251
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The physiological and pathophysiological role of PRMT1-mediated protein arginine methylation. Pharmacol Res 2009; 60:466-74. [DOI: 10.1016/j.phrs.2009.07.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 07/20/2009] [Accepted: 07/21/2009] [Indexed: 11/22/2022]
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252
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Jarmalavicius S, Trefzer U, Walden P. Differential arginine methylation of the G‐protein pathway suppressor GPS‐2 recognized by tumor‐specific T cells in melanoma. FASEB J 2009; 24:937-46. [DOI: 10.1096/fj.09-136283] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Saulius Jarmalavicius
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
| | - Uwe Trefzer
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
| | - Peter Walden
- Clinical Research Group Tumor ImmunologyDepartment of DermatologyCharité‐Universitätsmedizin BerlinBerlinGermany
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253
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Kim D, Lee J, Cheng D, Li J, Carter C, Richie E, Bedford MT. Enzymatic activity is required for the in vivo functions of CARM1. J Biol Chem 2009; 285:1147-52. [PMID: 19897492 DOI: 10.1074/jbc.m109.035865] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CARM1 is one of nine protein arginine methyltransferases that methylate arginine residues in proteins. CARM1 is recruited by many different transcription factors as a positive regulator. Gene targeting of CARM1 in mice has been performed, and knock-out mice, which are smaller than their wild-type littermates, die just after birth. It has been proposed that CARM1 has functions that are independent of its enzymatic activity. Indeed, CARM1 is found to interact with a number of proteins and may have a scaffolding function in this context. However, CARM1 methylates histone H3, PABP1, AIB1, and a number of splicing factors, which strongly suggests that its impact on transcription and splicing is primarily through its ability to modify these substrates. To unequivocally establish the importance of CARM1 enzymatic activity in vivo, we generated an enzyme-dead knock-in of this protein arginine methyltransferase. We determined that knock-in cells and mice have defects similar to those seen in their knock-out counterparts with respect to the time of embryo lethality, T cell development, adipocyte differentiation, and transcriptional coactivator activity. CARM1 requires its enzymatic activity for all of its known cellular functions. Thus, small molecule inhibitors of CARM1 will incapacitate all of the enzyme's cellular functions.
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Affiliation(s)
- Daehoon Kim
- Science Park-Research Division, The University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957, USA
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254
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Wu Q, Bruce AW, Jedrusik A, Ellis PD, Andrews RM, Langford CF, Glover DM, Zernicka-Goetz M. CARM1 is required in embryonic stem cells to maintain pluripotency and resist differentiation. Stem Cells 2009; 27:2637-2645. [PMID: 19544422 PMCID: PMC4135545 DOI: 10.1002/stem.131] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Histone H3 methylation at R17 and R26 recently emerged as a novel epigenetic mechanism regulating pluripotency in mouse embryos. Blastomeres of four-cell embryos with high H3 methylation at these sites show unrestricted potential, whereas those with lower levels cannot support development when aggregated in chimeras of like cells. Increasing histone H3 methylation, through expression of coactivator-associated-protein-arginine-methyltransferase 1 (CARM1) in embryos, elevates expression of key pluripotency genes and directs cells to the pluripotent inner cell mass. We demonstrate CARM1 is also required for the self-renewal and pluripotency of embryonic stem (ES) cells. In ES cells, CARM1 depletion downregulates pluripotency genes leading to their differentiation. CARM1 associates with Oct4/Pou5f1 and Sox2 promoters that display detectable levels of R17/26 histone H3 methylation. In CARM1 overexpressing ES cells, histone H3 arginine methylation is also at the Nanog promoter to which CARM1 now associates. Such cells express Nanog at elevated levels and delay their response to differentiation signals. Thus, like in four-cell embryo blastomeres, histone H3 arginine methylation by CARM1 in ES cells allows epigenetic modulation of pluripotency.
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Affiliation(s)
- Qiang Wu
- Wellcome Trust and Cancer Research UK Gurdon Institute
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Peter D. Ellis
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Robert M. Andrews
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | | | - David M. Glover
- Cancer Research UK Cell Cycle Genetics Research Group, University of Cambridge, Department of Genetics, Cambridge, United Kingdom
| | - Magdalena Zernicka-Goetz
- Wellcome Trust and Cancer Research UK Gurdon Institute
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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255
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Lu M, Yang J, Ren Z, Sabui S, Espejo A, Bedford MT, Jacobson RH, Jeruzalmi D, McMurray JS, Chen X. Crystal structure of the three tandem FF domains of the transcription elongation regulator CA150. J Mol Biol 2009; 393:397-408. [PMID: 19660470 PMCID: PMC3319151 DOI: 10.1016/j.jmb.2009.07.086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/27/2009] [Accepted: 07/29/2009] [Indexed: 10/20/2022]
Abstract
FF domains are small protein-protein interaction modules that have two flanking conserved phenylalanine residues. They are present in proteins involved in transcription, RNA splicing, and signal transduction, and often exist in tandem arrays. Although several individual FF domain structures have been determined by NMR, the tandem nature of most FF domains has not been revealed. Here we report the 2.7-A-resolution crystal structure of the first three FF domains of the human transcription elongation factor CA150. Each FF domain is composed of three alpha-helices and a 3(10) helix between alpha-helix 2 and alpha-helix 3. The most striking feature of the structure is that an FF domain is connected to the next by an alpha-helix that continues from helix 3 to helix 1 of the next. The consequent elongated arrangement allows exposure of many charged residues within the region that can be engaged in interaction with other molecules. Binding studies using a peptide ligand suggest that a specific conformation of the FF domains might be required to achieve higher-affinity binding. Additionally, we explore potential DNA binding of the FF construct used in this study. Overall, we provide the first crystal structure of an FF domain and insights into the tandem nature of the FF domains and suggest that, in addition to protein binding, FF domains might be involved in DNA binding.
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Affiliation(s)
- Ming Lu
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
- Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX 77030
| | - Jun Yang
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
- Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX 77030
| | - Zhiyong Ren
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Subir Sabui
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Alexsandra Espejo
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center Science Park, Smithville, TX 78957
| | - Mark T. Bedford
- Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX 77030
- Department of Carcinogenesis, University of Texas M.D. Anderson Cancer Center Science Park, Smithville, TX 78957
| | - Raymond H. Jacobson
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
- Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX 77030
| | - David Jeruzalmi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - John S. McMurray
- Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX 77030
- Department of Experimental Therapeutics, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
| | - Xiaomin Chen
- Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030
- Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX 77030
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256
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Feng Q, He B, Jung SY, Song Y, Qin J, Tsai SY, Tsai MJ, O'Malley BW. Biochemical control of CARM1 enzymatic activity by phosphorylation. J Biol Chem 2009; 284:36167-36174. [PMID: 19843527 DOI: 10.1074/jbc.m109.065524] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1) is a dual functional coregulator that facilitates transcription initiation by methylation of Arg(17) and Arg(26) of histone H3 and also dictates the subsequent coactivator complex disassembly by methylation of the steroid receptor coactivator family coactivators and p300/cAMP-response element-binding protein-binding protein. However, the regulation of CARM1 enzymatic activity and substrate specificity remains largely unknown. In this study, we report that CARM1 function is regulated by phosphorylation at Ser(217), a residue completely conserved in the type I protein arginine methyltransferase (PRMT) family of enzymes. Comparative analysis of the published CARM1 crystal structures reveals that the hydroxyl group of Ser(217) forms a strong hydrogen bond with the carbonyl oxygen atom of Tyr(154) to lock the cofactor S-adenosylmethionine inside the binding cavity. Phosphorylation of Ser(217) disrupts this hydrogen bond and subsequently abolishes S-adenosylmethionine binding and its methyltransferase activity. Importantly, Tyr(154) is also conserved in the type I PRMT family of enzymes, suggesting a general role of this hydrogen bond in maintaining the holo structure of the type I PRMT catalytic domain. Moreover, we found that phosphorylation at Ser(217) also promoted CARM1 cytoplasmic localization and that this translocation occurred mainly during mitosis. We propose that phosphorylation at Ser(217) serves as a molecular switch for controlling CARM1 enzymatic activity during the cell cycle.
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Affiliation(s)
- Qin Feng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Bin He
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Sung-Yun Jung
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Yongcheng Song
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030
| | - Jun Qin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Sophia Y Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Ming-Jer Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030.
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257
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Kuhn P, Xu W. Protein arginine methyltransferases: nuclear receptor coregulators and beyond. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 87:299-342. [PMID: 20374708 DOI: 10.1016/s1877-1173(09)87009-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein arginine methyltransferases (PRMTs) are a family of enzymes that play a crucial role in diverse cellular functions. Several PRMTs have been associated with gene expression regulation, in which PRMTs act as histone methyltransferases, secondary coregulators of transcription, or facilitate mRNA splicing and stability. Additional functions include modulation of protein localization, ribosomal assembly, and signal transduction. At the organismal level, several PRMTs appear to be important for development and may play an important role in cancer. The relationships between their cellular and organismal functions are poorly understood; at least in part due to the large body of enzymatic substrates for PRMTs and their transcriptional targets that remain to be determined. Specific PRMT inhibitors have been developed in recent years, which should help to shed light on their diverse biological roles. Connecting PRMT cellular functions with their global effects on an organism will facilitate development of novel treatments for human diseases.
