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Article ; Online: Effectors and effects of arginine methylation.

Wang, Yalong / Bedford, Mark T

2023 Volume 51, Issue 2, Page(s) 725–734

Abstract: ... dimethylarginine (SDMA). Methylarginine marks are catalyzed by members of the protein arginine methyltransferases ... With regards to protein-protein interactions, the major 'readers' of methylarginine marks are Tudor domain ... methylarginine readers and address other domains and complexes that sense methylarginine marks. ...

Abstract	Arginine methylation is a ubiquitous and relatively stable post-translational modification (PTM) that occurs in three types: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA). Methylarginine marks are catalyzed by members of the protein arginine methyltransferases (PRMTs) family of enzymes. Substrates for arginine methylation are found in most cellular compartments, with RNA-binding proteins forming the majority of PRMT targets. Arginine methylation often occurs in intrinsically disordered regions of proteins, which impacts biological processes like protein-protein interactions and phase separation, to modulate gene transcription, mRNA splicing and signal transduction. With regards to protein-protein interactions, the major 'readers' of methylarginine marks are Tudor domain-containing proteins, although additional domain types and unique protein folds have also recently been identified as methylarginine readers. Here, we will assess the current 'state-of-the-art' in the arginine methylation reader field. We will focus on the biological functions of the Tudor domain-containing methylarginine readers and address other domains and complexes that sense methylarginine marks.
MeSH term(s)	Arginine/chemistry ; Arginine/genetics ; Arginine/metabolism ; Methylation ; Protein Processing, Post-Translational ; Protein-Arginine N-Methyltransferases/chemistry ; Protein-Arginine N-Methyltransferases/genetics ; Protein-Arginine N-Methyltransferases/metabolism ; RNA-Binding Proteins/metabolism
Chemical Substances	Arginine (94ZLA3W45F) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319) ; RNA-Binding Proteins
Language	English
Publishing date	2023-10-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	184237-7
ISSN	1470-8752 ; 0300-5127
ISSN (online)	1470-8752
ISSN	0300-5127
DOI	10.1042/BST20221147
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Article ; Online: CARM1 arginine methyltransferase as a therapeutic target for cancer.

Santos, Margarida / Hwang, Jee Won / Bedford, Mark T

The Journal of biological chemistry

2023 Volume 299, Issue 9, Page(s) 105124

Abstract: Coactivator-associated arginine methyltransferase 1 (CARM1) is an arginine methyltransferase that posttranslationally modifies proteins that regulate multiple levels of RNA production and processing. Its substrates include histones, transcription factors, ...

Abstract	Coactivator-associated arginine methyltransferase 1 (CARM1) is an arginine methyltransferase that posttranslationally modifies proteins that regulate multiple levels of RNA production and processing. Its substrates include histones, transcription factors, coregulators of transcription, and splicing factors. CARM1 is overexpressed in many different cancer types, and often promotes transcription factor programs that are co-opted as drivers of the transformed cell state, a process known as transcription factor addiction. Targeting these oncogenic transcription factor pathways is difficult but could be addressed by removing the activity of the key coactivators on which they rely. CARM1 is ubiquitously expressed, and its KO is less detrimental in embryonic development than deletion of the arginine methyltransferases protein arginine methyltransferase 1 and protein arginine methyltransferase 5, suggesting that therapeutic targeting of CARM1 may be well tolerated. Here, we will summarize the normal in vivo functions of CARM1 that have been gleaned from mouse studies, expand on the transcriptional pathways that are regulated by CARM1, and finally highlight recent studies that have identified oncogenic properties of CARM1 in different biological settings. This review is meant to kindle an interest in the development of human drug therapies targeting CARM1, as there are currently no CARM1 inhibitors available for use in clinical trials.
MeSH term(s)	Animals ; Humans ; Mice ; Drug Delivery Systems ; Neoplasms/drug therapy ; Neoplasms/genetics ; Transcription Factors/metabolism ; Protein-Arginine N-Methyltransferases/antagonists & inhibitors ; Protein-Arginine N-Methyltransferases/genetics ; Protein-Arginine N-Methyltransferases/metabolism
Chemical Substances	coactivator-associated arginine methyltransferase 1 (EC 2.1.1.319) ; Transcription Factors ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319)
Language	English
Publishing date	2023-08-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105124
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Article ; Online: Screening for histone codebreakers.

Bedford, Mark T

The Journal of biological chemistry

2018 Volume 293, Issue 35, Page(s) 13766–13767

Abstract: ... molecule inhibitors have been identified for this enzyme, responsible for depositing the H3K36me2 mark ...

