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Identification and characterization of a highly conserved crenarchaeal protein lysine methyltransferase with broad substrate specificity. J Bacteriol 2012; 194:6917-26. [PMID: 23086207 DOI: 10.1128/jb.01535-12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Protein lysine methylation occurs extensively in the Crenarchaeota, a major kingdom in the Archaea. However, the enzymes responsible for this type of posttranslational modification have not been found. Here we report the identification and characterization of the first crenarchaeal protein lysine methyltransferase, designated aKMT, from the hyperthermophilic crenarchaeon Sulfolobus islandicus. The enzyme was capable of transferring methyl groups to selected lysine residues in a substrate protein using S-adenosyl-l-methionine (SAM) as the methyl donor. aKMT, a non-SET domain protein, is highly conserved among crenarchaea, and distantly related homologs also exist in Bacteria and Eukarya. aKMT was active over a wide range of temperatures, from ~25 to 90 °C, with an optimal temperature at ~60 to 70 °C. Amino acid residues Y9 and T12 at the N terminus appear to be the key residues in the putative active site of aKMT, as indicated by sequence conservation and site-directed mutagenesis. Although aKMT was identified based on its methylating activity on Cren7, the crenarchaeal chromatin protein, it exhibited broad substrate specificity and was capable of methylating a number of recombinant Sulfolobus proteins overproduced in Escherichia coli. The finding of aKMT will help elucidate mechanisms underlining extensive protein lysine methylation and the functional significance of posttranslational protein methylation in crenarchaea.
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152
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Epigenetic aspects of MDS and its molecular targeted therapy. Int J Hematol 2012; 97:175-82. [PMID: 23054654 DOI: 10.1007/s12185-012-1197-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/19/2012] [Accepted: 09/25/2012] [Indexed: 10/27/2022]
Abstract
The term "epigenetics" refers to clonally inherited stable variability in gene expression without underlying genetic changes. There are two well-known molecular mechanisms for epigenetic information: DNA methylation and histone modifications. Epigenetic changes have been recognized in the past decade as critical factors for physiological phenomena such as embryogenesis and the differentiation of normal cells. There is recent interest regarding the involvement of aberrant DNA methylation and histone modifications in mediating altered physiology in cancer. MDS is characterized by epigenetic changes, mutations in epigenetic regulators, and response to DNA methylation inhibitors, suggesting that epigenetic changes are unique features of MDS patients. In this article, recent progress in the understanding of MDS epigenetics and epigenetics-based therapies is reviewed.
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153
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Margaritis T, Oreal V, Brabers N, Maestroni L, Vitaliano-Prunier A, Benschop JJ, van Hooff S, van Leenen D, Dargemont C, Géli V, Holstege FCP. Two distinct repressive mechanisms for histone 3 lysine 4 methylation through promoting 3'-end antisense transcription. PLoS Genet 2012; 8:e1002952. [PMID: 23028359 PMCID: PMC3447963 DOI: 10.1371/journal.pgen.1002952] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 07/31/2012] [Indexed: 12/14/2022] Open
Abstract
Histone H3 di- and trimethylation on lysine 4 are major chromatin marks that correlate with active transcription. The influence of these modifications on transcription itself is, however, poorly understood. We have investigated the roles of H3K4 methylation in Saccharomyces cerevisiae by determining genome-wide expression-profiles of mutants in the Set1 complex, COMPASS, that lays down these marks. Loss of H3K4 trimethylation has virtually no effect on steady-state or dynamically-changing mRNA levels. Combined loss of H3K4 tri- and dimethylation results in steady-state mRNA upregulation and delays in the repression kinetics of specific groups of genes. COMPASS-repressed genes have distinct H3K4 methylation patterns, with enrichment of H3K4me3 at the 3′-end, indicating that repression is coupled to 3′-end antisense transcription. Further analyses reveal that repression is mediated by H3K4me3-dependent 3′-end antisense transcription in two ways. For a small group of genes including PHO84, repression is mediated by a previously reported trans-effect that requires the antisense transcript itself. For the majority of COMPASS-repressed genes, however, it is the process of 3′-end antisense transcription itself that is the important factor for repression. Strand-specific qPCR analyses of various mutants indicate that this more prevalent mechanism of COMPASS-mediated repression requires H3K4me3-dependent 3′-end antisense transcription to lay down H3K4me2, which seems to serve as the actual repressive mark. Removal of the 3′-end antisense promoter also results in derepression of sense transcription and renders sense transcription insensitive to the additional loss of SET1. The derepression observed in COMPASS mutants is mimicked by reduction of global histone H3 and H4 levels, suggesting that the H3K4me2 repressive effect is linked to establishment of a repressive chromatin structure. These results indicate that in S. cerevisiae, the non-redundant role of H3K4 methylation by Set1 is repression, achieved through promotion of 3′-end antisense transcription to achieve specific rather than global effects through two distinct mechanisms. In eukaryotes, DNA is packaged together with histones into nucleosomes. This packaging has a repressive role on gene expression. The N-termini of histones are subject to multiple modifications that affect DNA–dependent processes. The histone modification that has been predominantly linked with active transcription in all eukaryotes is histone H3 lysine 4 (H3K4) methylation. Here we investigate the functional effects of each H3K4 methylation state on transcription. Removal of the mark that is most characteristic for transcription, H3K4 trimethylation, has no effect on coding gene expression, in steady-state or dynamically changing conditions. Combined loss of H3K4 tri- and di-methylation does have an effect and leads to loss of repression of specific genes, the opposite of what is expected for global marks of active genes. The affected genes have antisense transcription. We show that there are two separate mechanisms through which H3K4 methylation represses transcription of protein-coding genes, one through antisense transcripts and one through the process of antisense transcription. In summary, we show how a general mark of active transcription can have specific repressive effects that are themselves also linked to repression through nucleosomes.
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Affiliation(s)
- Thanasis Margaritis
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vincent Oreal
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | - Nathalie Brabers
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Laetitia Maestroni
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
| | | | - Joris J. Benschop
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sander van Hooff
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dik van Leenen
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Catherine Dargemont
- Institut Jacques Monod, Université Paris Diderot, CNRS, Paris, France
- * E-mail: (CD); (VG); (FCPH)
| | - Vincent Géli
- Marseille Cancer Research Center (CRCM), U1068 Inserm, UMR7258 CNRS, Aix-Marseille Université, Institut Paoli-Calmettes, Marseille, France
- * E-mail: (CD); (VG); (FCPH)
| | - Frank C. P. Holstege
- Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail: (CD); (VG); (FCPH)
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154
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Paradowska AS, Miller D, Spiess AN, Vieweg M, Cerna M, Dvorakova-Hortova K, Bartkuhn M, Schuppe HC, Weidner W, Steger K. Genome wide identification of promoter binding sites for H4K12ac in human sperm and its relevance for early embryonic development. Epigenetics 2012; 7:1057-70. [PMID: 22894908 PMCID: PMC3466190 DOI: 10.4161/epi.21556] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Sperm chromatin reveals two characteristic features in that protamines are the predominant nuclear proteins and remaining histones are highly acetylated. Histone H4 acetylated at lysine 12 (H4K12ac) is localized in the post-acrosomal region, while protamine-1 is present within the whole nucleus. Chromatin immunoprecipitation in combination with promoter array analysis allowed genome-wide identification of H4K12ac binding sites. Previously, we reported enrichment of H4K12ac at CTCF binding sites and promoters of genes involved in developmental processes. Here, we demonstrate that H4K12ac is enriched predominantly between ± 2 kb from the transcription start site. In addition, we identified developmentally relevant H4K12ac-associated promoters with high expression levels of their transcripts stored in mature sperm. The highest expressed mRNA codes for testis-specific PHD finger protein-7 (PHF7), suggesting an activating role of H4K12ac in the regulatory elements of this gene. H4K12ac-associated genes revealed a weak correlation with genes expressed at 4-cell stage human embryos, while 23 H4K12ac-associated genes were activated in 8-cell embryo and 39 in the blastocyst. Genes activated in 4-cell embryos are involved in gene expression, histone fold and DNA-dependent transcription, while genes expressed in the blastocyst were classified as involved in developmental processes. Immunofluorescence staining detected H4K12ac from the murine male pronucleus to early stages of embryogenesis. Aberrant histone acetylation within developmentally important gene promoters in infertile men may reflect insufficient sperm chromatin compaction, which may result in inappropriate transfer of epigenetic information to the oocyte.