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Affiliation(s)
- Peter Kuhn
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin 53706, USA
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258
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Hernández H, Makarova OV, Makarov EM, Morgner N, Muto Y, Krummel DP, Robinson CV. Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP. PLoS One 2009; 4:e7202. [PMID: 19784376 PMCID: PMC2747018 DOI: 10.1371/journal.pone.0007202] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 08/13/2009] [Indexed: 12/24/2022] Open
Abstract
Most human protein-encoding genes contain multiple exons that are spliced together, frequently in alternative arrangements, by the spliceosome. It is established that U1 snRNP is an essential component of the spliceosome, in human consisting of RNA and ten proteins, several of which are post-translationally modified and exist as multiple isoforms. Unresolved and challenging to investigate are the effects of these post translational modifications on the dynamics, interactions and stability of the particle. Using mass spectrometry we investigate the composition and dynamics of the native human U1 snRNP and compare native and recombinant complexes to isolate the effects of various subunits and isoforms on the overall stability. Our data reveal differential incorporation of four protein isoforms and dynamic interactions of subunits U1-A, U1-C and Sm-B/B'. Results also show that unstructured post-translationally modified C-terminal tails are responsible for the dynamics of Sm-B/B' and U1-C and that their interactions with the Sm core are controlled by binding to different U1-70k isoforms and their phosphorylation status in vivo. These results therefore provide the important functional link between proteomics and structure as well as insight into the dynamic quaternary structure of the native U1 snRNP important for its function.
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Affiliation(s)
- Helena Hernández
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Olga V. Makarova
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Evgeny M. Makarov
- Division of Bioscience, School of Health and Social Care, Brunel University, Uxbridge, United Kingdom
| | - Nina Morgner
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Yutaka Muto
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Carol V. Robinson
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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259
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Jayne S, Rothgiesser KM, Hottiger MO. CARM1 but not its enzymatic activity is required for transcriptional coactivation of NF-kappaB-dependent gene expression. J Mol Biol 2009; 394:485-95. [PMID: 19769987 DOI: 10.1016/j.jmb.2009.09.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2009] [Revised: 09/08/2009] [Accepted: 09/15/2009] [Indexed: 02/05/2023]
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1) belongs to the protein arginine methyltransferase family. It was reported to methylate histone as well as non-histone proteins and thus to be involved in transcriptional activation and mRNA degradation/stability. Here we report the genetic complementation of carm1-/- cells with wild-type CARM1 or an enzymatic inactive mutant of CARM1 to investigate the requirement of CARM1 and its enzymatic activity for nuclear factor kappaB (NF-kappaB)-dependent gene expression. Using custom microarray and quantitative reverse transcription PCR, we could define a subset of NF-kappaB target genes that required CARM1 for their proper expression. Although several tumor necrosis factor-alpha- and phorbol-12-myristate-13-acetate/ionomycin-induced NF-kappaB target genes are CARM1 dependent, CARM1 enzymatic activity was dispensable for gene expression. Interestingly, CARM1 was not required for the stimulus-dependent recruitment of RelA/p65 to chromatin, suggesting that CARM1 is rather contributing in protein complex stabilization. Together, our results confirm the importance of CARM1 as transcriptional cofactor without the involvement of its catalytic activity.
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Affiliation(s)
- Sandrine Jayne
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zurich, Zurich, Switzerland
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260
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Copeland RA, Solomon ME, Richon VM. Protein methyltransferases as a target class for drug discovery. Nat Rev Drug Discov 2009; 8:724-32. [PMID: 19721445 DOI: 10.1038/nrd2974] [Citation(s) in RCA: 384] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The protein methyltransferases (PMTs) - which methylate protein lysine and arginine residues and have crucial roles in gene transcription - are emerging as an important group of enzymes that play key parts in normal physiology and human diseases. The collection of human PMTs is a large and diverse group of enzymes that have a common mechanism of catalysis. Here, we review the biological, biochemical and structural data that together present PMTs as a novel, chemically tractable target class for drug discovery.
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Affiliation(s)
- Robert A Copeland
- Epizyme, Inc., 840 Memorial Drive, Cambridge, Massachussets 02139, USA.
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261
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Ito T, Yadav N, Lee J, Furumatsu T, Yamashita S, Yoshida K, Taniguchi N, Hashimoto M, Tsuchiya M, Ozaki T, Lotz M, Bedford MT, Asahara H. Arginine methyltransferase CARM1/PRMT4 regulates endochondral ossification. BMC DEVELOPMENTAL BIOLOGY 2009; 9:47. [PMID: 19725955 PMCID: PMC2754437 DOI: 10.1186/1471-213x-9-47] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 09/02/2009] [Indexed: 01/20/2023]
Abstract
Background Chondrogenesis and subsequent endochondral ossification are processes tightly regulated by the transcription factor Sox9 (SRY-related high mobility group-Box gene 9), but molecular mechanisms underlying this activity remain unclear. Here we report that coactivator-associated arginine methyltransferase 1 (CARM1) regulates chondrocyte proliferation via arginine methylation of Sox9. Results CARM1-null mice display delayed endochondral ossification and decreased chondrocyte proliferation. Conversely, cartilage development of CARM1 transgenic mice was accelerated. CARM1 specifically methylates Sox9 at its HMG domain in vivo and in vitro. Arg-methylation of Sox9 by CARM1 disrupts interaction of Sox9 with beta-catenin, regulating Cyclin D1 expression and cell cycle progression of chondrocytes. Conclusion These results establish a role for CARM1 as an important regulator of chondrocyte proliferation during embryogenesis.
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Affiliation(s)
- Tatsuo Ito
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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262
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Burghes AHM, Beattie CE. Spinal muscular atrophy: why do low levels of survival motor neuron protein make motor neurons sick? Nat Rev Neurosci 2009; 10:597-609. [PMID: 19584893 PMCID: PMC2853768 DOI: 10.1038/nrn2670] [Citation(s) in RCA: 562] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many neurogenetic disorders are caused by the mutation of ubiquitously expressed genes. One such disorder, spinal muscular atrophy, is caused by loss or mutation of the survival motor neuron1 gene (SMN1), leading to reduced SMN protein levels and a selective dysfunction of motor neurons. SMN, together with partner proteins, functions in the assembly of small nuclear ribonucleoproteins (snRNPs), which are important for pre-mRNA splicing. It has also been suggested that SMN might function in the assembly of other ribonucleoprotein complexes. Two hypotheses have been proposed to explain the molecular dysfunction that gives rise to spinal muscular atrophy (SMA) and its specificity to a particular group of neurons. The first hypothesis states that the loss of SMN's well-known function in snRNP assembly causes an alteration in the splicing of a specific gene (or genes). The second hypothesis proposes that SMN is crucial for the transport of mRNA in neurons and that disruption of this function results in SMA.
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Affiliation(s)
- Arthur H M Burghes
- Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA.
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263
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Kousaka A, Mori Y, Koyama Y, Taneda T, Miyata S, Tohyama M. The distribution and characterization of endogenous protein arginine N-methyltransferase 8 in mouse CNS. Neuroscience 2009; 163:1146-57. [PMID: 19576965 DOI: 10.1016/j.neuroscience.2009.06.061] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 06/04/2009] [Accepted: 06/27/2009] [Indexed: 11/18/2022]
Abstract
Protein arginine N-methyltransferase (PRMT) 8 was first discovered from a database search for genes harboring four conserved methyltransferase motifs, which shares more than 80% homology to PRMT1 in amino acid [Lee J, Sayegh J, Daniel J, Clarke S, Bedford MT (2005) PRMT8, a new membrane-bound tissue-specific member of the protein arginine methyltransferase family. J Biol Chem 280:32890-32896]. Interestingly, its tissue distribution is strikingly restricted to mouse CNS. To characterize the function in the CNS neurons, we raised an antiserum against PRMT8 to perform immunohistochemistry (IHC) and Western blot analysis. By IHC, the immunoreactivity of endogenous PRMT8 was broadly distributed in the CNS neurons with markedly intense signals in the cerebellum, hippocampal formation, and cortex, but was not detected in the cerebellar granular layer. In some subset of the neurons, the immunoreactivity was observed in the dendrites and axon bundles. The subcellular localization of the immunoreactivity was dominantly nuclear, arguing against the original report that exogenously expressed PRMT8 localizes to the plasma membrane via the N-terminal myristoylation. A series of the exogenously expressed proteins with different in-frame translation initiation codons was tested for comparison with the endogenous protein in molecular size. The third initiator codon produced the protein that was equivalent in size to the endogenous and showed a similar localizing pattern in PC12 cells. In conclusion, PRMT8 is a neuron-specific nuclear enzyme and the N-terminus does not contain the glycine end for myristoylation target.
