scholarly journals Histone arginine methylations: their roles in chromatin dynamics and transcriptional regulation

2009 ◽  
Vol 29 (2) ◽  
pp. 131-141 ◽  
Author(s):  
Michael Litt ◽  
Yi Qiu ◽  
Suming Huang

PRMTs (protein arginine N-methyltransferases) specifically modify the arginine residues of key cellular and nuclear proteins as well as histone substrates. Like lysine methylation, transcriptional repression or activation is dependent upon the site and type of arginine methylation on histone tails. Recent discoveries imply that histone arginine methylation is an important modulator of dynamic chromatin regulation and transcriptional controls. However, under the shadow of lysine methylation, the roles of histone arginine methylation have been under-explored. The present review focuses on the roles of histone arginine methylation in the regulation of gene expression, and the interplays between histone arginine methylation, histone acetylation, lysine methylation and chromatin remodelling factors. In addition, we discuss the dynamic regulation of arginine methylation by arginine demethylases, and how dysregulation of PRMTs and their activities are linked to human diseases such as cancer.

2020 ◽  
Vol 48 (6) ◽  
pp. 2956-2968 ◽  
Author(s):  
Fan Liu ◽  
Ye Xu ◽  
Xiaoqing Lu ◽  
Pierre-Jacques Hamard ◽  
Daniel L Karl ◽  
...  

Abstract Protein arginine methyltransferase 5 (PRMT5) catalyzes the symmetric di-methylation of arginine residues in histones H3 and H4, marks that are generally associated with transcriptional repression. However, we found that PRMT5 inhibition or depletion led to more genes being downregulated than upregulated, indicating that PRMT5 can also act as a transcriptional activator. Indeed, the global level of histone H3K27me3 increases in PRMT5 deficient cells. Although PRMT5 does not directly affect PRC2 enzymatic activity, methylation of histone H3 by PRMT5 abrogates its subsequent methylation by PRC2. Treating AML cells with an EZH2 inhibitor partially restored the expression of approximately 50% of the genes that are initially downregulated by PRMT5 inhibition, suggesting that the increased H3K27me3 could directly or indirectly contribute to the transcription repression of these genes. Indeed, ChIP-sequencing analysis confirmed an increase in the H3K27me3 level at the promoter region of a quarter of these genes in PRMT5-inhibited cells. Interestingly, the anti-proliferative effect of PRMT5 inhibition was also partially rescued by treatment with an EZH2 inhibitor in several leukemia cell lines. Thus, PRMT5-mediated crosstalk between histone marks contributes to its functional effects.


2018 ◽  
Vol 4 (11) ◽  
pp. eaau1447 ◽  
Author(s):  
Ryan Hard ◽  
Nan Li ◽  
Wei He ◽  
Brian Ross ◽  
Gary C. H. Mo ◽  
...  

Posttranslational modifications (PTMs) play critical roles in regulating protein functions and mediating protein-protein interactions. An important PTM is lysine methylation that orchestrates chromatin modifications and regulates functions of non-histone proteins. Methyllysine peptides are bound by modular domains, of which chromodomains are representative. Here, we conducted the first large-scale study of chromodomains in the human proteome interacting with both histone and non-histone methyllysine peptides. We observed significant degenerate binding between chromodomains and histone peptides, i.e., different histone sites can be recognized by the same set of chromodomains, and different chromodomains can share similar binding profiles to individual histone sites. Such degenerate binding is not dictated by amino acid sequence or PTM motif but rather rooted in the physiochemical properties defined by the PTMs on the histone peptides. This molecular mechanism is confirmed by the accurate prediction of the binding specificity using a computational model that captures the structural and energetic patterns of the domain-peptide interaction. To further illustrate the power and accuracy of our model, we used it to effectively engineer an exceptionally strong H3K9me3-binding chromodomain and to label H3K9me3 in live cells. This study presents a systematic approach to deciphering domain-peptide recognition and reveals a general principle by which histone modifications are interpreted by reader proteins, leading to dynamic regulation of gene expression and other biological processes.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 2041-2041
Author(s):  
Xinyang Zhao ◽  
Animesh Parkanani ◽  
Jin Zhang ◽  
Richard Dunne ◽  
Andrew Xiao ◽  
...  