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Affiliation(s)
- Agnieszka S Paradowska
- Department of Urology, Pediatric Urology and Andrology, Justus Liebig University of Giessen, Giessen, Germany.
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155
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Gupta J, Kumar S, Li J, Krishna Murthy Karuturi R, Tikoo K. Histone H3 lysine 4 monomethylation (H3K4me1) and H3 lysine 9 monomethylation (H3K9me1): distribution and their association in regulating gene expression under hyperglycaemic/hyperinsulinemic conditions in 3T3 cells. Biochimie 2012; 94:2656-64. [PMID: 22951486 DOI: 10.1016/j.biochi.2012.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 08/02/2012] [Indexed: 10/28/2022]
Abstract
Hyperglycemia/hyperinsulinemia are leading cause for the induction type 2 diabetes and the role of post-translational histone modifications in dysregulating the expression of genes has emerged as potential important contributor in the progression of disease. The paradoxical nature of histone H3-Lysine 4 and Lysine 9 mono-methylation (H3K4me1 and H3K9me1) in both gene activation and repression motivated us to elucidate the functional relationship of these histone modifications in regulating expression of genes under hyperglycaemic/hyperinsulinemic condition. Chromatin immunoprecipitation-microarray analysis (ChIP-chip) was performed with H3 acetylation, H3K4me1 and H3K9me1 antibody. CLUSTER analysis of ChIP-chip (Chromatin immunoprecipitation-microarray analysis) data showed that mRNA expression and H3 acetylation/H3K4me1 levels on genes were inversely correlated with H3K9me1 levels on the transcribed regions, after 30 min of insulin stimulation under hyperglycaemic condition. Interestingly, we provide first evidence regarding regulation of histone de/acetylases and de/methylases; Myst4, Jmjd2b, Aof1 and Set by H3Ac, H3K4me1 and H3K9me1 under hyperinsulinemic/hyperglycaemic condition. ChIP-qPCR analysis shows association of increased H3Ac/H3K4me1 and decreased levels of H3K9me1 in up regulation of Myst4, Jmjd2, Set and Aof1 genes. We further analyse promoter occupancy of histone modifications by ChIP walking and observed increased occupancy of H3Ac/H3K4me1 on promoter region (-1000 to -1) of active genes and H3K9me1 on inactive genes under hyperglycemic/hyperinsulinemic condition. To best of our knowledge this is the first report that shows regulation of chromatin remodelling genes by alteration in the occupancy of histone H3Ac/H3K4/K9me on both promoter and transcribed regions.
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Affiliation(s)
- Jeena Gupta
- Laboratory of Chromatin Biology, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Mohali, Punjab, India
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156
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Wang Y, Shang Y. Epigenetic control of epithelial-to-mesenchymal transition and cancer metastasis. Exp Cell Res 2012; 319:160-9. [PMID: 22935683 DOI: 10.1016/j.yexcr.2012.07.019] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/23/2012] [Accepted: 07/25/2012] [Indexed: 12/22/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is vital for morphogenesis during embryonic development and is also critical for the conversion of early stage tumors into invasive malignancies. Several key inducers of EMT are transcription factors that repress the expression of E-cadherin, whose loss is a hallmark of EMT. Epigenetic regulation encompasses three types of changes: DNA methylation, histone modifications, and microRNAs, each of which has been shown to play a key role in controlling epithelial-mesenchymal transition and cancer metastasis. As we gain deeper understanding of epigenetic mechanisms controlling EMT processes and orchestrating all the metastatic steps, we broaden the therapeutic potentials of epigenetic drugs, such as DNA demethylating drugs and histone deacetylase/demethylase inhibitors, which can act upon metastasis-related genes, restoring their expression and biological functions.
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Affiliation(s)
- Yan Wang
- Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, 22 Qixiangtai Road, Tianjin 300070, China
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157
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Jenkins TG, Carrell DT. Dynamic alterations in the paternal epigenetic landscape following fertilization. Front Genet 2012; 3:143. [PMID: 23024648 PMCID: PMC3442791 DOI: 10.3389/fgene.2012.00143] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 07/13/2012] [Indexed: 12/14/2022] Open
Abstract
Embryonic development is a complex and dynamic process with frequent changes in gene expression, ultimately leading to cellular differentiation and commitment of various cell lines. These changes are likely preceded by changes to signaling cascades and/or alterations to the epigenetic program in specific cells. The process of epigenetic remodeling begins early in development. In fact, soon after the union of sperm and egg massive epigenetic changes occur across the paternal and maternal epigenetic landscape. The epigenome of these cells includes modifications to the DNA itself, in the form of DNA methylation, as well as nuclear protein content and modification, such as modifications to histones. Sperm chromatin is predominantly packaged by protamines, but following fertilization the sperm pronucleus undergoes remodeling in which maternally derived histones replace protamines, resulting in the relaxation of chromatin and ultimately decondensation of the paternal pronucleus. In addition, active DNA demethylation occurs across the paternal genome prior to the first cell division, effectively erasing many spermatogenesis derived methylation marks. This complex interplay begins the dynamic process by which two haploid cells unite to form a diploid organism. The biology of these events is central to the understanding of sexual reproduction, yet our knowledge regarding the mechanisms involved is extremely limited. This review will explore what is known regarding the post-fertilization epigenetic alterations of the paternal chromatin and the implications suggested by the available literature.
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Affiliation(s)
- Timothy G Jenkins
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
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158
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Pontvianne F, Blevins T, Chandrasekhara C, Feng W, Stroud H, Jacobsen SE, Michaels SD, Pikaard CS. Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis. Genes Dev 2012; 26:945-57. [PMID: 22549957 DOI: 10.1101/gad.182865.111] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Eukaryotes have hundreds of nearly identical 45S ribosomal RNA (rRNA) genes, each encoding the 18S, 5.8S, and 25S catalytic rRNAs. Because cellular demands for ribosomes and protein synthesis vary during development, the number of active rRNA genes is subject to dosage control. In genetic hybrids, one manifestation of dosage control is nucleolar dominance, an epigenetic phenomenon in which the rRNA genes of one progenitor are repressed. For instance, in Arabidopsis suecica, the allotetraploid hybrid of Arabidopsis thaliana and Arabidopsis arenosa, the A. thaliana-derived rRNA genes are selectively silenced. An analogous phenomenon occurs in nonhybrid A. thaliana, in which specific classes of rRNA gene variants are inactivated. An RNA-mediated knockdown screen identified SUVR4 {SUPPRESSOR OF VARIEGATION 3-9 [SU(VAR)3-9]-RELATED 4} as a histone H3 Lys 9 (H3K9) methyltransferase required for nucleolar dominance in A. suecica. H3K9 methyltransferases are also required for variant-specific silencing in A. thaliana, but SUVH5 [SU(VAR)3-9 HOMOLOG 5] and SUVH6, rather than SUVR4, are the key activities in this genomic context. Mutations disrupting the H3K27 methyltransferases ATXR5 or ATXR6 affect which rRNA gene variants are expressed or silenced, and in atxr5 atxr6 double mutants, dominance relationships among variants are reversed relative to wild type. Interestingly, these changes in gene expression are accompanied by changes in the relative abundance of the rRNA gene variants at the DNA level, including overreplication of the normally silenced class and decreased abundance of the normally dominant class. Collectively, our results indicate that histone methylation can affect both the doses of different variants and their differential silencing through the choice mechanisms that achieve dosage control.
