Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 6 de 6
Filter
Add more filters










Database
Language
Publication year range
1.
Nat Genet ; 56(6): 1193-1202, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38744974

ABSTRACT

Polycomb repressive complex 2 (PRC2) interacts with RNA in cells, but there is no consensus on how RNA regulates PRC2 canonical functions, including chromatin modification and the maintenance of transcription programs in lineage-committed cells. We assayed two separation-of-function mutants of the PRC2 catalytic subunit EZH2, defective in RNA binding but functional in methyltransferase activity. We find that part of the RNA-binding surface of EZH2 is required for chromatin modification, yet this activity is independent of RNA. Mechanistically, the RNA-binding surface within EZH2 is required for chromatin modification in vitro and in cells, through interactions with nucleosomal DNA. Contrarily, an RNA-binding-defective mutant exhibited normal chromatin modification activity in vitro and in lineage-committed cells, accompanied by normal gene repression activity. Collectively, we show that part of the RNA-binding surface of EZH2, rather than the RNA-binding activity per se, is required for the histone methylation in vitro and in cells, through interactions with the substrate nucleosome.


Subject(s)
Chromatin , Enhancer of Zeste Homolog 2 Protein , Histones , Nucleosomes , RNA , Enhancer of Zeste Homolog 2 Protein/metabolism , Enhancer of Zeste Homolog 2 Protein/genetics , Nucleosomes/metabolism , RNA/metabolism , RNA/genetics , Humans , Chromatin/metabolism , Chromatin/genetics , Histones/metabolism , Histones/genetics , Protein Binding , Methylation , Animals , Polycomb Repressive Complex 2/metabolism , Polycomb Repressive Complex 2/genetics , Mice , Mutation
2.
Cell Rep ; 43(3): 113858, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38416645

ABSTRACT

RNA has been implicated in the recruitment of chromatin modifiers, and previous studies have provided evidence in favor and against this idea. RNase treatment of chromatin is commonly used to study RNA-mediated regulation of chromatin modifiers, but the limitations of this approach remain unclear. RNase A treatment during chromatin immunoprecipitation (ChIP) reduces chromatin occupancy of the H3K27me3 methyltransferase Polycomb repressive complex 2 (PRC2). This led to suggestions of an "RNA bridge" between PRC2 and chromatin. Here, we show that RNase A treatment during ChIP causes the apparent loss of all facultative heterochromatin, including both PRC2 and H3K27me3 genome-wide. We track this observation to a gain of DNA from non-targeted chromatin, sequenced at the expense of DNA from facultative heterochromatin, which reduces ChIP signals. Our results emphasize substantial limitations in using RNase A treatment for mapping RNA-dependent chromatin occupancy and invalidate conclusions that were previously established for PRC2 based on this assay.


Subject(s)
Chromatin , Polycomb Repressive Complex 2 , Polycomb Repressive Complex 2/genetics , Polycomb Repressive Complex 2/metabolism , Histones/genetics , RNA/genetics , Heterochromatin , Ribonuclease, Pancreatic , Artifacts , DNA
3.
Proc Natl Acad Sci U S A ; 118(41)2021 10 12.
Article in English | MEDLINE | ID: mdl-34615715

ABSTRACT

Rotavirus genomes are distributed between 11 distinct RNA molecules, all of which must be selectively copackaged during virus assembly. This likely occurs through sequence-specific RNA interactions facilitated by the RNA chaperone NSP2. Here, we report that NSP2 autoregulates its chaperone activity through its C-terminal region (CTR) that promotes RNA-RNA interactions by limiting its helix-unwinding activity. Unexpectedly, structural proteomics data revealed that the CTR does not directly interact with RNA, while accelerating RNA release from NSP2. Cryo-electron microscopy reconstructions of an NSP2-RNA complex reveal a highly conserved acidic patch on the CTR, which is poised toward the bound RNA. Virus replication was abrogated by charge-disrupting mutations within the acidic patch but completely restored by charge-preserving mutations. Mechanistic similarities between NSP2 and the unrelated bacterial RNA chaperone Hfq suggest that accelerating RNA dissociation while promoting intermolecular RNA interactions may be a widespread strategy of RNA chaperone recycling.