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Affiliation(s)
- A Kousaka
- Department of Anatomy and Neuroscience, Graduate School of Medicine, The Osaka-Hamamatsu Joint Research Center for Child Mental Development, Osaka University, 2-2 Yamadaoka, Suita City, Osaka, Japan
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264
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Wolf SS. The protein arginine methyltransferase family: an update about function, new perspectives and the physiological role in humans. Cell Mol Life Sci 2009; 66:2109-21. [PMID: 19300908 PMCID: PMC11115746 DOI: 10.1007/s00018-009-0010-x] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 02/19/2009] [Accepted: 02/20/2009] [Indexed: 12/12/2022]
Abstract
Information about the family of protein arginine methyltransferases (PRMTs) has been growing rapidly over the last few years and the emerging role of arginine methylation involved in cellular processes like signaling, RNA processing, gene transcription, and cellular transport function has been investigated. To date, 11 PRMTs gene transcripts have been identified in humans. Almost all PRMTs have been shown to have enzymatic activity and to catalyze arginine methylation. This review will summarize the overall function of human PRMTs and include novel highlights on each family member.
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Affiliation(s)
- S S Wolf
- Bayer Schering Pharma AG, Global Drug Discovery, TRG Women's Healthcare, Muellerstr 178, 13353, Berlin, Germany.
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265
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Arginine methylation analysis of the splicing-associated SR protein SFRS9/SRP30C. Cell Mol Biol Lett 2009; 14:657-69. [PMID: 19557313 PMCID: PMC6275941 DOI: 10.2478/s11658-009-0024-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 06/10/2009] [Indexed: 11/20/2022] Open
Abstract
The human SFRS9/SRp30c belongs to the SR family of splicing regulators. Despite evidence that members of this protein family may be targeted by arginine methylation, this has yet to be experimentally addressed. In this study, we found that SFRS9 is a target for PRMT1-mediated arginine methylation in vitro, and that it is immunoprecipitated from HEK-293 lysates by antibodies that recognize both mono- and dimethylated arginines. We further observed that upon treatment with the methylation inhibitor Adox, the fluorescent EGFP-SFRS9 re-localizes to dot-like structures in the cell nucleus. In subsequent confocal analyses, we found that EGFP-SFRS9 localizes to nucleoli in Adox-treated cells. Our findings indicate the importance of arginine methylation for the subnuclear localization of SFRS9.
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266
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Bressan GC, Quaresma AJC, Moraes EC, Manfiolli AO, Passos DO, Gomes MD, Kobarg J. Functional association of human Ki-1/57 with pre-mRNA splicing events. FEBS J 2009; 276:3770-83. [PMID: 19523114 DOI: 10.1111/j.1742-4658.2009.07092.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The cytoplasmic and nuclear protein Ki-1/57 was first identified in malignant cells from Hodgkin's lymphoma. Despite studies showing its phosphorylation, arginine methylation, and interaction with several regulatory proteins, the functional role of Ki-1/57 in human cells remains to be determined. Here, we investigated the relationship of Ki-1/57 with RNA functions. Through immunoprecipitation assays, we verified the association of Ki-1/57 with the endogenous splicing proteins hnRNPQ and SFRS9 in HeLa cell extracts. We also found that recombinant Ki-1/57 was able to bind to a poly-U RNA probe in electrophoretic mobility shift assays. In a classic splicing test, we showed that Ki-1/57 can modify the splicing site selection of the adenoviral E1A minigene in a dose-dependent manner. Further confocal and fluorescence microscopy analysis revealed the localization of enhanced green fluorescent proteinKi-1/57 to nuclear bodies involved in RNA processing and or small nuclear ribonucleoprotein assembly, depending on the cellular methylation status and its N-terminal region. In summary, our findings suggest that Ki-1/57 is probably involved in cellular events related to RNA functions, such as pre-mRNA splicing.
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267
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Michaud-Levesque J, Richard S. Thrombospondin-1 is a transcriptional repression target of PRMT6. J Biol Chem 2009; 284:21338-46. [PMID: 19509293 DOI: 10.1074/jbc.m109.005322] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Protein arginine methyltransferase 6 (PRMT6) is known to catalyze the generation of asymmetric dimethylarginine in polypeptides. Although the cellular role of PRMT6 is not well understood, it has been implicated in human immunodeficiency virus pathogenesis, DNA repair, and transcriptional regulation. PRMT6 is known to methylate histone H3 Arg-2 (H3R2), and this negatively regulates the lysine methylation of H3K4 resulting in gene repression. To identify in a nonbiased manner genes regulated by PRMT6 expression, we performed a microarray analysis on U2OS osteosarcoma cells transfected with control and PRMT6 small interfering RNAs. We identified thrombospondin-1 (TSP-1), a potent natural inhibitor of angiogenesis, as a transcriptional repression target of PRMT6. Moreover, we show that PRMT6-deficient U2OS cells exhibited cell migration defects that were rescued by blocking the secreted TSP-1 with a neutralizing peptide or blocking alpha-TSP-1 antibody. PRMT6 associates with the TSP-1 promoter and regulates the balance of methylation of H3R2 and H3K4, such that in PRMT6-deficient cells H3R2 was hypomethylated and H3K4 was trimethylated at the TSP-1 promoter. Using a TSP-1 promoter reporter gene, we further show that PRMT6 directly regulates the TSP-1 promoter activity. These findings show that TSP-1 is a transcriptional repression target of PRMT6 and suggest that neutralizing the activity of PRMT6 could inhibit tumor progression and therefore may be of cancer therapeutic significance.
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Affiliation(s)
- Jonathan Michaud-Levesque
- Terry Fox Molecular Oncology Group and the Bloomfield Center for Research on Aging, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, and Departments of Oncology and Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
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268
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Optimization of pyrazole inhibitors of Coactivator Associated Arginine Methyltransferase 1 (CARM1). Bioorg Med Chem Lett 2009; 19:2924-7. [DOI: 10.1016/j.bmcl.2009.04.075] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2009] [Revised: 04/09/2009] [Accepted: 04/17/2009] [Indexed: 11/22/2022]
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269
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Lupien M, Eeckhoute J, Meyer CA, Krum SA, Rhodes DR, Liu XS, Brown M. Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol 2009; 29:3413-23. [PMID: 19364822 PMCID: PMC2698732 DOI: 10.1128/mcb.00020-09] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/16/2009] [Accepted: 03/29/2009] [Indexed: 01/24/2023] Open
Abstract
Proper activation of transcriptional networks in complex organisms is central to the response to stimuli. We demonstrate that the selective activation of a subset of the estrogen receptor alpha (ERalpha) cistrome in MCF7 breast cancer cells provides specificity to the estradiol (E2) response. ERalpha-specific enhancers that are subject to E2-induced coactivator-associated arginine methyltransferase 1 (CARM1) action are critical to E2-stimulated gene expression. This is true for both FoxA1-dependent and independent enhancers. In contrast, a subset of E2-suppressed genes are controlled by FoxA1-independent ERalpha binding sites. Nonetheless, these are sites of E2-induced CARM1 activity. In addition, the MCF7 RNA polymerase II cistrome reveals preferential occupancy of E2-regulated promoters prior to stimulation. Interestingly, E2-suppressed genes tend to lie in otherwise silent genomic regions. Together, our results suggest that the transcriptional response to E2 in breast cancer cells is dependent on the interplay between polymerase II pre-occupied promoters and the subset of the ERalpha cistrome associated with coactivation.
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Affiliation(s)
- Mathieu Lupien
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney St., Boston, MA 02115, USA
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270
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Kofler M, Schuemann M, Merz C, Kosslick D, Schlundt A, Tannert A, Schaefer M, Lührmann R, Krause E, Freund C. Proline-rich sequence recognition: I. Marking GYF and WW domain assembly sites in early spliceosomal complexes. Mol Cell Proteomics 2009; 8:2461-73. [PMID: 19483244 DOI: 10.1074/mcp.m900191-mcp200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proline-rich sequences (PRS) and their recognition domains have emerged as transposable protein interaction modules during eukaryotic evolution. They are especially abundant in proteins associated with pre-mRNA splicing and likely assist in the formation of the spliceosome by binding to GYF and WW domains. Here we profile PRS-mediated interactions of the CD2BP2/52K GYF domain by a site-specific peptide inhibitor and stable isotope labeling/mass spectrometry analysis. Several PRS hubs with multiple proline-rich motifs exist that can recruit GYF and/or WW domains. Saturating the PRS sites by an isolated GYF domain inhibited splicing at the level of A complex formation. The interactions mediated by PRS are therefore important to the early phases of spliceosomal assembly.