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159
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Zou Y, Ma X, Huang Y, Hong L, Chiao JW. Effect of phenylhexyl isothiocyanate on aberrant histone H3 methylation in primary human acute leukemia. J Hematol Oncol 2012; 5:36. [PMID: 22747680 PMCID: PMC3413588 DOI: 10.1186/1756-8722-5-36] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 06/07/2012] [Indexed: 11/29/2022] Open
Abstract
Background We have previously studied the histone acetylation in primary human leukemia cells. However, histone H3 methylation in these cells has not been characterized. Methods This study examined the methylation status at histone H3 lysine 4 (H3K4) and histone H3 lysine 9 (H3K9) in primary acute leukemia cells obtained from patients and compared with those in the non-leukemia and healthy cells. We further characterized the effect of phenylhexyl isothiocyanate (PHI), Trichostatin A (TSA), and 5-aza-2’-deoxycytidine (5-Aza) on the cells. Results We found that methylation of histone H3K4 was virtually undetectable, while methylation at H3K9 was significantly higher in primary human leukemia cells. The histone H3K9 hypermethylation and histone H3K4 hypomethylation were observed in both myeloid and lymphoid leukemia cells. PHI was found to be able to normalize the methylation level in the primary leukemia cells. We further showed that PHI was able to enhance the methyltransferase activity of H3K4 and decrease the activity of H3K9 methyltransferase. 5-Aza had similar effect on H3K4, but minimal effect on H3K9, whereas TSA had no effect on H3K4 and H3K9 methyltransferases. Conclusions This study revealed opposite methylation level of H3K4 and H3K9 in primary human leukemia cells and demonstrated for the first time that PHI has different effects on the methyltransferases for H3K4 and H3K9.
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Affiliation(s)
- Yong Zou
- Department of Hematology, Zhangzhou Hospital of Fujian Medical University, Zhangzhou, Fujian Province, 363000, China
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160
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Takawa M, Cho HS, Hayami S, Toyokawa G, Kogure M, Yamane Y, Iwai Y, Maejima K, Ueda K, Masuda A, Dohmae N, Field HI, Tsunoda T, Kobayashi T, Akasu T, Sugiyama M, Ohnuma SI, Atomi Y, Ponder BAJ, Nakamura Y, Hamamoto R. Histone lysine methyltransferase SETD8 promotes carcinogenesis by deregulating PCNA expression. Cancer Res 2012; 72:3217-27. [PMID: 22556262 DOI: 10.1158/0008-5472.can-11-3701] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although the physiologic significance of lysine methylation of histones is well known, whether lysine methylation plays a role in the regulation of nonhistone proteins has not yet been examined. The histone lysine methyltransferase SETD8 is overexpressed in various types of cancer and seems to play a crucial role in S-phase progression. Here, we show that SETD8 regulates the function of proliferating cell nuclear antigen (PCNA) protein through lysine methylation. We found that SETD8 methylated PCNA on lysine 248, and either depletion of SETD8 or substitution of lysine 248 destabilized PCNA expression. Mechanistically, lysine methylation significantly enhanced the interaction between PCNA and the flap endonuclease FEN1. Loss of PCNA methylation retarded the maturation of Okazaki fragments, slowed DNA replication, and induced DNA damage, and cells expressing a methylation-inactive PCNA mutant were more susceptible to DNA damage. An increase of methylated PCNA was found in cancer cells, and the expression levels of SETD8 and PCNA were correlated in cancer tissue samples. Together, our findings reveal a function for lysine methylation on a nonhistone protein and suggest that aberrant lysine methylation of PCNA may play a role in human carcinogenesis.
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Affiliation(s)
- Masashi Takawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, and National Cancer Center Hospital, Chuo-ku, Tokyo, Japan
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161
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Epigenetic reprogramming of embryos derived from sperm frozen at −20°C. SCIENCE CHINA-LIFE SCIENCES 2012; 55:349-57. [DOI: 10.1007/s11427-012-4309-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 03/26/2012] [Indexed: 01/29/2023]
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162
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Park KE, Inerowicz HD, Wang X, Li Y, Koser S, Cabot RA. Identification of karyopherin α1 and α7 interacting proteins in porcine tissue. PLoS One 2012; 7:e38990. [PMID: 22720010 PMCID: PMC3374799 DOI: 10.1371/journal.pone.0038990] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/17/2012] [Indexed: 11/19/2022] Open
Abstract
Specialized trafficking systems in eukaryotic cells serve a critical role in partitioning intracellular proteins between the nucleus and cytoplasm. Cytoplasmic proteins (including chromatin remodeling enzymes and transcription factors) must gain access to the nucleus to exert their functions to properly program fundamental cellular events ranging from cell cycle progression to gene transcription. Knowing that nuclear import mediated by members of the karyopherin α family of transport receptors plays a critical role in regulating development and differentiation, we wanted to determine the identity of proteins that are trafficked by this karyopherin α pathway. To this end, we performed a GST pull-down assay using porcine orthologs of karyopherin α1 (KPNA1) and karyopherin α7 (KPNA7) and prey protein derived from porcine fibroblast cells and used a liquid chromatography and tandem mass spectrometry (LC-MS/MS) approach to determine the identity of KPNA1 and KPNA7 interacting proteins. Our screen revealed that the proteins that interact with KPNA1 and KPNA7 are generally nuclear proteins that possess nuclear localization signals. We further validated two candidate proteins from this screen and showed that they are able to be imported into the nucleus in vivo and also interact with members of the karyopherin α family of proteins in vitro. Our results also reveal the utility of using a GST pull-down approach coupled with LC-MS/MS to screen for protein interaction partners in a non-traditional model system.
