RNAs — Physical and functional modulators of chromatin reader proteins

Hiragami-Hamada, Kyoko; Fischle, Wolfgang

doi:10.1016/j.bbagrm.2014.03.015

Cited by 12 publications

(9 citation statements)

References 59 publications

(117 reference statements)

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“…The CD is a highly conserved protein module most recognized for targeting methylated histone tails ( Blus et al, 2011 ; Fischle et al, 2003 ). Although several lines of evidence suggest that the CD binds DNA and RNA in addition to targeting methylated histones, its biological relevance and physiological roles are poorly understood ( Hiragami-Hamada and Fischle, 2014 ). In this study, we demonstrated that Suv39h1-CD not only recognizes H3K9me3, but also binds RNA and DNA (with a higher affinity to ssRNA than to dsDNA), indicating that RNA may also be crucial for Suv39h1 recruitment/function.…”

Section: Discussionmentioning

confidence: 99%

Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly

Shirai

Kawaguchi

Shimojo

et al. 2017

eLife

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SUV39H is the major histone H3 lysine 9 (H3K9)-specific methyltransferase that targets pericentric regions and is crucial for assembling silent heterochromatin. SUV39H recognizes trimethylated H3K9 (H3K9me3) via its chromodomain (CD), and enriched H3K9me3 allows SUV39H to target specific chromosomal regions. However, the detailed targeting mechanisms, especially for naïve chromatin without preexisting H3K9me3, are poorly understood. Here we show that Suv39h1’s CD (Suv39h1-CD) binds nucleic acids, and this binding is important for its function in heterochromatin assembly. Suv39h1-CD had higher binding affinity for RNA than DNA, and its ability to bind nucleic acids was independent of its H3K9me3 recognition. Suv39h1 bound major satellite RNAs in vivo, and knockdown of major satellite RNAs lowered Suv39h1 retention on pericentromere. Suv39h1 mutational studies indicated that both the nucleic acid–binding and H3K9me–binding activities of Suv39h1-CD were crucial for its pericentric heterochromatin assembly. These results suggest that chromatin-bound RNAs contribute to creating SUV39H’s target specificity.DOI: http://dx.doi.org/10.7554/eLife.25317.001

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Section: Discussionmentioning

confidence: 99%

Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly

Shirai

Kawaguchi

Shimojo

et al. 2017

eLife

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“…These interactions play important roles in the demarcation of chromatin domains, establishment of specific regional chromatin structures, and regulation of gene expression (Bonasio et al 2010;Smolle et al 2013;Hiragami-Hamada and Fischle 2014) and further highlight the importance of associated factor-mediated processes in the targeting of histone modifiers.…”

Section: Conflicting Reports On Specificity Of Histone Modifiersmentioning

confidence: 99%

Histone target selection within chromatin: an exemplary case of teamwork

2014

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Histone modifiers like acetyltransferases, methyltransferases, and demethylases are critical regulators of most DNA-based nuclear processes, de facto controlling cell cycle progression and cell fate. These enzymes perform very precise post-translational modifications on specific histone residues, which in turn are recognized by different effector modules/proteins. We now have a better understanding of how these enzymes exhibit such specificity. As they often reside in multisubunit complexes, they use associated factors to target their substrates within chromatin structure and select specific histone mark-bearing nucleosomes. In this review, we cover the current understanding of how histone modifiers select their histone targets. We also explain how different experimental approaches can lead to conflicting results about the histone specificity and function of these enzymes.

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“…Early discoveries supported a notion that lncRNA regulate transcription via chromatin modulations 33 . Additionally, several lncRNAs have been found to target directly or indirectly on specific transcription factors 34 .…”

Section: Functional Diversity Of Immune-related Lncrnasmentioning

confidence: 94%

Functional diversity of long non-coding RNAs in immune regulation

Geng

Tan

2016

Genes & Diseases

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Precise and dynamic regulation of gene expression is a key feature of immunity. In recent years, rapid advances in transcriptome profiling analysis have led to recognize long non-coding RNAs (lncRNAs) as an additional layer of gene regulation context. In the immune system, lncRNAs are found to be widely expressed in immune cells including monocytes, macrophages, dendritic cells (DC), neutrophils, T cells and B cells during their development, differentiation and activation. However, the functional importance of immune-related lncRNAs is just emerging to be characterized. In this review, we discuss the up-to-date knowledge of lncRNAs in immune regulation.

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RNAs — Physical and functional modulators of chromatin reader proteins

Cited by 12 publications

References 59 publications

Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly

Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly

Histone target selection within chromatin: an exemplary case of teamwork

Functional diversity of long non-coding RNAs in immune regulation

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