Abstract	The lysine methyltransferase NSD2 is overexpressed and carries gain-of-function mutations in a number of different cancers, making it an attractive therapeutic target. However, no specific small molecule inhibitors have been identified for this enzyme, responsible for depositing the H3K36me2 mark on histones. A new study reports a robust platform for high-throughput screening (HTS) assays to facilitate this discovery.
MeSH term(s)	Drug Discovery/methods ; Drug Evaluation, Preclinical/methods ; Enzyme Inhibitors/pharmacology ; Epigenesis, Genetic/drug effects ; High-Throughput Screening Assays/methods ; Histone Code/drug effects ; Histone-Lysine N-Methyltransferase/antagonists & inhibitors ; Histone-Lysine N-Methyltransferase/metabolism ; Histones/genetics ; Histones/metabolism ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Repressor Proteins/antagonists & inhibitors ; Repressor Proteins/metabolism
Chemical Substances	Enzyme Inhibitors ; Histones ; Repressor Proteins ; Histone-Lysine N-Methyltransferase (EC 2.1.1.43) ; NSD2 protein, human (EC 2.1.1.43)
Language	English
Publishing date	2018-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.H118.005132
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Article ; Online: The Role of the PRMT5-SND1 Axis in Hepatocellular Carcinoma.

Wright, Tanner / Wang, Yalong / Bedford, Mark T

Epigenomes

2021 Volume 5, Issue 1

Abstract: ... methylation marks in cells. The staphylococcal nuclease and Tudor domain-containing 1 (SND1) effector protein ... is a key reader of the marks deposited by PRMT5. Both PRMT5 and SND1 are broadly expressed and ...

Abstract	Arginine methylation is an essential post-translational modification (PTM) deposited by protein arginine methyltransferases (PRMTs) and recognized by Tudor domain-containing proteins. Of the nine mammalian PRMTs, PRMT5 is the primary enzyme responsible for the deposition of symmetric arginine methylation marks in cells. The staphylococcal nuclease and Tudor domain-containing 1 (SND1) effector protein is a key reader of the marks deposited by PRMT5. Both PRMT5 and SND1 are broadly expressed and their deregulation is reported to be associated with a range of disease phenotypes, including cancer. Hepatocellular carcinoma (HCC) is an example of a cancer type that often displays elevated PRMT5 and SND1 levels, and there is evidence that hyperactivation of this axis is oncogenic. Importantly, this pathway can be tempered with small-molecule inhibitors that target PRMT5, offering a therapeutic node for cancer, such as HCC, that display high PRMT5-SND1 axis activity. Here we summarize the known activities of this writer-reader pair, with a focus on their biological roles in HCC. This will help establish a foundation for treating HCC with PRMT5 inhibitors and also identify potential biomarkers that could predict sensitivity to this type of therapy.
Language	English
Publishing date	2021-01-05
Publishing country	Switzerland
Document type	Journal Article
ISSN	2075-4655
ISSN (online)	2075-4655
DOI	10.3390/epigenomes5010002
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Article ; Online: Pan-methylarginine antibody generation using PEG linked GAR motifs as antigens.

Wang, Yalong / Person, Maria D / Bedford, Mark T

Methods (San Diego, Calif.)

2021 Volume 200, Page(s) 80–86

Abstract: ... of methylarginine marks. Using these antibodies, we observed substrate scavenging by PRMT1, when PRMT5 activity is ...

Abstract	Arginine methylation is a prevalent posttranslational modification which is deposited by a family of protein arginine methyltransferases (PRMTs), and is found in three different forms in mammalian cells: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA). Pan-methylarginine antibodies are critical for identifying proteins that are methylated on arginine residues, and are also used for evaluating signaling pathways that modulate this methyltransferase activity. Although good pan-MMA, -ADMA and -SDMA antibodies have been developed over the years, there is still room for improvement. Here we use a novel antigen approach, which involves the separation of short methylated motifs with inert polyethylene glycol (PEG) linkers, to generate a set of pan antibodies to the full range of methylarginine marks. Using these antibodies, we observed substrate scavenging by PRMT1, when PRMT5 activity is blocked. Specifically, we find that the splicing factor SmD1 displays increased ADMA levels upon PRMT5 inhibitor treatment. Furthermore, when the catalysis of both SDMA and ADMA is blocked with small molecule inhibitors, we demonstrate that SmD1 and SMN no longer interact. This could partially explain the synergistic effect of PRMT5 and type I PRMT inhibition on RNA splicing and cancer cell growth.
MeSH term(s)	Animals ; Antibodies/genetics ; Arginine/metabolism ; Mammals/metabolism ; Methylation ; Polyethylene Glycols ; Protein Processing, Post-Translational ; Protein-Arginine N-Methyltransferases/metabolism
Chemical Substances	Antibodies ; Polyethylene Glycols (3WJQ0SDW1A) ; Arginine (94ZLA3W45F) ; Protein-Arginine N-Methyltransferases (EC 2.1.1.319)
Language	English
Publishing date	2021-06-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1066584-5
ISSN	1095-9130 ; 1046-2023
ISSN (online)	1095-9130
ISSN	1046-2023
DOI	10.1016/j.ymeth.2021.06.005
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Article ; Online: A complete methyl-lysine binding aromatic cage constructed by two domains of PHF2.