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Affiliation(s)
- Ki-Eun Park
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - H. Dorota Inerowicz
- Bindley Biosciences Center, Proteomics Core Facility, Purdue University, West Lafayette, Indiana, United States of America
| | - Xin Wang
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Yanfang Li
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Stephanie Koser
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Ryan A. Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, Indiana, United States of America
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163
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Liu T, Huang Y, Huang Q, Jiang L, Guo L, Liu Z. Use of human amniotic epithelial cells as a feeder layer to support undifferentiated growth of mouse spermatogonial stem cells via epigenetic regulation of the Nanog and Oct-4 promoters. ACTA BIOLOGICA HUNGARICA 2012; 63:167-79. [PMID: 22695517 DOI: 10.1556/abiol.63.2012.2.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Spermatogonial stem cells (SSCs) are defined by unique properties like other stem cells. However, there are two major challenges: long-term cultivation of normal SSCs into stable cell lines and maintaining the SSCs as undifferentiated and capable of self-renewal. Here, we compared different culture methods for mouse SSCs isolated and cultured from testicular tissue. We found that human amniotic epithelial cells (hAECs) can behave as feeder cells, allowing mouse SSCs to maintain a high level of alkaline phosphatase (AP) activity when cultured long-term. Also, we observed that expression of Nanog, Oct-4 and other important stem cells markers were higher in mouse SSCs cultured on hAECs compared to those cultured on MEF or without any feeder cells. Furthermore, we demonstrated that the CpG islands of the Nanog and Oct-4 promoters were hypomethylated in cells cultured on hAECs. In addition, mouse SSCs cultured on hAECs exhibited higher levels of H3AC and H3K4Me3 in the Nanog and Oct-4 promoters than those cultured on MEF or without feeder cells. Taken together, these results suggest that the hAEC-induced epigenetic modifications at the Nanog and Oct-4 locus could be a key mechanism for maintaining mouse SSCs in an undifferentiated state capable of self-renewal.
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Affiliation(s)
- Te Liu
- School of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
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164
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Chao SB, Chen L, Li JC, Ou XH, Huang XJ, Wen S, Sun QY, Gao GL. Defective histone H3K27 trimethylation modification in embryos derived from heated mouse sperm. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2012; 18:476-482. [PMID: 22568956 DOI: 10.1017/s1431927612000396] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The mouse sperm genome is resistant to in vitro heat treatment, and embryos derived from heated sperm can support full-term embryonic development, but the blastocyst rate and implantation rate are lower compared to embryos derived from fresh sperm. In the present study, the patterns of DNA methylation, histone H4K12 (ACH4K12) acetylation, H3K9 trimethylation (H3K9-TriM), and H3K27 trimethylation (H3K27-TriM) in preimplantation embryos derived from 65 °C-heated sperm were investigated. Although no evident changes in global DNA methylation, histone H4K12 (ACH4K12) acetylation, and H3K9 trimethylation (H3K9-TriM) were found, significantly lower levels of H3K27-TriM, which was thought to be one of the reasons for low efficiency of mouse cloning, were found in the inner cell mass of heated-sperm derived blastocysts. Thus, defective modification of H3K27-TriM might contribute to compromised development of embryos derived from heated sperm.
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Affiliation(s)
- Shi-Bin Chao
- Center of Reproductive Medicine, The First Affiliated Hospital of NanChang University, NanChang, China
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165
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Abstract
Repetitive sequences, especially transposon-derived interspersed repetitive elements, account for a large fraction of the genome in most eukaryotes. Despite the repetitive nature, these transposable elements display quantitative and qualitative differences even among species of the same lineage. Although transposable elements contribute greatly as a driving force to the biological diversity during evolution, they can induce embryonic lethality and genetic disorders as a result of insertional mutagenesis and genomic rearrangement. Temporary relaxation of the epigenetic control of retrotransposons during early germline development opens a risky window that can allow retrotransposons to escape from host constraints and to propagate abundantly in the host genome. Because germline mutations caused by retrotransposon activation are heritable and thus can be deleterious to the offspring, an adaptive strategy has evolved in host cells, especially in the germline. In this review, we will attempt to summarize general defense mechanisms deployed by the eukaryotic genome, with an emphasis on pathways utilized by the male germline to confer retrotransposon silencing.
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Affiliation(s)
- Jianqiang Bao
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, USA
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166
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Perisic T, Holsboer F, Rein T, Zschocke J. The CpG island shore of the GLT-1 gene acts as a methylation-sensitive enhancer. Glia 2012; 60:1345-55. [PMID: 22593010 DOI: 10.1002/glia.22353] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/18/2012] [Indexed: 12/25/2022]
Abstract
Astrocytic lineage commitment and brain region-dependent specialization of glia are partly ascribed to epigenetic processes. Clearance of glutamate is an essential task, which astrocytes assume in a temporal-spatial fashion by distinct glutamate transporter expression. Glutamate transporter subtype 1 (GLT-1) is predominant in cortex (CTX), while it plays an inferior role in cerebellum (CER). Here, we set out to identify regulatory elements that could account for the differences in brain region-specific activity as well as response to dexamethasone (DEX) or epigenetic factors. We found a distal promoter element at the shore of the CpG island exhibiting enhancer function in response to DEX in reporter gene assays. This shore region showed slight enrichment in repressive trimethyl-histone H3 (Lys27) and under-representation of acetyl-histone H4 (H4ac) marks in DEX nonresponsive CER astrocytes as determined by chromatin immunoprecipitation. In addition, CpG sites of the shore region displayed higher methylation in CER than in CTX cells. Targeted in vitro methylation of CpG sites within the shore abrogated the stimulatory effects of DEX. Interestingly, the shore was characterized by a pronounced epigenetic plasticity in CTX cells since DEX exposure elicited an increase of H4ac in CTX in comparison to DEX nonresponsive CER. The transcriptional activity of this region was also affected by histone deacetylase inhibitors in a methylation- and brain region-dependent manner. Together, our study highlights the impact of an epigenetically adaptive DNA element of the GLT-1 promoter being decisive for brain region-specific activity and reactivity.
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Affiliation(s)
- Tatjana Perisic
- Chaperone Research Group, Max Planck Institute of Psychiatry, Munich, Germany
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167
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Rassoulzadegan M, Cuzin F. The making of an organ: RNA mediated developmental controls in mice. Organogenesis 2012; 6:33-6. [PMID: 20592863 DOI: 10.4161/org.6.1.11094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 12/22/2009] [Accepted: 12/22/2009] [Indexed: 11/19/2022] Open
Abstract
Based initially on the observation of inheritance patterns at variance with Mendel's first law, hereditary epigenetic variations were evidenced in the mouse. Modulating the transcription of a locus, they are induced by RNAs with sequence homology to the transcript. RNAs transferred by the gamete, including sperm, to the fertilized egg appeared to be responsible for transgenerational maintenance of the variant phenotypes. Instances of RNA-dependent variations so far analyzed in the mouse-a pathological deviation of heart development and a syndrome of gigantism initiated by hyperproliferation of embryonic stem cells-suggest a general dependence of organogenesis on epigenetic controls of gene expression. "I conclude it is impossible to say we know the limit of variation."-Charles Darwin. One of the most fascinating visions offered to the biologist is to watch the fertilized egg ingeniously unfolding a program to create a novel being. Development takes place by activating networks of gene activation that result in the proper adjustment of cell growth and functional differentiation. How is the whole process started? Thoughts are generally centered on the activation of critical genes at the early stages due to a newly acquired organization of their chromatin structures. Is the embryo induced to start a given program by molecules contributed by the maternal and paternal gametes? While genetic determinants are clearly essential, the epigenetic landscape largely dominates our current way of thinking. In this essay, we will focus on the evidence showing that RNA molecules are present in the gametes and that RNA can modulate the robust genetic program of organ formation in the mouse.