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Affiliation(s)
- Michael Kofler
- Protein Engineering Group, Leibniz Institute for Molecular Pharmacology and Freie Universität Berlin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
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271
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Perreault A, Gascon S, D'Amours A, Aletta JM, Bachand F. A methyltransferase-independent function for Rmt3 in ribosomal subunit homeostasis. J Biol Chem 2009; 284:15026-37. [PMID: 19359250 DOI: 10.1074/jbc.m109.004812] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Schizosaccharomyces pombe Rmt3 is a member of the protein-arginine methyltransferase (PRMT) family and is the homolog of human PRMT3. We previously characterized Rmt3 as a ribosomal protein methyltransferase based on the identification of the 40 S Rps2 (ribosomal protein S2) as a substrate of Rmt3. RMT3-null cells produce nonmethylated Rps2 and show mis-regulation of the 40 S/60 S ribosomal subunit ratio due to a small subunit deficit. For this study, we have generated a series of RMT3 alleles that express various amino acid substitutions to characterize the functional domains of Rmt3 in Rps2 binding, Rps2 arginine methylation, and small ribosomal subunit production. Notably, catalytically inactive versions of Rmt3 restored the ribosomal subunit imbalance detected in RMT3-null cells. Consistent with a methyltransferase-independent function for Rmt3 in small ribosomal subunit production, the expression of an Rps2 variant in which the identified methylarginine residues were substituted with lysines showed normal levels of 40 S subunit. Importantly, substitutions within the zinc finger domain of Rmt3 that abolished Rps2 binding did not rescue the 40 S ribosomal subunit deficit of RMT3-null cells. Our findings suggest that the Rmt3-Rps2 interaction, rather than Rps2 methylation, is important for the function of Rmt3 in the regulation of small ribosomal subunit production.
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Affiliation(s)
- Audrey Perreault
- RNA Group, Department of Biochemistry, Université de Sherbrooke, Québec J1H 5N4, Canada
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272
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Shao J, Xu D, Tsai SN, Wang Y, Ngai SM. Computational identification of protein methylation sites through bi-profile Bayes feature extraction. PLoS One 2009; 4:e4920. [PMID: 19290060 PMCID: PMC2654709 DOI: 10.1371/journal.pone.0004920] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Accepted: 02/19/2009] [Indexed: 11/21/2022] Open
Abstract
Protein methylation is one type of reversible post-translational modifications (PTMs), which plays vital roles in many cellular processes such as transcription activity, DNA repair. Experimental identification of methylation sites on proteins without prior knowledge is costly and time-consuming. In silico prediction of methylation sites might not only provide researches with information on the candidate sites for further determination, but also facilitate to perform downstream characterizations and site-specific investigations. In the present study, a novel approach based on Bi-profile Bayes feature extraction combined with support vector machines (SVMs) was employed to develop the model for Prediction of Protein Methylation Sites (BPB-PPMS) from primary sequence. Methylation can occur at many residues including arginine, lysine, histidine, glutamine, and proline. For the present, BPB-PPMS is only designed to predict the methylation status for lysine and arginine residues on polypeptides due to the absence of enough experimentally verified data to build and train prediction models for other residues. The performance of BPB-PPMS is measured with a sensitivity of 74.71%, a specificity of 94.32% and an accuracy of 87.98% for arginine as well as a sensitivity of 70.05%, a specificity of 77.08% and an accuracy of 75.51% for lysine in 5-fold cross validation experiments. Results obtained from cross-validation experiments and test on independent data sets suggest that BPB-PPMS presented here might facilitate the identification and annotation of protein methylation. Besides, BPB-PPMS can be extended to build predictors for other types of PTM sites with ease. For public access, BPB-PPMS is available at http://www.bioinfo.bio.cuhk.edu.hk/bpbppms.
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Affiliation(s)
- Jianlin Shao
- Department of Biology, The Chinese University of Hong Kong, Hong Kong, China
| | - Dong Xu
- Department of Mathematics & Scientific Computing Key Laboratory of Shanghai Universities, Shanghai Normal University, Shanghai, China
| | - Sau-Na Tsai
- Department of Biology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yifei Wang
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Sai-Ming Ngai
- Department of Biology, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Plant Molecular Biology and Agricultural Biotechnology, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail:
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273
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Heinke R, Spannhoff A, Meier R, Trojer P, Bauer I, Jung M, Sippl W. Virtual screening and biological characterization of novel histone arginine methyltransferase PRMT1 inhibitors. ChemMedChem 2009; 4:69-77. [PMID: 19085993 DOI: 10.1002/cmdc.200800301] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Lysine and arginine methyltransferases participate in the posttranslational modification of histones and regulate key cellular functions. Protein arginine methyltransferase 1 (PRMT1) has been identified as an essential component of mixed lineage leukemia (MLL) oncogenic complexes, revealing its potential as a novel therapeutic target in human cancer. The first potent arginine methyltransferase inhibitors were recently discovered by random- and target-based screening approaches. Herein we report virtual and biological screening for novel inhibitors of PRMT1. Structure-based virtual screening (VS) of the Chembridge database composed of 328 000 molecules was performed with a combination of ligand- and target-based in silico approaches. Nine inhibitors were identified from the top-scored docking solutions; these were experimentally tested using human PRMT1 and an antibody-based assay with a time-resolved fluorescence readout. Among several aromatic amines, an aliphatic amine and an amide were also found to be active in the micromolar range.
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Affiliation(s)
- Ralf Heinke
- Universität Halle-Wittenberg, Department of Pharmaceutical Chemistry, Wolfgang-Langenbeckstrasse 4, 06120 Halle/Saale, Germany
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274
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Herrmann F, Pably P, Eckerich C, Bedford MT, Fackelmayer FO. Human protein arginine methyltransferases in vivo--distinct properties of eight canonical members of the PRMT family. J Cell Sci 2009; 122:667-77. [PMID: 19208762 DOI: 10.1242/jcs.039933] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Methylation of arginine residues is a widespread post-translational modification of proteins catalyzed by a small family of protein arginine methyltransferases (PRMTs). Functionally, the modification appears to regulate protein functions and interactions that affect gene regulation, signalling and subcellular localization of proteins and nucleic acids. All members have been, to different degrees, characterized individually and their implication in cellular processes has been inferred from characterizing substrates and interactions. Here, we report the first comprehensive comparison of all eight canonical members of the human PRMT family with respect to subcellular localization and dynamics in living cells. We show that the individual family members differ significantly in their properties, as well as in their substrate specificities, suggesting that they fulfil distinctive, non-redundant functions in vivo. In addition, certain PRMTs display different subcellular localization in different cell types, implicating cell- and tissue-specific mechanisms for regulating PRMT functions.
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Affiliation(s)
- Frank Herrmann
- EMBL-CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), c/Dr. Aiguader 88, 08003 Barcelona, Spain
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275
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Abstract
The covalent marking of proteins by methyl group addition to arginine residues can promote their recognition by binding partners or can modulate their biological activity. A small family of gene products that catalyze such methylation reactions in eukaryotes (PRMTs) works in conjunction with a changing cast of associated subunits to recognize distinct cellular substrates. These reactions display many of the attributes of reversible covalent modifications such as protein phosphorylation or protein lysine methylation; however, it is unclear to what extent protein arginine demethylation occurs. Physiological roles for protein arginine methylation have been established in signal transduction, mRNA splicing, transcriptional control, DNA repair, and protein translocation.
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276
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Distinct protein arginine methyltransferases promote ATP-dependent chromatin remodeling function at different stages of skeletal muscle differentiation. Mol Cell Biol 2009; 29:1909-21. [PMID: 19188441 DOI: 10.1128/mcb.00742-08] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Temporal regulation of gene expression is a hallmark of cellular differentiation pathways, yet the mechanisms controlling the timing of expression for different classes of differentiation-specific genes are not well understood. We previously demonstrated that the class II arginine methyltransferase Prmt5 was required for skeletal muscle differentiation at the early stages of myogenesis (C. S. Dacwag, Y. Ohkawa, S. Pal, S. Sif, and A. N. Imbalzano, Mol. Cell. Biol. 27:384-394, 2007). Specifically, when Prmt5 levels were reduced, the ATP-dependent SWI/SNF chromatin-remodeling enzymes could not interact with or remodel the promoter of myogenin, an essential early gene. Here we investigated the requirement for Prmt5 and the class I arginine methyltransferase Carm1/Prmt4 in the temporal control of myogenesis. Both arginine methyltransferases could bind to and modify histones at late-gene regulatory sequences. However, the two enzymes showed sequential requirements for gene expression. Prmt5 was required for early-gene expression but dispensable for late-gene expression. Carm1/Prmt4 was required for late- but not for early-gene expression. The reason for the requirement for Carm1/Prmt4 at late genes was to facilitate SWI/SNF chromatin-remodeling enzyme interaction and remodeling at late-gene loci. Thus, distinct arginine methyltransferases are employed at different times of skeletal muscle differentiation for the purpose of facilitating ATP-dependent chromatin-remodeling enzyme interaction and function at myogenic genes.