Horton, John R / Zhou, Jujun / Chen, Qin / Zhang, Xing / Bedford, Mark T / Cheng, Xiaodong

The Journal of biological chemistry

2022 Volume 299, Issue 2, Page(s) 102862

Abstract: ... related kinase 1 (VRK1). The Jumonji domain erases the repressive dimethylation mark from histone H3 ...

Abstract	The N-terminal half of PHF2 harbors both a plant homeodomain (PHD) and a Jumonji domain. The PHD recognizes both histone H3 trimethylated at lysine 4 and methylated nonhistone proteins including vaccinia-related kinase 1 (VRK1). The Jumonji domain erases the repressive dimethylation mark from histone H3 lysine 9 (H3K9me2) at select promoters. The N-terminal amino acid sequences of H3 (AR
MeSH term(s)	Histones/chemistry ; Lysine/chemistry ; Methylation ; Peptides/chemistry ; Protein Binding ; Protein Domains ; Homeodomain Proteins/chemistry
Chemical Substances	Histones ; Lysine (K3Z4F929H6) ; Peptides ; Homeodomain Proteins
Language	English
Publishing date	2022-12-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102862
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Article ; Online: Loss of the methylarginine reader function of SND1 confers resistance to hepatocellular carcinoma.

Wright, Tanner / Wang, Yalong / Stratton, Sabrina A / Sebastian, Manu / Liu, Bin / Johnson, David G / Bedford, Mark T

The Biochemical journal

2023 Volume 480, Issue 22, Page(s) 1805–1816

Abstract: ... methylarginine marks through its Tudor domain. Specifically, it recognizes methylation marks deposited by protein ... whose mutant SND1 can no longer recognize PRMT5-catalyzed methylarginine marks. Quantitative PCR analysis ...

Abstract	Staphylococcal nuclease Tudor domain containing 1 (SND1) protein is an oncogene that 'reads' methylarginine marks through its Tudor domain. Specifically, it recognizes methylation marks deposited by protein arginine methyltransferase 5 (PRMT5), which is also known to promote tumorigenesis. Although SND1 can drive hepatocellular carcinoma (HCC), it is unclear whether the SND1 Tudor domain is needed to promote HCC. We sought to identify the biological role of the SND1 Tudor domain in normal and tumorigenic settings by developing two genetically engineered SND1 mouse models, an Snd1 knockout (Snd1 KO) and an Snd1 Tudor domain-mutated (Snd1 KI) mouse, whose mutant SND1 can no longer recognize PRMT5-catalyzed methylarginine marks. Quantitative PCR analysis of normal, KO, and KI liver samples revealed a role for the SND1 Tudor domain in regulating the expression of genes encoding major acute phase proteins, which could provide mechanistic insight into SND1 function in a tumor setting. Prior studies indicated that ectopic overexpression of SND1 in the mouse liver dramatically accelerates the development of diethylnitrosamine (DEN)-induced HCC. Thus, we tested the combined effects of DEN and SND1 loss or mutation on the development of HCC. We found that both Snd1 KO and Snd1 KI mice were partially protected against malignant tumor development following exposure to DEN. These results support the development of small molecule inhibitors that target the SND1 Tudor domain or the use of upstream PRMT5 inhibitors, as novel treatments for HCC.
MeSH term(s)	Animals ; Mice ; Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/pathology ; Endonucleases/genetics ; Liver Neoplasms/genetics ; Liver Neoplasms/pathology ; Nuclear Proteins/metabolism ; Transcription Factors ; Genetic Predisposition to Disease
Chemical Substances	Endonucleases (EC 3.1.-) ; Nuclear Proteins ; Transcription Factors ; Snd1 protein, mouse (EC 3.1.-)
Language	English
Publishing date	2023-10-30
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BCJ20230384
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Article ; Online: The Role of the PRMT5–SND1 Axis in Hepatocellular Carcinoma