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168
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Jenkins TG, Carrell DT. The sperm epigenome and potential implications for the developing embryo. Reproduction 2012; 143:727-34. [PMID: 22495887 DOI: 10.1530/rep-11-0450] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent work in the field of male fertility has yielded significant increases in our understanding of the sperm epigenome and its potential role in embryonic development. These new findings have enabled a broad classification of a normal epigenetic state in the male gamete and have provided insight into the possible etiologies of some idiopathic male infertility cases. Histone retention and modification, protamine incorporation into the chromatin, DNA methylation, and spermatozoal RNA transcripts appear to play important roles in the epigenetic state of mature sperm. These epigenetic factors may reveal a historical record of spermatogenesis, portend future functions in embryogenesis, and help to elucidate mechanism of pluripotency. In contrast to the once held dogma regarding the importance of the paternal epigenome, the unique epigenetic landscape in sperm appears to serve more than the gamete itself and is likely influential in the developing embryo. In fact, growing evidence suggests that mature sperm provide appropriate epigenetic marks that drive specific genes toward activation and contribute to the pluripotent state of the embryonic cells. Although not definitive, the current literature provides evidence for the role of the sperm epigenome in the embryo. Future work must be focused on the characterization of epigenetic abnormalities commonly found in individuals with compromised fertility to further establish this role. Additionally, studies should target the effects of environment and aging on the sperm epigenetic program and subsequent fertility loss to determine the etiology of aberrant epigenetic profiles.
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Affiliation(s)
- Timothy G Jenkins
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, 675 Arapeen Drive, Suite 205, Salt Lake City,Utah 801-581-3740, USA
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169
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Chao SB, Guo L, Ou XH, Luo SM, Wang ZB, Schatten H, Gao GL, Sun QY. Heated spermatozoa: effects on embryonic development and epigenetics. Hum Reprod 2012; 27:1016-24. [DOI: 10.1093/humrep/des005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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170
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Cho HS, Shimazu T, Toyokawa G, Daigo Y, Maehara Y, Hayami S, Ito A, Masuda K, Ikawa N, Field HI, Tsuchiya E, Ohnuma SI, Ponder BA, Yoshida M, Nakamura Y, Hamamoto R. Enhanced HSP70 lysine methylation promotes proliferation of cancer cells through activation of Aurora kinase B. Nat Commun 2012; 3:1072. [PMID: 22990868 PMCID: PMC3658001 DOI: 10.1038/ncomms2074] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/20/2012] [Indexed: 01/17/2023] Open
Abstract
Although heat-shock protein 70 (HSP70), an evolutionarily highly conserved molecular chaperone, is known to be post-translationally modified in various ways such as phosphorylation, ubiquitination and glycosylation, physiological significance of lysine methylation has never been elucidated. Here we identify dimethylation of HSP70 at Lys-561 by SETD1A. Enhanced HSP70 methylation was detected in various types of human cancer by immunohistochemical analysis, although the methylation was barely detectable in corresponding non-neoplastic tissues. Interestingly, methylated HSP70 predominantly localizes to the nucleus of cancer cells, whereas most of the HSP70 protein locates to the cytoplasm. Nuclear HSP70 directly interacts with Aurora kinase B (AURKB) in a methylation-dependent manner and promotes AURKB activity in vitro and in vivo. We also find that methylated HSP70 has a growth-promoting effect in cancer cells. Our findings demonstrate a crucial role of HSP70 methylation in human carcinogenesis.
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Affiliation(s)
- Hyun-Soo Cho
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639, Japan
- These authors contributed equally to this work
| | - Tadahiro Shimazu
- Chemical Genomics Research Group, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako
351-0198, Japan
- These authors contributed equally to this work
| | - Gouji Toyokawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639, Japan
- Department of Surgery and Science, Graduate School of Medical Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka
812-8582, Japan
| | - Yataro Daigo
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639, Japan
- Department of Medical Oncology, Shiga University of Medical Science, Otsu
520-2192, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka
812-8582, Japan
| | - Shinya Hayami
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639, Japan
| | - Akihiro Ito
- Chemical Genomics Research Group, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako
351-0198, Japan
| | - Ken Masuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639, Japan
| | - Noriko Ikawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639, Japan
| | - Helen I. Field
- Department of Genetics, University of Cambridge, Downing Street, Cambridge
CB2 3EH, UK
| | - Eiju Tsuchiya
- Department of Pathology, Saitama Cancer Center, 818 Komuro, Inamachi, Kita-Adachi, Saitama
362-0806, Japan
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Kanagawa
241-0815, Japan
| | - Shin-ichi Ohnuma
- Institute of Ophthalmology, University College London, 11-43 Bath Street, London
EC1V 9EL, UK
| | - Bruce A.J. Ponder
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Robinson Way, Cambridge
CB2 0RE, UK
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako
351-0198, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639, Japan
- Section of Hematology/Oncology, The University of Chicago, 900 E 57th Street, KCBD6126, Chicago, Illinois
60637, USA
| | - Ryuji Hamamoto
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo
108-8639, Japan
- Department of Oncology, Cancer Research UK Cambridge Research Institute, University of Cambridge, Robinson Way, Cambridge
CB2 0RE, UK
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171
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Daze KD, Pinter T, Beshara CS, Ibraheem A, Minaker SA, Ma MCF, Courtemanche RJM, Campbell RE, Hof F. Supramolecular hosts that recognize methyllysines and disrupt the interaction between a modified histone tail and its epigenetic reader protein. Chem Sci 2012. [DOI: 10.1039/c2sc20583a] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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172
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Batra V, Devasagayam TPA. Interaction between γ-radiation and dietary folate starvation metabolically reprograms global hepatic histone H3 methylation at lysine 4 and lysine 27 residues. Food Chem Toxicol 2011; 50:464-72. [PMID: 22154853 DOI: 10.1016/j.fct.2011.11.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/24/2011] [Accepted: 11/24/2011] [Indexed: 01/14/2023]
Abstract
The objective of the present study was to investigate the regulatory control of histone H3 methylation at lysine 4 (H3K4) and lysine 27 (H3K27) residues in response to the effect of folate deficiency and gamma (γ)-radiation. Male Swiss mice maintained on folate sufficient diet (FSD) and folate free diet (FFD) based on AIN-93M formula, were subjected to 2-4 Gy total body γ-irradiation. There was a significant decrease in liver folate levels with concomitant depletion of S-adenosylmethionine (SAM) reserves. Folate deficiency and γ-radiation together induced H3K4 histone methyltransferase (H3K4HMTase) and suppressed H3K27 histone methyltransferase (H3K27HMTase) activities in a dose and time dependent manner. Our studies suggested radiation induced metabolic reprogramming of H3K4/H3K27 methylation patterns in FFD animals. We showed that radiation toxicity diverted one-carbon (C1) flux in FFD fed animals towards H3K4 methylation. Present work on methylation pattern of histone lysine residues gains particular importance as methylation of H3K4 residues is associated with euchromatin while methylated H3K27 residues promote gene silencing. In conclusion, our study suggests that maintenance of genomic histone methylation under γ-radiation stress might be a very dynamic, progressive process that could be modulated by dietary folate deficiency leading to formation of epigenetically reprogrammed cells.
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Affiliation(s)
- Vipen Batra
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400 085, India.
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173
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Abstract
Many studies have shown that microRNA expression in cancer may be regulated by epigenetic events. Recently, we found that in lung cancer miR-212 was strongly down-regulated. However, mechanisms involved in the regulation of miR-212 expression are unknown. Therefore, we addressed this point by investigating the molecular mechanisms of miR-212 silencing in lung cancer. We identified histone modifications rather than DNA hypermethylation as epigenetic events that regulate miR-212 levels in NSCLC. Moreover, we found that miR-212 silencing in vivo is closely associated with the severity of the disease.