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277
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Lee YH, Stallcup MR. Minireview: protein arginine methylation of nonhistone proteins in transcriptional regulation. Mol Endocrinol 2009; 23:425-33. [PMID: 19164444 DOI: 10.1210/me.2008-0380] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Endocrine regulation frequently culminates in altered transcription of specific genes. The signal transduction pathways, which transmit the endocrine signal from cell surface to the transcription machinery, often involve posttranslational modifications of proteins. Although phosphorylation has been by far the most widely studied protein modification, recent studies have indicated important roles for other types of modification, including protein arginine methylation. Ten different protein arginine methyltransferase (PRMT) family members have been identified in mammalian cells, and numerous substrates are being identified for these PRMTs. Whereas major attention has been focused on the methylation of histones and its role in chromatin remodeling and transcriptional regulation, there are many nonhistone substrates methylated by PRMTs. This review primarily focuses on recent progress on the roles of the nonhistone protein methylation in transcription. Protein methylation of coactivators, transcription factors, and signal transducers, among other proteins, plays important roles in transcriptional regulation. Protein methylation may affect protein-protein interaction, protein-DNA or protein-RNA interaction, protein stability, subcellular localization, or enzymatic activity. Thus, protein arginine methylation is critical for regulation of transcription and potentially for various physiological/pathological processes.
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Affiliation(s)
- Young-Ho Lee
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Los Angeles, California 90089-9176, USA
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278
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Tini M, Naeem H, Torchia J. Biochemical analysis of arginine methylation in transcription. Methods Mol Biol 2009; 523:235-47. [PMID: 19381935 DOI: 10.1007/978-1-59745-190-1_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Protein arginine methylation has emerged as an important mechanism for regulating the functions of proteins involved in diverse aspects of gene regulation such as transcriptional activation and repression, mRNA processing and nuclear-cytoplasmic shuttling. This modification is catalyzed by the PRMT family of enzymes which utilize intracellular S-adenosyl methionine as a cofactor to dimethylate-specific arginines found within many target proteins.The establishment of in vitro biochemical assays as well as the development of modification-specific antibodies, and more recently mass spectrometry, have increased our understanding of the mechanism of catalysis of the PRMT family of enzymes. In the following discussion, we present some of the more commonly used in vivo and in vitro techniques which can be utilized to study the mechanism of arginine methylation and its role in transcription.
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Affiliation(s)
- Marc Tini
- Department of Physiology and Pharmacology, The University of Western Ontario, London, Ontario, Canada
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279
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Allan M, Manku S, Therrien E, Nguyen N, Styhler S, Robert MF, Goulet AC, Petschner AJ, Rahil G, Robert Macleod A, Déziel R, Besterman JM, Nguyen H, Wahhab A. N-Benzyl-1-heteroaryl-3-(trifluoromethyl)-1H-pyrazole-5-carboxamides as inhibitors of co-activator associated arginine methyltransferase 1 (CARM1). Bioorg Med Chem Lett 2008; 19:1218-23. [PMID: 19131248 DOI: 10.1016/j.bmcl.2008.12.075] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 12/16/2008] [Accepted: 12/17/2008] [Indexed: 11/25/2022]
Abstract
A series of N-benzyl-1-heteroaryl-3-(trifluoromethyl)-1H-pyrazole-5-carboxamides targeting co-activator associated arginine methyltransferase 1 (CARM1) have been designed and synthesized. The potency of these inhibitors was influenced by the nature of the heteroaryl fragment with the thiophene analogues being superior to thiazole, pyridine, isoindoline and benzofuran based inhibitors.
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Affiliation(s)
- Martin Allan
- MethylGene Inc., Department of Medicinal Chemistry, 7220 rue Frederick-Banting, Montreal, Que., Canada H4S 2A1
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280
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Patel SB, Bellini M. The assembly of a spliceosomal small nuclear ribonucleoprotein particle. Nucleic Acids Res 2008; 36:6482-93. [PMID: 18854356 PMCID: PMC2582628 DOI: 10.1093/nar/gkn658] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The U1, U2, U4, U5 and U6 small nuclear ribonucleoprotein particles (snRNPs) are essential elements of the spliceosome, the enzyme that catalyzes the excision of introns and the ligation of exons to form a mature mRNA. Since their discovery over a quarter century ago, the structure, assembly and function of spliceosomal snRNPs have been extensively studied. Accordingly, the functions of splicing snRNPs and the role of various nuclear organelles, such as Cajal bodies (CBs), in their nuclear maturation phase have already been excellently reviewed elsewhere. The aim of this review is, then, to briefly outline the structure of snRNPs and to synthesize new and exciting developments in the snRNP biogenesis pathways.
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Affiliation(s)
- Snehal Bhikhu Patel
- Biochemistry and College of Medicine and Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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281
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Spannhoff A, Sippl W, Jung M. Cancer treatment of the future: inhibitors of histone methyltransferases. Int J Biochem Cell Biol 2008; 41:4-11. [PMID: 18773966 DOI: 10.1016/j.biocel.2008.07.024] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 07/01/2008] [Accepted: 07/08/2008] [Indexed: 10/21/2022]
Abstract
Cancer in humans is the result of a multi-step process. This process often involves the activation of oncogenes and/or the inactivation of tumor suppressor genes. These two steps arise not only due to mutations, but can also be the result of a translocation or an altered transcription rate. One important mechanism is the occurrence of epigenetic alterations like promotor methylation (which may lead to tumor suppressor silencing) or decreased histone acetylation (which can result in the downregulation of proteins involved in apoptosis). Today, histone acetylation and DNA methylation are epigenetic modifications which have been linked closely to the pathology of human cancers and inhibitors of both enzyme classes for clinical use are at hand. In contrast, other fields of epigenetics still lack of similarly thorough knowledge. This is especially true for the group of histone methyltransferases and their inhibitors. Since connections between histone methylation patterns and cancer progression have been recognized, histone methyltransferases represent promising targets for future cancer treatment.
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Affiliation(s)
- Astrid Spannhoff
- Albert-Ludwigs-Universität Freiburg, Institute of Pharmaceutical Sciences, Albertstr. 25, 79104 Freiburg, Germany
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282
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Goulet I, Boisvenue S, Mokas S, Mazroui R, Côté J. TDRD3, a novel Tudor domain-containing protein, localizes to cytoplasmic stress granules. Hum Mol Genet 2008; 17:3055-74. [PMID: 18632687 PMCID: PMC2536506 DOI: 10.1093/hmg/ddn203] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Our previous work has demonstrated that the Tudor domain of the ‘survival of motor neuron’ protein and the Tudor domain-containing protein 3 (TDRD3) are highly similar and that they both have the ability to interact with arginine-methylated polypeptides. TDRD3 has been identified among genes whose overexpression has a strong predictive value for poor prognosis of estrogen receptor-negative breast cancers, although its precise function remains unknown. TDRD3 is a modular protein, and in addition to its Tudor domain, it harbors a putative nucleic acid recognition motif and a ubiquitin-associated domain. We report here that TDRD3 localizes predominantly to the cytoplasm, where it co-sediments with the fragile X mental retardation protein on actively translating polyribosomes. We also demonstrate that TDRD3 accumulates into stress granules (SGs) in response to various cellular stresses. Strikingly, the Tudor domain of TDRD3 was found to be both required and sufficient for its recruitment to SGs, and the methyl-binding surface in the Tudor domain is important for this process. Pull down experiments identified five novel TDRD3 interacting partners, most of which are potentially methylated RNA-binding proteins. Our findings revealed that two of these proteins, SERPINE1 mRNA-binding protein 1 and DEAD/H box-3 (a gene often deleted in Sertoli-cell-only syndrome), are also novel constituents of cytoplasmic SGs. Taken together, we report the first characterization of TDRD3 and its functional interaction with at least two proteins implicated in human genetic diseases and present evidence supporting a role for arginine methylation in the regulation of SG dynamics.
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Affiliation(s)
- Isabelle Goulet
- Department of Cellular and Molecular Medicine and Centre for Neuromuscular Disease, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8M5
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283
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Pyrazole inhibitors of coactivator associated arginine methyltransferase 1 (CARM1). Bioorg Med Chem Lett 2008; 18:4438-41. [PMID: 18619839 DOI: 10.1016/j.bmcl.2008.06.026] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/06/2008] [Accepted: 06/09/2008] [Indexed: 11/20/2022]
Abstract
This study reports the identification and Hits to Leads optimization of inhibitors of coactivator associated arginine methyltransferase (CARM1). Compound 7b is a potent, selective inhibitor of CARM1.