Abstract The AML1/Runx1 protein is required for definitive hematopoiesis and for the maturation of adult megakaryocytic cells. Alterations of the Runx1 gene by mutations, deletions and chromosome translocations are associated with several types of acute leukemia. Runx1 functions as both an activator and repressor of gene transcription with promoter and cell type context dependency. Likely, this relates to the ability of Runx1 to interact with a variety of transcription factors such as MEF, C/EBPa, Ets-1 and GATA-1 and also with repressor proteins such as Groucho, mSin3 and HDACs. Runx1 is post-translationally modified through acetylation and phosphorylation, and the acetylable and phosphorylable forms of Runx1 can activate transcription to higher level in Runx1 dependent reporter assays when HATs or Erk2 are coexpressed. Runx1 has also been shown to be methylated on lysine residues by SUV39H1 methyltransferase in fibroblasts. Based on the presence of a SGRGK motif in the runt domain of Runx1, we have been examining whether Runx1 is methylated on arginine residues by the protein arginine methyltransferases (PRMT). We have found that PRMT1 and PRMT5 are associated with Runx1 in AML cells by co-immunoprecipitation assays and using in vitro by GST-pulldown assays with in vitro translated PRMT(s) have shown that the interactions are direct. Using a luciferase gene reporter assay, we show that PRMT1 acts synergistically with p300 to activate Runx1 mediated transcription in response to cell proliferation signals. We have mapped the arginine methylation sites in Runx1 using GST-Runx1 fusion proteins, site-specific mutagenesis and mass spectrometry analysis. We have found three potential arginine methylation sites, one in the Runt domain, and two in the Runx1 carboxy-terminal region. Interestingly, one of these sites is in the region shown to interact with both the mSIN3A transcriptional repression complex and with p300. This suggests that arginine methylation of Runx1 may affects its transcriptional activating and repressing functions. Chromatin immunoprecipitation assays are underway to show how arginine methylation of Runx1 affects its activities in hematopoietic cells. Additional studies examining the effects of cross-talk between arginine methylation, lysine acetylation and serine phosphorylation has on Runx1 functions (biological and biochemical) will be presented.


2013 ◽  
Vol 41 (3) ◽  
pp. 727-740 ◽  
Author(s):  
Hannah K. Long ◽  
Neil P. Blackledge ◽  
Robert J. Klose

Vertebrate DNA can be chemically modified by methylation of the 5 position of the cytosine base in the context of CpG dinucleotides. This modification creates a binding site for MBD (methyl-CpG-binding domain) proteins which target chromatin-modifying activities that are thought to contribute to transcriptional repression and maintain heterochromatic regions of the genome. In contrast with DNA methylation, which is found broadly across vertebrate genomes, non-methylated DNA is concentrated in regions known as CGIs (CpG islands). Recently, a family of proteins which encode a ZF-CxxC (zinc finger-CxxC) domain have been shown to specifically recognize non-methylated DNA and recruit chromatin-modifying activities to CGI elements. For example, CFP1 (CxxC finger protein 1), MLL (mixed lineage leukaemia protein), KDM (lysine demethylase) 2A and KDM2B regulate lysine methylation on histone tails, whereas TET (ten-eleven translocation) 1 and TET3 hydroxylate methylated cytosine bases. In the present review, we discuss the most recent advances in our understanding of how ZF-CxxC domain-containing proteins recognize non-methylated DNA and describe their role in chromatin modification at CGIs.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 794-794
Author(s):  
Fan Liu ◽  
Xinyang Zhao ◽  
Fabiana Perna ◽  
Lan Wang ◽  
Priya Koppikar ◽  
...  

Abstract Abstract 794 Background: The cytoplasmic, non-receptor JAK2 tyrosine kinase is mutated at amino acid residue 617 (from valine to phenylalanine) in most patients with myeloproliferative neoplasms (MPNs), resulting in a constitutively activated kinase that phosphorylates STAT proteins in the absence of upstream signals. Overexpression of JAK2V617F leads to cytokine-independent growth of Ba/F3 cells and the JAK2V617F transgenic and knockin mice develop a disease phenotype resembling human polycythemia vera. Results: We hypothesized that the JAK2V617F occurs so consistently in MPNs because it gains some functional property. The type II arginine methyltransferase PRMT5 was initially identified because of its interaction with JAK2 in a yeast two hybrid screen. We examined the interaction between JAK2 and PRMT5 and found that JAK2V617F and JAK2K539L (another active JAK2 kinase) bound PRMT5 more strongly than did wild-type JAK2. PRMT5 mediates the symmetrical dimethylation of arginine residues within histones H2A and H4 and methylates other cellular proteins as well, such as p53. The oncogenic forms of JAK2 acquire the ability to phosphorylate PRMT5, which greatly impaired its methyltransferase activity. We have shown the in vivo importance of this post-translation modification as treating JAK2V617F-positive cells (but not the wild-type JAK2-harboring cells) with different JAK2 inhibitors significantly increased histone arginine methylation levels. To define the effect of inhibiting PRMT5 activity on hematopoiesis, we knocked down PRMT5 in human cord blood derived CD34+ cells using shRNA and observed increased colony formation and erythroid differentiation; In contrast, PRMT5 overexpression in these cells led to reduced colony formation and inhibition of erythroid differentiation. Furthermore, overexpression of PRMT5, especially a phosphorylation site mutant form of PRMT5 (PRMT5M6), diminishes the proliferative and erythroid generating capacity of JAK2V617F+ CD34+ cells isolated from MPN patients to a greater degree than normal cord blood CD34+ cells. Importantly, we found marked increase in PRMT5 phosphorylation in JAK2V617F-positive MPN patents relative to normal cord blood CD34+ cells, suggesting that this phosphorylation is important for the myeloproliferation phenotype. Conclusion: we show that the oncogenic mutant forms of JAK2 kinase, such as JAK2V617F and JAK2K539L, are not simply constitutively active forms of wild-type JAK2, rather they have specific gains-of-function that allow them to phosphorylate PRMT5 and down-regulate its enzymatic activity. Inhibition of PRMT5 contributes to the myeloproliferation and erythroid differentiation promoting effects of JAK2V617F. This gain-of –function mutation results in cross-talk between oncogenic kinases and histone arginine methylation. Taken together, we demonstrate a novel link between the mutant JAK2 kinases and PRMT5 methyltransferase activity, which contributes to MPN pathogenesis. Further insights about the shared gene expression profile of JAK2 inhibition vs. PRMT5 knockdown will be presented to understand the basics for the behavior change in hematopoietic stem/progenitor cells brought about by these two interventions. Disclosures: No relevant conflicts of interest to declare.