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174
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Epigenetic regulation of CIITA expression in human T-cells. Biochem Pharmacol 2011; 82:1430-7. [DOI: 10.1016/j.bcp.2011.05.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 05/18/2011] [Accepted: 05/26/2011] [Indexed: 11/18/2022]
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175
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Nowacki M, Shetty K, Landweber LF. RNA-Mediated Epigenetic Programming of Genome Rearrangements. Annu Rev Genomics Hum Genet 2011; 12:367-89. [PMID: 21801022 DOI: 10.1146/annurev-genom-082410-101420] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
RNA, normally thought of as a conduit in gene expression, has a novel mode of action in ciliated protozoa. Maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. This opportunity for RNA-mediated genome rearrangement and DNA repair is profound in the ciliate Oxytricha, which deletes 95% of its germline genome during development in a process that severely fragments its chromosomes and then sorts and reorders the hundreds of thousands of pieces remaining. Oxytricha's somatic nuclear genome is therefore an epigenome formed through RNA templates and signals arising from the previous generation. Furthermore, this mechanism of RNA-mediated epigenetic inheritance can function across multiple generations, and the discovery of maternal template RNA molecules has revealed new biological roles for RNA and has hinted at the power of RNA molecules to sculpt genomic information in cells.
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Affiliation(s)
- Mariusz Nowacki
- Institute of Cell Biology, University of Bern, CH-3012 Bern, Switzerland.
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176
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Zhou D, Pan YX. Gestational low protein diet selectively induces the amino acid response pathway target genes in the liver of offspring rats through transcription factor binding and histone modifications. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:549-56. [DOI: 10.1016/j.bbagrm.2011.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 06/27/2011] [Accepted: 07/06/2011] [Indexed: 12/19/2022]
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177
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Methylation and acetylation of histones during spermatogenesis. YI CHUAN = HEREDITAS 2011; 33:939-46. [DOI: 10.3724/sp.j.1005.2011.00939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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178
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Epigenetic mechanisms in developmental programming of adult disease. Drug Discov Today 2011; 16:1007-18. [PMID: 21945859 DOI: 10.1016/j.drudis.2011.09.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Revised: 07/05/2011] [Accepted: 09/09/2011] [Indexed: 12/13/2022]
Abstract
Adverse insults during intrauterine life can result in permanent changes in the physiology and metabolism of the offspring, which in turn leads to an increased risk of disease in adulthood. This is an adaptational response by the fetus to changes in the environmental signals that it receives during early life to ensure its survival and prepare itself for postnatal life. Increasing evidence suggests that the epigenetic regulation of gene expression patterns has a crucial role in the developmental programming of adult disease. This review summarizes recent studies of epigenetic mechanisms and focuses particularly on studies that explore identifiable epigenetic biomarkers in the promoters of specific disease-associated genes. Such biomarkers would enable early recognition of children who might be at risk of developing adult disease with fetal origins.
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179
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Rubio A, Sánchez-Mut JV, García E, Velasquez ZD, Oliver J, Esteller M, Avila J. Epigenetic control of somatostatin and cortistatin expression by β amyloid peptide. J Neurosci Res 2011; 90:13-20. [PMID: 21922516 DOI: 10.1002/jnr.22731] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/26/2011] [Accepted: 06/02/2011] [Indexed: 01/06/2023]
Abstract
β Amyloid, present in senile plaques, has been related largely to neuronal loss in the brain of patients with Alzheimer's disease. However, how neurons respond to β amyloid insults is still poorly understood. Here we show that β amyloid increases somatostatin and cortistatin gene expression mainly through an increase in histone 3 lysine 4 methylation (H3K4me3), a modification associated with transcriptional activation. Somatostatin and cortistatin partially decreased β amyloid toxicity in primary cortical neurons in culture. Thus we suggest that neurons respond to β amyloid insults by releasing somatostatin and cortistatin, which will act as a protective agent against β amyloid toxicity. Our results suggest a relevant function for both neuropeptides against β amyloid toxicity, providing new insights into Alzheimer's disease.
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Affiliation(s)
- Alicia Rubio
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/Nicolás Cabrera 1, Universidad Autónoma de Madrid, Campus Cantoblanco, Madrid, Spain
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180
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Burkhart KB, Guang S, Buckley BA, Wong L, Bochner AF, Kennedy S. A pre-mRNA-associating factor links endogenous siRNAs to chromatin regulation. PLoS Genet 2011; 7:e1002249. [PMID: 21901112 PMCID: PMC3161925 DOI: 10.1371/journal.pgen.1002249] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 07/02/2011] [Indexed: 11/30/2022] Open
Abstract
In plants and fungi, small RNAs silence gene expression in the nucleus by establishing repressive chromatin states. The role of endogenous small RNAs in metazoan nuclei is largely unknown. Here we show that endogenous small interfering RNAs (endo-siRNAs) direct Histone H3 Lysine 9 methylation (H3K9me) in Caenorhabditis elegans. In addition, we report the identification and characterization of nuclear RNAi defective (nrde)-1 and nrde-4. Endo-siRNA–driven H3K9me requires the nuclear RNAi pathway including the Argonaute (Ago) NRDE-3, the conserved nuclear RNAi factor NRDE-2, as well as NRDE-1 and NRDE-4. Small RNAs direct NRDE-1 to associate with the pre-mRNA and chromatin of genes, which have been targeted by RNAi. NRDE-3 and NRDE-2 are required for the association of NRDE-1 with pre-mRNA and chromatin. NRDE-4 is required for NRDE-1/chromatin association, but not NRDE-1/pre-mRNA association. These data establish that NRDE-1 is a novel pre-mRNA and chromatin-associating factor that links small RNAs to H3K9 methylation. In addition, these results demonstrate that endo-siRNAs direct chromatin modifications via the Nrde pathway in C. elegans. Chromatin consists of DNA and proteins. Chromatin can exist in many different states. The state of chromatin in highly regulated in order to ensure that genes are expressed correctly. RNAs play an important role in the regulation of chromatin. For example, in plants and fungi small RNAs drive the formation of heterochromatin, a repressive chromatin state. Many types of small RNAs have been identified in animal cells, but the functions of these small RNAs are largely unknown. Using the nematode C. elegans as a model system, we identified a small RNA pathway that regulates the state of chromatin. We report the identification of two new factors, termed NRDE-1 and NRDE-4, which act in this nuclear small RNA pathway. NRDE-1 and NRDE-4 link small RNAs to chromatin regulation. Additionally, we show that endogenously expressed small RNAs, termed the endo-siRNAs, direct the post-translational modification of histone proteins, which are core components of chromatin. These results establish a direct connection between small RNAs and chromatin regulation in animals.