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284
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Pandit S, Wang D, Fu XD. Functional integration of transcriptional and RNA processing machineries. Curr Opin Cell Biol 2008; 20:260-5. [PMID: 18436438 PMCID: PMC2701685 DOI: 10.1016/j.ceb.2008.03.001] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 03/10/2008] [Indexed: 12/23/2022]
Abstract
Cotranscriptional RNA processing not only permits temporal RNA processing before the completion of transcription but also allows sequential recognition of RNA processing signals on nascent transcripts threading out from the elongating RNA polymerase II (RNAPII) complex. Rapid progress in recent years has established multiple contacts that physically connect the transcription and RNA processing machineries, which centers on the C-terminal domain (CTD) of the largest subunit of RNAPII. Although cotranscriptional RNA processing has been substantiated, the evidence for 'reciprocal' coupling starts to emerge, which emphasizes functional integration of transcription and RNA processing machineries in a mutually beneficial manner for efficient and regulated gene expression.
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Affiliation(s)
- Shatakshi Pandit
- Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0651, United States
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285
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Kumar GVP, Selvi R, Kishore AH, Kundu TK, Narayana C. Surface-enhanced Raman spectroscopic studies of coactivator-associated arginine methyltransferase 1. J Phys Chem B 2008; 112:6703-7. [PMID: 18461904 DOI: 10.1021/jp711594z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We report, for the first time, the surface-enhanced Raman spectra of an important enzyme, coactivator-associated arginine methyltransferase 1 (CARM1), involved in various biological activities such as tumor suppressor function and stem cell differentiation. We have employed surface-enhanced Raman scattering (SERS) to obtain insight into the structural details of CARM1 by adsorbing it to silver (Ag) nanoparticles. The enzyme retains its activity even after its adsorption onto Ag nanoparticles. We observe strong SERS modes arising from amide vibrations and aromatic ring amino acids. The SERS spectra revealed amide I bands at 1637 cm(-1) and 1666 cm(-1), which arise as a result of the alpha helix of the protein and the polypeptide backbone vibration of a random coil, respectively. In order to confirm the amide vibrations, we have performed SERS on deuterated CARM1, which exhibits a clear red shift in amide band positions. The SERS spectra may provide useful information, which could be harnessed to study the functional interactions of CARM1 with small molecule modulators.
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Affiliation(s)
- G V Pavan Kumar
- Light Scattering Laboratory, Chemistry and Physics of Material Unit, Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur, Bangalore,-560064, India
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286
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Denman RB. Protein Methyltransferase Activities in Commercial In vitro Translation Systems. ACTA ACUST UNITED AC 2008; 144:223-33. [DOI: 10.1093/jb/mvn061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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287
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Brosch G, Loidl P, Graessle S. Histone modifications and chromatin dynamics: a focus on filamentous fungi. FEMS Microbiol Rev 2008; 32:409-39. [PMID: 18221488 PMCID: PMC2442719 DOI: 10.1111/j.1574-6976.2007.00100.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 11/13/2007] [Indexed: 12/19/2022] Open
Abstract
The readout of the genetic information of eukaryotic organisms is significantly regulated by modifications of DNA and chromatin proteins. Chromatin alterations induce genome-wide and local changes in gene expression and affect a variety of processes in response to internal and external signals during growth, differentiation, development, in metabolic processes, diseases, and abiotic and biotic stresses. This review aims at summarizing the roles of histone H1 and the acetylation and methylation of histones in filamentous fungi and links this knowledge to the huge body of data from other systems. Filamentous fungi show a wide range of morphologies and have developed a complex network of genes that enables them to use a great variety of substrates. This fact, together with the possibility of simple and quick genetic manipulation, highlights these organisms as model systems for the investigation of gene regulation. However, little is still known about regulation at the chromatin level in filamentous fungi. Understanding the role of chromatin in transcriptional regulation would be of utmost importance with respect to the impact of filamentous fungi in human diseases and agriculture. The synthesis of compounds (antibiotics, immunosuppressants, toxins, and compounds with adverse effects) is also likely to be regulated at the chromatin level.
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Affiliation(s)
- Gerald Brosch
- Division of Molecular Biology, Biocenter, Innsbruck Medical University, Fritz-Pregl-Strasse 3, Innsbruck, Austria
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288
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Hua Y, Vickers TA, Okunola HL, Bennett CF, Krainer AR. Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am J Hum Genet 2008; 82:834-48. [PMID: 18371932 DOI: 10.1016/j.ajhg.2008.01.014] [Citation(s) in RCA: 448] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 01/04/2008] [Accepted: 01/10/2008] [Indexed: 12/20/2022] Open
Abstract
Survival of motor neuron 2, centromeric (SMN2) is a gene that modifies the severity of spinal muscular atrophy (SMA), a motor-neuron disease that is the leading genetic cause of infant mortality. Increasing inclusion of SMN2 exon 7, which is predominantly skipped, holds promise to treat or possibly cure SMA; one practical strategy is the disruption of splicing silencers that impair exon 7 recognition. By using an antisense oligonucleotide (ASO)-tiling method, we systematically screened the proximal intronic regions flanking exon 7 and identified two intronic splicing silencers (ISSs): one in intron 6 and a recently described one in intron 7. We analyzed the intron 7 ISS by mutagenesis, coupled with splicing assays, RNA-affinity chromatography, and protein overexpression, and found two tandem hnRNP A1/A2 motifs within the ISS that are responsible for its inhibitory character. Mutations in these two motifs, or ASOs that block them, promote very efficient exon 7 inclusion. We screened 31 ASOs in this region and selected two optimal ones to test in human SMN2 transgenic mice. Both ASOs strongly increased hSMN2 exon 7 inclusion in the liver and kidney of the transgenic animals. Our results show that the high-resolution ASO-tiling approach can identify cis-elements that modulate splicing positively or negatively. Most importantly, our results highlight the therapeutic potential of some of these ASOs in the context of SMA.
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Affiliation(s)
- Yimin Hua
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
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289
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CARM1 promotes adipocyte differentiation by coactivating PPARgamma. EMBO Rep 2008; 9:193-8. [PMID: 18188184 DOI: 10.1038/sj.embor.7401151] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 11/16/2007] [Accepted: 11/19/2007] [Indexed: 11/08/2022] Open
Abstract
The coactivator-associated arginine methyltransferase 1 (CARM1) is recruited to gene promoters by many transcription factors. To identify new pathways that use CARM1, we carried out a comprehensive transcriptome analysis of CARM1-knockout embryos. By using complementary DNA microarrays and serial analysis of gene expression, we identified various genes involved in lipid metabolism that were underrepresented in CARM1-knockout embryos, indicating an important role for this coactivator in adipose tissue biology. We also observed that the amount of brown fat in CARM1-knockout embryos is reduced. Furthermore, cells lacking CARM1 have a severely curtailed potential to differentiate into mature adipocytes. Reporter experiments and chromatin immunoprecipitation analysis show that CARM1 regulates these processes by acting as a coactivator for peroxisome proliferator-activated receptor gamma (PPARgamma). Together, these results show that CARM1 promotes adipocyte differentiation by coactivating PPARgamma-mediated transcription and thus might be important in energy balance.
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290
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Pearson JL, Robinson TJ, Muñoz MJ, Kornblihtt AR, Garcia-Blanco MA. Identification of the cellular targets of the transcription factor TCERG1 reveals a prevalent role in mRNA processing. J Biol Chem 2008; 283:7949-61. [PMID: 18187414 DOI: 10.1074/jbc.m709402200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The transcription factor TCERG1 (also known as CA150) associates with RNA polymerase II holoenzyme and alters the elongation efficiency of reporter transcripts. TCERG1 is also found as a component of highly purified spliceosomes and has been implicated in splicing. To elucidate the function of TCERG1, we used short interfering RNA-mediated knockdown followed by en masse gene expression analysis to identify its cellular targets. Analysis of data from HEK293 and HeLa cells identified high confidence targets of TCERG1. We found that targets of TCERG1 were enriched in microRNA-binding sites, suggesting the possibility of post-transcriptional regulation. Consistently, reverse transcription-PCR analysis revealed that many of the changes observed upon TCERG1 knockdown were because of differences in alternative mRNA processing of the 3'-untranslated regions. Furthermore, a novel computational approach, which can identify alternatively processed events from conventional microarray data, showed that TCERG1 led to widespread alterations in mRNA processing. These findings provide the strongest support to date for a role of TCERG1 in mRNA processing and are consistent with proposals that TCERG1 couples transcription and processing.