Tanner Wright / Yalong Wang / Mark T. Bedford

Epigenomes, Vol 5, Iss 2, p

2021 Volume 2

Abstract	Arginine methylation is an essential post-translational modification (PTM) deposited by protein arginine methyltransferases (PRMTs) and recognized by Tudor domain-containing proteins. Of the nine mammalian PRMTs, PRMT5 is the primary enzyme responsible for the deposition of symmetric arginine methylation marks in cells. The staphylococcal nuclease and Tudor domain-containing 1 (SND1) effector protein is a key reader of the marks deposited by PRMT5. Both PRMT5 and SND1 are broadly expressed and their deregulation is reported to be associated with a range of disease phenotypes, including cancer. Hepatocellular carcinoma (HCC) is an example of a cancer type that often displays elevated PRMT5 and SND1 levels, and there is evidence that hyperactivation of this axis is oncogenic. Importantly, this pathway can be tempered with small-molecule inhibitors that target PRMT5, offering a therapeutic node for cancer, such as HCC, that display high PRMT5–SND1 axis activity. Here we summarize the known activities of this writer–reader pair, with a focus on their biological roles in HCC. This will help establish a foundation for treating HCC with PRMT5 inhibitors and also identify potential biomarkers that could predict sensitivity to this type of therapy.
Keywords	arginine methylation ; PRMT5 ; SND1 ; Tudor-SN ; p100 ; HCC ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	571
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Functional characterization of QT interval associated

Gunamalai, Lavanya / Singh, Parul / Berg, Brian / Shi, Leilei / Sanchez, Ernesto / Smith, Alexa / Breton, Ghislain / Bedford, Mark T / Balciunas, Darius / Kapoor, Ashish

bioRxiv : the preprint server for biology

2024

Abstract: Several empirical and theoretical studies suggest presence of multiple enhancers per gene that collectively regulate gene expression, and that common sequence variation impacting on the activities of these enhancers is a major source of inter-individual ... ...

Abstract	Several empirical and theoretical studies suggest presence of multiple enhancers per gene that collectively regulate gene expression, and that common sequence variation impacting on the activities of these enhancers is a major source of inter-individual variability in gene expression. However, for vast majority of genes, enhancers and the underlying regulatory variation remains unknown. Even for the genes with well-characterized enhancers, the nature of the combined effects from multiple enhancers and their variants, when known, on gene expression regulation remains unexplored. Here, we have evaluated the combined effects from five
Language	English
Publishing date	2024-03-14
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.11.584440
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Article ; Online: Molecular Basis for SPINDOC-Spindlin1 Engagement and Its Role in Transcriptional Attenuation.

Zhao, Fan / Deng, Yafang / Yang, Fen / Yan, Yan / Feng, Fan / Peng, Bo / Gao, Juntao / Bedford, Mark T / Li, Haitao

Journal of molecular biology

2023 Volume 436, Issue 7, Page(s) 168371

Abstract: ... such as H3 "K4me3-K9me3" bivalent mark. Further ChIP-seq and RT-qPCR indicated that SPINDOC could promote ...

Abstract	Spindlin1 is a histone reader with three Tudor-like domains and its transcriptional co-activator activity could be attenuated by SPINDOC. The first two Tudors are involved in histone methylation readout, while the function of Tudor 3 is largely unknown. Here our structural and binding studies revealed an engagement mode of SPINDOC-Spindlin1, in which a hydrophobic motif of SPINDOC, DOCpep3, stably interacts with Spindlin1 Tudor 3, and two neighboring K/R-rich motifs, DOCpep1 and DOCpep2, bind to the acidic surface of Spindlin1 Tudor 2. Although DOCpep3-Spindlin1 engagement is compatible with histone readout, an extended SPINDOC fragment containing the K/R-rich region attenuates histone or TCF4 binding by Spindlin1 due to introduced competition. This inhibitory effect is more pronounced for weaker binding targets but not for strong ones such as H3 "K4me3-K9me3" bivalent mark. Further ChIP-seq and RT-qPCR indicated that SPINDOC could promote genomic relocation of Spindlin1, thus modulate downstream gene transcription. Collectively, we revealed multivalent engagement between SPINDOC and Spindlin1, in which a hydrophobic motif acts as the primary binding site for stable SPINDOC-Spindlin1 association, while K/R-rich region modulates the target selectivity of Spindlin1 via competitive inhibition, therefore attenuating the transcriptional co-activator activity of Spindlin1.
MeSH term(s)	Binding Sites ; Cell Cycle Proteins/chemistry ; Cell Cycle Proteins/metabolism ; Co-Repressor Proteins/chemistry ; Co-Repressor Proteins/metabolism ; Gene Expression Regulation ; Histones/metabolism ; Methylation ; Microtubule-Associated Proteins/chemistry ; Microtubule-Associated Proteins/metabolism ; Phosphoproteins/chemistry ; Phosphoproteins/metabolism ; Protein Binding ; Transcription, Genetic ; Tudor Domain ; Humans ; Protein Interaction Mapping ; Protein Interaction Domains and Motifs
Chemical Substances	Cell Cycle Proteins ; Co-Repressor Proteins ; Histones ; Microtubule-Associated Proteins ; Phosphoproteins ; spindlin ; SPINDOC protein, human
Language	English
Publishing date	2023-11-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168371
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