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Affiliation(s)
- Kirk B. Burkhart
- Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Shouhong Guang
- Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Bethany A. Buckley
- Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Lily Wong
- Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Aaron F. Bochner
- Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Scott Kennedy
- Laboratory of Genetics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- Department of Pharmacology, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- * E-mail:
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181
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Andresen E, Günther G, Bullwinkel J, Lange C, Heine H. Increased expression of beta-defensin 1 (DEFB1) in chronic obstructive pulmonary disease. PLoS One 2011; 6:e21898. [PMID: 21818276 PMCID: PMC3139569 DOI: 10.1371/journal.pone.0021898] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 06/08/2011] [Indexed: 12/21/2022] Open
Abstract
On-going airway inflammation is characteristic for the pathophysiology of chronic obstructive pulmonary disease (COPD). However, the key factors determining the decrease in lung function, an important clinical parameter of COPD, are not clear. Genome-wide linkage analyses provide evidence for significant linkage to airway obstruction susceptibility loci on chromosome 8p23, the location of the human defensin gene cluster. Moreover, a genetic variation in the defensin beta 1 (DEFB1) gene was found to be associated with COPD. Therefore, we hypothesized that DEFB1 is differently regulated and expressed in human lungs during COPD progression. Gene expression of DEFB1 was assessed in bronchial epithelium and BAL fluid cells of healthy controls and patients with COPD and using bisulfite sequencing and ChIP analysis, the epigenetic control of DEFB1 mRNA expression was investigated. We can demonstrate that DEFB1 mRNA expression was significantly increased in bronchopulmonary specimen of patients with COPD (n = 34) vs. healthy controls (n = 10) (p<0.0001). Furthermore, a significant correlation could be detected between DEFB1 and functional parameters such as FEV1 (p = 0.0024) and the FEV1/VC ratio (p = 0.0005). Upregulation of DEFB1 mRNA was paralleled by changes in HDAC1-3, HDAC5 and HDAC8 mRNA expression. Whereas bisulfite sequencing revealed no differences in the methylation state of DEFB1 promoter between patients with COPD and controls, ChIP analysis showed that enhanced DEFB1 mRNA expression was associated with the establishment of an active histone code. Thus, expression of human DEFB1 is upregulated and related to the decrease in pulmonary function in patients with COPD.
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Affiliation(s)
- Ellen Andresen
- Section of Immunoregulation, Division of Innate Immunity, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Gunar Günther
- Division of Clinical Infection Diseases, Department of Pneumology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Jörn Bullwinkel
- Division of Immunoepigenetics, Department of Immunology and Cell Biology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Christoph Lange
- Division of Clinical Infection Diseases, Department of Pneumology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Holger Heine
- Section of Immunoregulation, Division of Innate Immunity, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
- * E-mail:
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182
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SCF(FBXO22) regulates histone H3 lysine 9 and 36 methylation levels by targeting histone demethylase KDM4A for ubiquitin-mediated proteasomal degradation. Mol Cell Biol 2011; 31:3687-99. [PMID: 21768309 DOI: 10.1128/mcb.05746-11] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Reversible methylation of lysine residues has emerged as a central mechanism for epigenetic regulation and is a component of the "histone code," which engenders histones with gene regulatory information. KDM4A is a histone demethylase that targets tri- and dimethylation marks on histone H3 lysines 9 and 36. While the abundance of KDM4A oscillates in the cell cycle, little is known how this enzyme is regulated to achieve targeted effects on specific histone residues in chromatin. Here, we report that a previously unstudied SCF(FBXO22) ubiquitin ligase complex controls the activity of KDM4A by targeting it for proteasomal turnover. FBXO22 functions as a receptor for KDM4A by recognizing its catalytic JmjN/JmjC domains via its intracellular signal transduction (FIST) domain. Modulation of FBXO22 levels by RNA interference or overexpression leads to increased or decreased levels of KDM4A, respectively. Changes in KDM4A abundance correlate with alterations in histone H3 lysine 9 and 36 methylation levels, and transcription of a KDM4A target gene, ASCL2. Taken together, these results demonstrate that SCF(FBXO22) regulates changes in histone H3 marks and cognate transcriptional control pathways by controlling KDM4A levels, and they suggest a potential role for FBXO22 in development, differentiation, and disease through spatial and temporal control of KDM4A activity.
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183
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Islam K, Zheng W, Yu H, Deng H, Luo M. Expanding cofactor repertoire of protein lysine methyltransferase for substrate labeling. ACS Chem Biol 2011; 6:679-84. [PMID: 21495674 DOI: 10.1021/cb2000567] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lysine methyltransferases (PKMTs) play crucial roles in normal physiology and disease processes. Profiling PKMT targets is an important but challenging task. With cancer-relevant G9a as a target, we have demonstrated success in developing S-adenosyl-L-methionine (SAM) analogues, particularly (E)-hex-2-en-5-ynyl SAM (Hey-SAM), as cofactors for engineered G9a. Hey-SAM analogue in combination with G9a Y1154A mutant modifies the same set of substrates as their native counterparts with remarkable efficiency. (E)-Hex-2-en-5-ynylated substrates undergo smooth click reaction with an azide-based probe. This approach is thus suitable for substrate characterization of G9a and expected to further serve as a starting point to evolve other PKMTs to utilize a similar set of cofactors.
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Affiliation(s)
- Kabirul Islam
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - Weihong Zheng
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - Haiqiang Yu
- Proteomics Resource Center, Rockefeller University, New York, New York 10065, United States
| | - Haiteng Deng
- Proteomics Resource Center, Rockefeller University, New York, New York 10065, United States
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Minkui Luo
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, United States
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184
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Li H, Luan S. The cyclophilin AtCYP71 interacts with CAF-1 and LHP1 and functions in multiple chromatin remodeling processes. MOLECULAR PLANT 2011; 4:748-58. [PMID: 21596687 DOI: 10.1093/mp/ssr036] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Chromatin is the primary carrier of epigenetic information in higher eukaryotes. AtCYP71 contains both cyclophilin domain and WD40 repeats. Loss of AtCYP71 function causes drastic pleiotropic phenotypic defects. Here, we show that AtCYP71 physically interacts with FAS1 and LHP1, respectively, to modulate their distribution on chromatin. The lhp1 cyp71 double mutant showed more severe phenotypes than the single mutants, suggesting that AtCYP71 and LHP1 synergistically control plant development. Such synergism was in part illustrated by the observation that LHP1 association with its specific target loci requires AtCYP71 function. We also demonstrate that AtCYP71 physically interacts with FAS1 and is indispensable for FAS1 targeting to the KNAT1 locus. Together, our data suggest that AtCYP71 is involved in fundamental processes of chromatin assembly and histone modification in plants.
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Affiliation(s)
- Hong Li
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
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185
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Abstract
Protozoa constitute the earliest branch of the eukaryotic lineage, and several groups of protozoans are serious parasites of humans and other animals. Better understanding of biochemical pathways that are either in common with or divergent from those of higher eukaryotes is integral in the defense against these parasites. In yeast and humans, the posttranslational methylation of arginine residues in proteins affects myriad cellular processes, including transcription, RNA processing, DNA replication and repair, and signal transduction. The protein arginine methyltransferases (PRMTs) that catalyze these reactions, which are unique to the eukaryotic kingdom of organisms, first become evident in protozoa. In this review, we focus on the current understanding of arginine methylation in multiple species of parasitic protozoa, including Trichomonas, Entamoeba, Toxoplasma, Plasmodium, and Trypanosoma spp., and discuss how arginine methylation may play important and unique roles in each type of parasite. We mine available genomic and transcriptomic data to inventory the families of PRMTs in different parasites and the changes in their abundance during the life cycle. We further review the limited functional studies on the roles of arginine methylation in parasites, including epigenetic regulation in Apicomplexa and RNA processing in trypanosomes. Interestingly, each of the parasites considered herein has significantly differing sets of PRMTs, and we speculate on the importance of this diversity in aspects of parasite biology, such as differentiation and antigenic variation.