2011 ◽  
Vol 17 (2) ◽  
pp. 237-244 ◽  
Author(s):  
Jiang Wu ◽  
Nan Xie ◽  
You Feng ◽  
Y. George Zheng

Methylation of arginine residues, catalyzed by protein arginine methyltransferases (PRMTs), is one important protein posttranslational modification involved in epigenetic regulation of gene expression. A fast and effective assay for PRMT can provide valuable information for dissecting the biological functions of PRMTs, as well as for screening small-molecule inhibitors of arginine methylation. Currently, among the methods used for PRMT activity measurement, many contain laborious separation procedures, which restrict the applications of these assays for high-throughput screening (HTS) in drug discovery. The authors report here a mix-and-measure method to measure PRMT activity based on the principle of scintillation proximity assay (SPA). In this assay, 3H-AdoMet was used as methyl donor, and biotin-modified histone H4 peptide served as a methylation substrate. Following the methylation reaction catalyzed by PRMTs, streptavidin-coated SPA beads were added to the reaction solution, and SPA signals were detected by a MicroBeta scintillation counter. No separation step is needed, which simplifies the assay procedure and greatly enhances the assay speed. Particularly, the miniaturization and robustness suggest that this method is suited for HTS of PRMT inhibitors.


2000 ◽  
Vol 150 (4) ◽  
pp. 707-718 ◽  
Author(s):  
Chi Y. Yun ◽  
Xiang-Dong Fu

Mammalian serine and arginine–rich (SR) proteins play important roles in both constitutive and regulated splicing, and SR protein–specific kinases (SRPKs) are conserved from humans to yeast. Here, we demonstrate a novel function of the single conserved SR protein kinase Sky1p in nuclear import in budding yeast. The yeast SR-like protein Npl3p is known to enter the nucleus through a composite nuclear localization signal (NLS) consisting of a repetitive arginine- glycine-glycine (RGG) motif and a nonrepetitive sequence. We found that the latter is the site for phosphorylation by Sky1p and that this phosphorylation regulates nuclear import of Npl3p by modulating the interaction of the RGG motif with its nuclear import receptor Mtr10p. The RGG motif is also methylated on arginine residues, but methylation does not affect the Npl3p–Mtr10p interaction in vitro. Remarkably, arginine methylation interferes with Sky1p-mediated phosphorylation, thereby indirectly influencing the Npl3p–Mtr10p interaction in vivo and negatively regulating nuclear import of Npl3p. These results suggest that nuclear import of Npl3p is coordinately influenced by methylation and phosphorylation in budding yeast, which may represent conserved components in the dynamic regulation of RNA processing in higher eukaryotic cells.


2019 ◽  
Vol 23 (15) ◽  
pp. 1663-1670 ◽  
Author(s):  
Chunyan Ao ◽  
Shunshan Jin ◽  
Yuan Lin ◽  
Quan Zou

Protein methylation is an important and reversible post-translational modification that regulates many biological processes in cells. It occurs mainly on lysine and arginine residues and involves many important biological processes, including transcriptional activity, signal transduction, and the regulation of gene expression. Protein methylation and its regulatory enzymes are related to a variety of human diseases, so improved identification of methylation sites is useful for designing drugs for a variety of related diseases. In this review, we systematically summarize and analyze the tools used for the prediction of protein methylation sites on arginine and lysine residues over the last decade.


Sign in / Sign up

Export Citation Format

Share Document