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Affiliation(s)
- James L Pearson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
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291
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Affiliation(s)
- Mark T. Bedford
- Department of Carcinogenesis, The University of Texas M. D. Anderson Cancer Center, Smithville, TX 78957, USA
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292
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Iberg AN, Espejo A, Cheng D, Kim D, Michaud-Levesque J, Richard S, Bedford MT. Arginine methylation of the histone H3 tail impedes effector binding. J Biol Chem 2007; 283:3006-3010. [PMID: 18077460 DOI: 10.1074/jbc.c700192200] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Histone tail post-translational modification results in changes in cellular processes, either by generating or blocking docking sites for histone code readers or by altering the higher order chromatin structure. H3K4me3 is known to mark the promoter regions of active transcription. Proteins bind H3K4 in a methyl-dependent manner and aid in the recruitment of histone-remodeling enzymes and transcriptional cofactors. The H3K4me3 binders harbor methyl-specific chromatin binding domains, including plant homeodomain, Chromo, and tudor domains. Structural analysis of the plant homeodomains present in effector proteins, as well as the WD40 repeats of WDR5, reveals critical contacts between residues in these domains and H3R2. The intimate contact between H3R2 and these domain types leads to the hypothesis that methylation of this arginine residue antagonizes the binding of effector proteins to the N-terminal tail of H3. Here we show that H3 tail binding effector proteins are indeed sensitive to H3R2 methylation and that PRMT6, not CARM1/PRMT4, is the primary methyltransferase acting on this site. We have tested the expression of a select group of H3K4 effector-regulated genes in PRMT6 knockdown cells and found that their levels are altered. Thus, PRMT6 methylates H3R2 and is a negative regulator of N-terminal H3 tail binding.
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Affiliation(s)
- Aimee N Iberg
- The University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957
| | - Alexsandra Espejo
- The University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957
| | - Donghang Cheng
- The University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957
| | - Daehoon Kim
- The University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957
| | | | - Stephane Richard
- Terry Fox Molecular Oncology Group, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Mark T Bedford
- The University of Texas M.D. Anderson Cancer Center, Science Park-Research Division, Smithville, Texas 78957.
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293
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Goulet I, Gauvin G, Boisvenue S, Côté J. Alternative Splicing Yields Protein Arginine Methyltransferase 1 Isoforms with Distinct Activity, Substrate Specificity, and Subcellular Localization. J Biol Chem 2007; 282:33009-21. [PMID: 17848568 DOI: 10.1074/jbc.m704349200] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PRMT1 is the predominant member of a family of protein arginine methyltransferases (PRMTs) that have been implicated in various cellular processes, including transcription, RNA processing, and signal transduction. It was previously reported that the human PRMT1 pre-mRNA was alternatively spliced to yield three isoforms with distinct N-terminal sequences. Close inspection of the genomic organization in the 5'-end of the PRMT1 gene revealed that it can produce up to seven protein isoforms, all varying in their N-terminal domain. A detailed biochemical characterization of these variants revealed that unique N-terminal sequences can influence catalytic activity as well as substrate specificity. In addition, our results uncovered the presence of a functional nuclear export sequence in PRMT1v2. Finally, we find that the relative balance of PRMT1 isoforms is altered in breast cancer.
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Affiliation(s)
- Isabelle Goulet
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada
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294
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Yue WW, Hassler M, Roe SM, Thompson-Vale V, Pearl LH. Insights into histone code syntax from structural and biochemical studies of CARM1 methyltransferase. EMBO J 2007; 26:4402-12. [PMID: 17882261 PMCID: PMC2034666 DOI: 10.1038/sj.emboj.7601856] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 08/09/2007] [Indexed: 12/15/2022] Open
Abstract
Coactivator-associated arginine methyltransferase (CARM1) is a transcriptional coactivator that methylates Arg17 and Arg26 in histone H3. CARM1 contains a conserved protein arginine methyltransferase (PRMT) catalytic core flanked by unique pre- and post-core regions. The crystal structures of the CARM1 catalytic core in the apo and holo states reveal cofactor-dependent formation of a substrate-binding groove providing a specific access channel for arginine to the active site. The groove is supported by the first eight residues of the post-core region (C-extension), not present in other PRMTs. In vitro methylation assays show that the C-extension is essential for all histone H3 methylation activity, whereas the pre-core region is required for methylation of Arg26, but not Arg17. Kinetic analysis shows Arg17 methylation is potentiated by pre-acetylation of Lys18, and this is reflected in k(cat) rather than K(m). Together with the absence of specificity subsites in the structure, this suggests an electrostatic sensing mechanism for communicating the modification status of vicinal residues as part of the syntax of the 'histone code.'
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Affiliation(s)
- Wyatt W Yue
- Cancer Research-UK DNA Repair Enzyme Research Group, Section of Structural Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Markus Hassler
- Cancer Research-UK DNA Repair Enzyme Research Group, Section of Structural Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
- Cancer Research-UK Centre for Cell and Molecular Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - S Mark Roe
- Cancer Research-UK DNA Repair Enzyme Research Group, Section of Structural Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Vivienne Thompson-Vale
- Cancer Research-UK DNA Repair Enzyme Research Group, Section of Structural Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
| | - Laurence H Pearl
- Cancer Research-UK DNA Repair Enzyme Research Group, Section of Structural Biology, Chester Beatty Laboratories, Institute of Cancer Research, London, UK
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295
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Sayegh J, Webb K, Cheng D, Bedford MT, Clarke SG. Regulation of protein arginine methyltransferase 8 (PRMT8) activity by its N-terminal domain. J Biol Chem 2007; 282:36444-53. [PMID: 17925405 DOI: 10.1074/jbc.m704650200] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human protein arginine methyltransferase PRMT8 has been recently described as a type I enzyme in brain that is localized to the plasma membrane by N-terminal myristoylation. The amino acid sequence of human PRMT8 is almost 80% identical to human PRMT1, the major protein arginine methyltransferase activity in mammalian cells. However, the activity of a recombinant PRMT8 GST fusion protein toward methyl-accepting substrates is much lower than that of a GST fusion of PRMT1. We show here that both His-tagged and GST fusion species lacking the initial 60 amino acid residues of PRMT8 have enhanced enzymatic activity, suggesting that the N-terminal domain may regulate PRMT8 activity. This conclusion is supported by limited proteolysis experiments showing an increase in the activity of the digested full-length protein, consistent with the loss of the N-terminal domain. In contrast, the activity of the N-terminal truncated protein was slightly diminished by limited proteolysis. Significantly, we detect automethylation at two sites in the N-terminal domain, as well as binding sites for SH3 domain-containing proteins. We suggest that the N-terminal domain may function as an autoregulator that may be displaced by interaction with one or more physiological inducers.
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Affiliation(s)
- Joyce Sayegh
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California 90095-1569, USA
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296
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Borrelli S, Testoni B, Callari M, Alotto D, Castagnoli C, Romano RA, Sinha S, Viganò AM, Mantovani R. Reciprocal regulation of p63 by C/EBP delta in human keratinocytes. BMC Mol Biol 2007; 8:85. [PMID: 17903252 PMCID: PMC2148061 DOI: 10.1186/1471-2199-8-85] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 09/28/2007] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Genetic experiments have clarified that p63 is a key transcription factor governing the establishment and maintenance of multilayered epithelia. Key to our understanding of p63 strategy is the identification of target genes. We perfomed an RNAi screening in keratinocytes for p63, followed by profiling analysis. RESULTS C/EBPdelta, member of a family with known roles in differentiation pathways, emerged as a gene repressed by p63. We validated C/EBPdelta as a primary target of DeltaNp63alpha by RT-PCR and ChIP location analysis in HaCaT and primary cells. C/EBPdelta is differentially expressed in stratification of human skin and it is up-regulated upon differentiation of HaCaT and primary keratinocytes. It is bound to and activates the DeltaNp63 promoter. Overexpression of C/EBPdelta leads to alteration in the normal profile of p63 isoforms, with the emergence of DeltaNp63beta and gamma, and of the TA isoforms, with different kinetics. In addition, there are changes in the expression of most p63 targets. Inactivation of C/EBPdelta leads to gene expression modifications, in part due to the concomitant repression of DeltaNp63alpha. Finally, C/EBPdelta is found on the p63 targets in vivo by ChIP analysis, indicating that coregulation is direct. CONCLUSION Our data highlight a coherent cross-talk between these two transcription factors in keratinocytes and a large sharing of common transcriptional targets.
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Affiliation(s)
- Serena Borrelli
- Dipartimento di Scienze Biomolecolari e Biotecnologie. U. di Milano. Via Celoria 26, 20133 Milano, Italy
| | - Barbara Testoni
- Dipartimento di Scienze Biomolecolari e Biotecnologie. U. di Milano. Via Celoria 26, 20133 Milano, Italy
| | - Maurizio Callari
- Dipartimento di Scienze Biomolecolari e Biotecnologie. U. di Milano. Via Celoria 26, 20133 Milano, Italy
| | - Daniela Alotto
- Dipartimento di Chirurgia Plastica-Banca della Cute, Ospedale CTO, Torino, Italy
| | - Carlotta Castagnoli
- Dipartimento di Chirurgia Plastica-Banca della Cute, Ospedale CTO, Torino, Italy
| | | | | | - Alessandra M Viganò
- Dipartimento di Scienze Biomolecolari e Biotecnologie. U. di Milano. Via Celoria 26, 20133 Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Scienze Biomolecolari e Biotecnologie. U. di Milano. Via Celoria 26, 20133 Milano, Italy
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297
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Troffer-Charlier N, Cura V, Hassenboehler P, Moras D, Cavarelli J. Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains. EMBO J 2007; 26:4391-401. [PMID: 17882262 PMCID: PMC2034665 DOI: 10.1038/sj.emboj.7601855] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 08/21/2007] [Indexed: 11/08/2022] Open
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1), a protein arginine methyltransferase recruited by several transcription factors, methylates a large variety of proteins and plays a critical role in gene expression. We report, in this paper, four crystal structures of isolated modules of CARM1. The 1.7 A crystal structure of the N-terminal domain of CARM1 reveals an unexpected PH domain, a scaffold frequently found to regulate protein-protein interactions in a large variety of biological processes. Three crystal structures of the CARM1 catalytic module, two free and one cofactor-bound forms (refined at 2.55 A, 2.4 A and 2.2 A, respectively) reveal large structural modifications including disorder to order transition, helix to strand transition and active site modifications. The N-terminal and the C-terminal end of CARM1 catalytic module contain molecular switches that may inspire how CARM1 regulates its biological activities by protein-protein interactions.