Subject(s)
Genome, Viral/genetics , RNA Folding/genetics , RNA, Viral/genetics , Rotavirus/growth & development , Viral Genome Packaging/genetics , Viral Nonstructural Proteins/metabolism , Cryoelectron Microscopy , Models, Molecular , Molecular Chaperones/metabolism , RNA-Binding Proteins/metabolism , Ribonucleoproteins/metabolism , Rotavirus/genetics , Rotavirus/metabolism
4.
Bioinformatics ; 36(22-23): 5530-5532, 2021 Apr 01.
Article in English | MEDLINE | ID: mdl-33346827

ABSTRACT

SUMMARY: Unbiased detection of protein-protein and protein-RNA interactions within ribonucleoprotein complexes are enabled through crosslinking followed by mass spectrometry. Yet, different methods detect different types of molecular interactions and therefore require the usage of different software packages with limited compatibility. We present crisscrosslinkeR, an R package that maps both protein-protein and protein-RNA interactions detected by different types of approaches for crosslinking with mass spectrometry. crisscrosslinkeR produces output files that are compatible with visualization using popular software packages for the generation of publication-quality figures. AVAILABILITY AND IMPLEMENTATION: crisscrosslinkeR is a free and open-source package, available through GitHub: github.com/egmg726/crisscrosslinker. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

5.
Nat Struct Mol Biol ; 26(3): 237-247, 2019 03.
Article in English | MEDLINE | ID: mdl-30833789

ABSTRACT

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that maintains cell identity during development in multicellular organisms by marking repressed genes and chromatin domains. In addition to four core subunits, PRC2 comprises multiple accessory subunits that vary in their composition during cellular differentiation and define two major holo-PRC2 complexes: PRC2.1 and PRC2.2. PRC2 binds to RNA, which inhibits its enzymatic activity, but the mechanism of RNA-mediated inhibition of holo-PRC2 is poorly understood. Here we present in vivo and in vitro protein-RNA interaction maps and identify an RNA-binding patch within the allosteric regulatory site of human and mouse PRC2, adjacent to the methyltransferase center. RNA-mediated inhibition of holo-PRC2 is relieved by allosteric activation of PRC2 by H3K27me3 and JARID2-K116me3 peptides. Both holo-PRC2.1 and holo-PRC2.2 bind RNA, providing a unified model to explain how RNA and allosteric stimuli antagonistically regulate the enzymatic activity of PRC2.


Subject(s)
Histones/metabolism , Polycomb Repressive Complex 2/metabolism , RNA-Binding Proteins/metabolism , RNA/metabolism , Animals , Binding Sites/physiology , Cells, Cultured , Embryonic Stem Cells/metabolism , Humans , Methylation , Mice , Protein Interaction Maps/physiology
6.
Neuropsychopharmacology ; 41(3): 695-703, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26119471

ABSTRACT

Brain imaging has revealed links between prefrontal activity during risky decision-making and striatal dopamine receptors. Specifically, striatal dopamine D2-like receptor availability is correlated with risk-taking behavior and sensitivity of prefrontal activation to risk in the Balloon Analogue Risk Task (BART). The extent to which these associations, involving a single neurochemical measure, reflect more general effects of dopaminergic functioning on risky decision making, however, is unknown. Here, 65 healthy participants provided genotypes and performed the BART during functional magnetic resonance imaging. For each participant, dopamine function was assessed using a gene composite score combining known functional variation across five genes involved in dopaminergic signaling: DRD2, DRD3, DRD4, DAT1, and COMT. The gene composite score was negatively related to dorsolateral prefrontal cortical function during risky decision making, and nonlinearly related to earnings on the task. Iterative permutations of all possible allelic variations (7777 allelic combinations) was tested on brain function in an independently defined region of the prefrontal cortex and confirmed empirical validity of the composite score, which yielded stronger association than 95% of all other possible combinations. The gene composite score also accounted for a greater proportion of variability in neural and behavioral measures than the independent effects of each gene variant, indicating that the combined effects of functional dopamine pathway genes can provide a robust assessment, presumably reflecting the cumulative and potentially interactive effects on brain function. Our findings support the view that the links between dopaminergic signaling, prefrontal function, and decision making vary as a function of dopamine signaling capacity.


Subject(s)
Decision Making/physiology , Dopamine/metabolism , Genetic Variation , Prefrontal Cortex/physiology , Risk-Taking , Adolescent , Adult , Brain Mapping , Catechol O-Methyltransferase/genetics , Dopamine Plasma Membrane Transport Proteins/genetics , Female , Humans , Magnetic Resonance Imaging , Male , Middle Aged , Neuropsychological Tests , Receptors, Dopamine D2/genetics , Receptors, Dopamine D3/genetics , Receptors, Dopamine D4/genetics , Young Adult
SELECTION OF CITATIONS
SEARCH DETAIL
...