Novel Structural and Functional Mode of a Knot Essential for RNA Binding Activity of the Esa1 Presumed Chromodomain

Shimojo, Hideaki; Sano, Norihiko; Moriwaki, Yoshihito; Okuda, Masahiko; Horikoshi, Masami; Nishimura, Yoshifumi

doi:10.1016/j.jmb.2008.03.021

Cited by 44 publications

(46 citation statements)

References 50 publications

(62 reference statements)

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“…TT and the Esa1 knotted Tudor domain, bind other DNA sequences besides methylated lysines (20,23). The 53BP1 TT Tudor domain 1, the key domain for DNA binding, has a pI of 9.8, whereas the pI of the Tudor domain 2 is 4.4, and the overall pI of 53BP1…”

Section: Resultsmentioning

confidence: 99%

“…TT and Esa1 knotted Tudor domain depends on multiple types of interactions, including hydrophobic, cation-, ring stacking, and hydrogen bond interactions (20,23). Rad9…”

Section: Structural Model Of the Rbbp1 Tudor Domain-dnamentioning

confidence: 99%

“…These three proteins have been proposed to play similar roles in DNA damage signaling and repair (21). DNA/RNA binding affinity is critical for the role of the Esa1 knotted Tudor domain (23). Some proteins, such as TDRD and TUDOR, have tandem Tudor domains, which cooperatively recognize combinational histone marks (24).…”

mentioning

confidence: 99%

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Retinoblastoma-binding Protein 1 Has an Interdigitated Double Tudor Domain with DNA Binding Activity

Gong

Wang

Perrett

et al. 2014

Journal of Biological Chemistry

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Background: Retinoblastoma-binding protein 1 (RBBP1), a tumor suppressor, has a Tudor domain with unknown function. Results: The Tudor domain adopts an interdigitated double Tudor structure with DNA binding activity. Conclusion:The Tudor domain of the RBBP1 family is a DNA binding module. Significance: Our research provides further structural insights into RBBP1 function and the diversity of Tudor domains.

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Section: Resultsmentioning

confidence: 99%

“…TT and Esa1 knotted Tudor domain depends on multiple types of interactions, including hydrophobic, cation-, ring stacking, and hydrogen bond interactions (20,23). Rad9…”

Section: Structural Model Of the Rbbp1 Tudor Domain-dnamentioning

confidence: 99%

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Retinoblastoma-binding Protein 1 Has an Interdigitated Double Tudor Domain with DNA Binding Activity

Gong

Wang

Perrett

et al. 2014

Journal of Biological Chemistry

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“…2D) and possibly catalytically inactive versions of the JOR/JmjC domain (Jacobs and Khorasanizadeh 2002;Maurer-Stroh et al 2003;Brehm et al 2004;Shimojo et al 2008). By far, chromolike domains constitute the most versatile class of methylated histone-binding domains, recognizing methylation at H3K4, H3K9, H3K27, H3K36, and H4K20.…”

Section: Protein Methylation-dependent Systemsmentioning

confidence: 99%

Protein and DNA Modifications: Evolutionary Imprints of Bacterial Biochemical Diversification and Geochemistry on the Provenance of Eukaryotic Epigenetics

Aravind

Burroughs

Zhang

et al. 2014

Cold Spring Harbor Perspectives in Biology

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Epigenetic information, which plays a major role in eukaryotic biology, is transmitted by covalent modifications of nuclear proteins (e.g., histones) and DNA, along with poorly understood processes involving cytoplasmic/secreted proteins and RNAs. The origin of eukaryotes was accompanied by emergence of a highly developed biochemical apparatus for encoding, resetting, and reading covalent epigenetic marks in proteins such as histones and tubulins. The provenance of this apparatus remained unclear until recently. Developments in comparative genomics show that key components of eukaryotic epigenetics emerged as part of the extensive biochemical innovation of secondary metabolism and intergenomic/interorganismal conflict systems in prokaryotes, particularly bacteria. These supplied not only enzymatic components for encoding and removing epigenetic modifications, but also readers of some of these marks. Diversification of these prokaryotic systems and subsequently eukaryotic epigenetics appear to have been considerably influenced by the great oxygenation event in the Earth's history.

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“…This might indicate that interaction with RNA might be a common feature that is necessary for MOF function conserved from yeast to flies. 44 The results mentioned above clearly showed that the roX RNAs are stable members of the MSL complex; they actually seem to be even more stably associated with the rest of the complex than MLE-the protein required for their stability and association with other MSL proteins in vivo. 40,45 Their stability, however is compromised in mutants with a single residue change that renders MLE incapable of hydrolyzing NTPs.…”

Section: Rna Independent Role Of Rox?mentioning

confidence: 91%

roX RNAs: Non-coding regulators of the male X chromosome in flies

Ilık

Akhtar²

2009

RNA Biology

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The roX RNAs represent one of the paradigm examples of large non-coding RNAs involved in chromatin regulation. Interestingly, roX genes have a dual life. The RNA product is part of the MSL complex required for dosage compensation of the male X chromosome in Drosophila while the genomic location is used as a binding platform for MSL complex assembly. In this review we discuss both aspects of roX function and propose an integrated model for possible mechanisms how these RNAs might be involved in epigenetic regulation of the male X chromosome.

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Novel Structural and Functional Mode of a Knot Essential for RNA Binding Activity of the Esa1 Presumed Chromodomain

Cited by 44 publications

References 50 publications

Retinoblastoma-binding Protein 1 Has an Interdigitated Double Tudor Domain with DNA Binding Activity

Retinoblastoma-binding Protein 1 Has an Interdigitated Double Tudor Domain with DNA Binding Activity

Protein and DNA Modifications: Evolutionary Imprints of Bacterial Biochemical Diversification and Geochemistry on the Provenance of Eukaryotic Epigenetics

roX RNAs: Non-coding regulators of the male X chromosome in flies

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