests that modification of these residues would prevent binding, and this has been confirmed experimentally 47 .…”

Section: Crosstalk Of Paired Readersmentioning

confidence: 69%

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Insights into newly discovered marks and readers of epigenetic information

2016

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The field of chromatin biology has been advancing at an accelerated pace. Recent discoveries of previously uncharacterized sites and types of post-translational modifications (PTMs) and the identification of new sets of proteins responsible for the deposition, removal, and reading of these marks continue raising the complexity of an already exceedingly complicated biological phenomenon. In this Perspective article we examine the biological importance of new types and sites of histone PTMs and summarize the molecular mechanisms of chromatin engagement by newly discovered epigenetic readers. We also highlight the imperative role of structural insights in understanding PTM–reader interactions and discuss future directions to enhance the knowledge of PTM readout.

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Section: Crosstalk Of Paired Readersmentioning

confidence: 69%

“…The ORC1b PHD finger sequence is embedded in the sequence of BAH, and this unique assembly of readers recognizes unmodified histone H3 tail (residues 1–8) 47 . In the BAH–PHD–H3 complex, the peptide adopts an extended conformation and occupies a long groove at the interface of the readers (Fig.…”

Section: Crosstalk Of Paired Readersmentioning

confidence: 99%

Insights into newly discovered marks and readers of epigenetic information

2016

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“…Maize ZMET2, mouse ORC1, and Arabidopsis ORC1b utilize their BAH domains to recognize H3K9me2, H4K20me2, and unmodified H3, respectively (Supplementary Fig. 5a–c ) 29 , 47 , 48 . Here, we revealed that SHL BAH is engaged in H3K27me3 recognition, similar to the BAH domain of BAHD1 protein 49 .…”

Section: Discussionmentioning

confidence: 99%

“…The Arabidopsis ORC1b BAH domain together with a PHD finger combinatorially recognize unmodified H3 using a different interface (Supplementary Fig. 5c ) 47 , suggesting a distinct histone binding interface other than the aromatic cage.…”

Section: Discussionmentioning

confidence: 99%

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL

Qian

Scheid

et al. 2018

Nat Commun

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The ability of a cell to dynamically switch its chromatin between different functional states constitutes a key mechanism regulating gene expression. Histone mark “readers” display distinct binding specificity to different histone modifications and play critical roles in regulating chromatin states. Here, we show a plant-specific histone reader SHORT LIFE (SHL) capable of recognizing both H3K27me3 and H3K4me3 via its bromo-adjacent homology (BAH) and plant homeodomain (PHD) domains, respectively. Detailed biochemical and structural studies suggest a binding mechanism that is mutually exclusive for either H3K4me3 or H3K27me3. Furthermore, we show a genome-wide co-localization of SHL with H3K27me3 and H3K4me3, and that BAH-H3K27me3 and PHD-H3K4me3 interactions are important for SHL-mediated floral repression. Together, our study establishes BAH-PHD cassette as a dual histone methyl-lysine binding module that is distinct from others in recognizing both active and repressive histone marks.

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“…Thus, it is likely that the Tudor-SN interface recognition mode is conserved among at least a subgroup of eTudor domain proteins. Notably, the interface of BAH-PHD or Ankyrin-Chromo has also been reported to recognize unmodified ligands (24,25). For germline-specific TDRD family proteins, methylation-independent and methylation-dependent eTudor-PIWI interactions may act in a cooperative temporal-spatial fashion and together facilitate the formation of the piRNA machinery and optimal biogenesis of piRNAs.…”

Section: Significance Of Arginine Methylation-independent Tdrd2-piwil1mentioning

confidence: 99%

Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2

Liu

Izumi

Huang

et al. 2017

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

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The P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway plays a central role in transposon silencing and genome protection in the animal germline. A family of Tudor domain proteins regulates the piRNA pathway through direct Tudor domain-PIWI interactions. Tudor domains are known to fulfill this function by binding to methylated PIWI proteins in an arginine methylation-dependent manner. Here, we report a mechanism of methylation-independent Tudor domain-PIWI interaction. Unlike most other Tudor domains, the extended Tudor domain of mammalian Tudor domain-containing protein 2 (TDRD2) preferentially recognizes an unmethylated arginine-rich sequence from PIWI-like protein 1 (PIWIL1). Structural studies reveal an unexpected Tudor domain-binding mode for the PIWIL1 sequence in which the interface of Tudor and staphylococcal nuclease domains is primarily responsible for PIWIL1 peptide recognition. Mutations disrupting the TDRD2-PIWIL1 interaction compromise piRNA maturation via 3'-end trimming in vitro. Our work presented here reveals the molecular divergence of the interactions between different Tudor domain proteins and PIWI proteins.

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Structural Basis for the Unique Multivalent Readout of Unmodified H3 Tail by Arabidopsis ORC1b BAH-PHD Cassette

Cited by 19 publications

References 31 publications

Insights into newly discovered marks and readers of epigenetic information

Insights into newly discovered marks and readers of epigenetic information

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL

Structural basis for arginine methylation-independent recognition of PIWIL1 by TDRD2

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