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Affiliation(s)
- Nathalie Troffer-Charlier
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
| | - Vincent Cura
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
| | - Pierre Hassenboehler
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
| | - Dino Moras
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
| | - Jean Cavarelli
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
- Laboratoire de Biologie et Génomique Structurales, IGBMC (CNRS/INSERM/ULP), 1 rue Laurent Fries, BP 10142, Ilkirch 67404, France. Tel.: +33 388 65 5793; Fax: +33 388 65 3276; E-mail:
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298
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Iyer LM, Anantharaman V, Wolf MY, Aravind L. Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int J Parasitol 2007; 38:1-31. [PMID: 17949725 DOI: 10.1016/j.ijpara.2007.07.018] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 07/26/2007] [Accepted: 07/30/2007] [Indexed: 11/18/2022]
Abstract
Comparative genomics of parasitic protists and their free-living relatives are profoundly impacting our understanding of the regulatory systems involved in transcription and chromatin dynamics. While some parts of these systems are highly conserved, other parts are rapidly evolving, thereby providing the molecular basis for the variety in the regulatory adaptations of eukaryotes. The gross number of specific transcription factors and chromatin proteins are positively correlated with proteome size in eukaryotes. However, the individual types of specific transcription factors show an enormous variety across different eukaryotic lineages. The dominant families of specific transcription factors even differ between sister lineages, and have been shaped by gene loss and lineage-specific expansions. Recognition of this principle has helped in identifying the hitherto unknown, major specific transcription factors of several parasites, such as apicomplexans, Entamoeba histolytica, Trichomonas vaginalis, Phytophthora and ciliates. Comparative analysis of predicted chromatin proteins from protists allows reconstruction of the early evolutionary history of histone and DNA modification, nucleosome assembly and chromatin-remodeling systems. Many key catalytic, peptide-binding and DNA-binding domains in these systems ultimately had bacterial precursors, but were put together into distinctive regulatory complexes that are unique to the eukaryotes. In the case of histone methylases, histone demethylases and SWI2/SNF2 ATPases, proliferation of paralogous families followed by acquisition of novel domain architectures, seem to have played a major role in producing a diverse set of enzymes that create and respond to an epigenetic code of modified histones. The diversification of histone acetylases and DNA methylases appears to have proceeded via repeated emergence of new versions, most probably via transfers from bacteria to different eukaryotic lineages, again resulting in lineage-specific diversity in epigenetic signals. Even though the key histone modifications are universal to eukaryotes, domain architectures of proteins binding post-translationally modified-histones vary considerably across eukaryotes. This indicates that the histone code might be "interpreted" differently from model organisms in parasitic protists and their relatives. The complexity of domain architectures of chromatin proteins appears to have increased during eukaryotic evolution. Thus, Trichomonas, Giardia, Naegleria and kinetoplastids have relatively simple domain architectures, whereas apicomplexans and oomycetes have more complex architectures. RNA-dependent post-transcriptional silencing systems, which interact with chromatin-level regulatory systems, show considerable variability across parasitic protists, with complete loss in many apicomplexans and partial loss in Trichomonas vaginalis. This evolutionary synthesis offers a robust scaffold for future investigation of transcription and chromatin structure in parasitic protists.
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Affiliation(s)
- Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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299
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Gonsalvez GB, Tian L, Ospina JK, Boisvert FM, Lamond AI, Matera AG. Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins. ACTA ACUST UNITED AC 2007; 178:733-40. [PMID: 17709427 PMCID: PMC2064538 DOI: 10.1083/jcb.200702147] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Small nuclear ribonucleoproteins (snRNPs) are core components of the spliceosome. The U1, U2, U4, and U5 snRNPs each contain a common set of seven Sm proteins. Three of these Sm proteins are posttranslationally modified to contain symmetric dimethylarginine (sDMA) residues within their C-terminal tails. However, the precise function of this modification in the snRNP biogenesis pathway is unclear. Several lines of evidence suggest that the methyltransferase protein arginine methyltransferase 5 (PRMT5) is responsible for sDMA modification of Sm proteins. We found that in human cells, PRMT5 and a newly discovered type II methyltransferase, PRMT7, are each required for Sm protein sDMA modification. Furthermore, we show that the two enzymes function nonredundantly in Sm protein methylation. Lastly, we provide in vivo evidence demonstrating that Sm protein sDMA modification is required for snRNP biogenesis in human cells.
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Affiliation(s)
- Graydon B Gonsalvez
- Department of Genetics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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300
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Troffer-Charlier N, Cura V, Hassenboehler P, Moras D, Cavarelli J. Expression, purification, crystallization and preliminary crystallographic study of isolated modules of the mouse coactivator-associated arginine methyltransferase 1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:330-3. [PMID: 17401209 PMCID: PMC2330207 DOI: 10.1107/s1744309107011785] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Accepted: 03/13/2007] [Indexed: 11/10/2022]
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1) plays a crucial role in gene expression as a coactivator of several nuclear hormone receptors and also of non-nuclear receptor systems. Its recruitment by the transcriptional machinery induces protein methylation, leading to chromatin remodelling and gene activation. CARM1(28-507) and two structural states of CARM1(140-480) were expressed, purified and crystallized. Crystals of CARM1(28-507) belong to space group P6(2)22, with unit-cell parameters a = b = 136.0, c = 125.3 A; they diffract to beyond 2.5 A resolution using synchrotron radiation and contain one monomer in the asymmetric unit. The structure of CARM1(28-507) was solved by multiple isomorphous replacement and anomalous scattering methods. Crystals of apo CARM1(140-480) belong to space group I222, with unit-cell parameters a = 74.6, b = 99.0, c = 207.4 A; they diffract to beyond 2.7 A resolution and contain two monomers in the asymmetric unit. Crystals of CARM1(140-480) in complex with S-adenosyl-L-homocysteine belong to space P2(1)2(1)2, with unit-cell parameters a = 74.6, b = 98.65, c = 206.08 A; they diffract to beyond 2.6 A resolution and contain four monomers in the asymmetric unit. The structures of apo and holo CARM1(140-480) were solved by molecular-replacement techniques from the structure of CARM1(28-507).
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Affiliation(s)
- Nathalie Troffer-Charlier
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie et Génomique Structurales, 1 Rue Laurent Fries, Illkirch, F-67404, France; INSERM, U596, Illkirch, F-67400, France; CNRS, UMR7104, Illkirch, F-67400, France; Université Louis Pasteur, Faculté des Sciences de la Vie, Strasbourg, F-67000, France
| | - Vincent Cura
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie et Génomique Structurales, 1 Rue Laurent Fries, Illkirch, F-67404, France; INSERM, U596, Illkirch, F-67400, France; CNRS, UMR7104, Illkirch, F-67400, France; Université Louis Pasteur, Faculté des Sciences de la Vie, Strasbourg, F-67000, France
| | - Pierre Hassenboehler
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie et Génomique Structurales, 1 Rue Laurent Fries, Illkirch, F-67404, France; INSERM, U596, Illkirch, F-67400, France; CNRS, UMR7104, Illkirch, F-67400, France; Université Louis Pasteur, Faculté des Sciences de la Vie, Strasbourg, F-67000, France
| | - Dino Moras
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie et Génomique Structurales, 1 Rue Laurent Fries, Illkirch, F-67404, France; INSERM, U596, Illkirch, F-67400, France; CNRS, UMR7104, Illkirch, F-67400, France; Université Louis Pasteur, Faculté des Sciences de la Vie, Strasbourg, F-67000, France
| | - Jean Cavarelli
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Département de Biologie et Génomique Structurales, 1 Rue Laurent Fries, Illkirch, F-67404, France; INSERM, U596, Illkirch, F-67400, France; CNRS, UMR7104, Illkirch, F-67400, France; Université Louis Pasteur, Faculté des Sciences de la Vie, Strasbourg, F-67000, France
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