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186
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Strenkert D, Schmollinger S, Sommer F, Schulz-Raffelt M, Schroda M. Transcription factor-dependent chromatin remodeling at heat shock and copper-responsive promoters in Chlamydomonas reinhardtii. THE PLANT CELL 2011; 23:2285-301. [PMID: 21705643 PMCID: PMC3160021 DOI: 10.1105/tpc.111.085266] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 05/09/2011] [Accepted: 06/07/2011] [Indexed: 05/19/2023]
Abstract
How transcription factors affect chromatin structure to regulate gene expression in response to changes in environmental conditions is poorly understood in the green lineage. To shed light on this issue, we used chromatin immunoprecipitation and formaldehyde-assisted isolation of regulatory elements to investigate the chromatin structure at target genes of HSF1 and CRR1, key transcriptional regulators of the heat shock and copper starvation responses, respectively, in the unicellular green alga Chlamydomonas reinhardtii. Generally, we detected lower nucleosome occupancy, higher levels of histone H3/4 acetylation, and lower levels of histone H3 Lys 4 (H3K4) monomethylation at promoter regions of active genes compared with inactive promoters and transcribed and intergenic regions. Specifically, we find that activated HSF1 and CRR1 transcription factors mediate the acetylation of histones H3/4, nucleosome eviction, remodeling of the H3K4 mono- and dimethylation marks, and transcription initiation/elongation. By this, HSF1 and CRR1 quite individually remodel and activate target promoters that may be inactive and embedded into closed chromatin (HSP22F/CYC6) or weakly active and embedded into partially opened (CPX1) or completely opened chromatin (HSP70A/CRD1). We also observed HSF1-independent histone H3/4 deacetylation at the RBCS2 promoter after heat shock, suggesting interplay of specific and presumably more generally acting factors to adapt gene expression to the new requirements of a changing environment.
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187
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Fatima N, Ahmed SH, Salhan S, Rehman SMF, Kaur J, Owais M, Chauhan SS. Study of methyl transferase (G9aMT) and methylated histone (H3-K9) expressions in unexplained recurrent spontaneous abortion (URSA) and normal early pregnancy. Mol Hum Reprod 2011; 17:693-701. [PMID: 21606120 DOI: 10.1093/molehr/gar038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated the expression of methyl transferase G9a and methylated histone H3-K9 in fresh human decidual/endometrial tissue of 12 normal early pregnancies and 15 unexplained recurrent spontaneous abortions (URSA). The samples were obtained through dilatation and curettage and collected as per strict inclusion-exclusion criteria. The tissue was subjected to immunohistochemical analysis (IHC), western blotting (WB) and RT-PCR analysis. The results demonstrated methyl transferase G9a to have a lower expression in abortions when compared with that in normal pregnancy (P < 0.05). The sensitivity of RT-PCR, IHC and WB were respectively 66.67, 75 and 71.43%, while specificity of the same were 66.67, 60 and 78.92%, respectively. Methylated histone H3-K9 was significantly lower (P < 0.0001) in URSA tissues than in controls. This study suggests that methylation may cause URSA and indicates the need for further work to explore the role of methylation in URSA and its possible prevention through locally acting methylating/demethylating agents.
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Affiliation(s)
- Nishat Fatima
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India.
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188
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Feng Y, Wang J, Asher S, Hoang L, Guardiani C, Ivanov I, Zheng YG. Histone H4 acetylation differentially modulates arginine methylation by an in Cis mechanism. J Biol Chem 2011; 286:20323-34. [PMID: 21502321 DOI: 10.1074/jbc.m110.207258] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Histone H4 undergoes extensive post-translational modifications (PTMs) at its N-terminal tail. Many of these PTMs profoundly affect the on and off status of gene transcription. The molecular mechanism by which histone PTMs modulate genetic and epigenetic processes is not fully understood. In particular, how a PTM mark affects the presence and level of other histone modification marks needs to be addressed and is essential for better understanding the molecular basis of histone code hypothesis. To dissect the interplaying relationship between different histone modification marks, we investigated how individual lysine acetylations and their different combinations at the H4 tail affect Arg-3 methylation in cis. Our data reveal that the effect of lysine acetylation on arginine methylation depends on the site of acetylation and the type of methylation. Although certain acetylations present a repressive impact on PRMT1-mediated methylation (type I methylation), lysine acetylation generally is correlated with enhanced methylation by PRMT5 (type II dimethylation). In particular, Lys-5 acetylation decreases the activity of PRMT1 but increases that of PRMT5. Furthermore, circular dichroism study and computer simulation demonstrate that hyperacetylation increases the content of ordered secondary structures at the H4 tail region. These findings provide new insights into the regulatory mechanism of Arg-3 methylation by H4 acetylation and unravel the complex intercommunications that exist between different the PTM marks in cis. The divergent activities of PRMT1 and PRMT5 with respect to different acetyl-H4 substrates suggest that type I and type II protein-arginine methyltransferases use distinct molecular determinants for substrate recognition and catalysis.
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Affiliation(s)
- You Feng
- Department of Chemistry and Biology, Program of Molecular Basis of Diseases, Georgia State University, Atlanta, Georgia 30302, USA
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189
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Han A, Lee KH, Hyun S, Lee NJ, Lee SJ, Hwang H, Yu J. Methylation-mediated control of aurora kinase B and Haspin with epigenetically modified histone H3 N-terminal peptides. Bioorg Med Chem 2011; 19:2373-7. [DOI: 10.1016/j.bmc.2011.02.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 02/08/2011] [Accepted: 02/09/2011] [Indexed: 11/26/2022]
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190
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Creamer KM, Partridge JF. RITS-connecting transcription, RNA interference, and heterochromatin assembly in fission yeast. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:632-46. [PMID: 21823226 DOI: 10.1002/wrna.80] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In recent years, a bevy of evidence has been unearthed indicating that 'silent' heterochromatin is not as transcriptionally inert as once thought. In the unicellular yeast Schizosaccharomyces pombe, the processing of transcripts derived from centromeric repeats into homologous short interfering RNA (siRNA) is essential for the formation of centromeric heterochromatin. Deletion of genes required for siRNA biogenesis showed that core components of the canonical RNA interference (RNAi) pathway are essential for centromeric heterochromatin assembly as well as for centromere function. Subsequent purification of the RNA-induced initiation of transcriptional gene silencing (RITS) complex provided the critical link between siRNAs and heterochromatin assembly, with RITS acting as a physical bridge between noncoding RNA scaffolds and chromatin. Here, we review current understanding of how RITS promotes heterochromatin formation and how it participates in transcription-coupled silencing. WIREs RNA 2011 2 632-646 DOI: 10.1002/wrna.80 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Kevin M Creamer
- Integrated Program in Biomedical Sciences, University of Tennessee Health Science Center, Memphis, USA
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191
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Veiseth SV, Rahman MA, Yap KL, Fischer A, Egge-Jacobsen W, Reuter G, Zhou MM, Aalen RB, Thorstensen T. The SUVR4 histone lysine methyltransferase binds ubiquitin and converts H3K9me1 to H3K9me3 on transposon chromatin in Arabidopsis. PLoS Genet 2011; 7:e1001325. [PMID: 21423664 PMCID: PMC3053343 DOI: 10.1371/journal.pgen.1001325] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Accepted: 02/03/2011] [Indexed: 12/11/2022] Open
Abstract
Chromatin structure and gene expression are regulated by posttranslational modifications (PTMs) on the N-terminal tails of histones. Mono-, di-, or trimethylation of lysine residues by histone lysine methyltransferases (HKMTases) can have activating or repressive functions depending on the position and context of the modified lysine. In Arabidopsis, trimethylation of lysine 9 on histone H3 (H3K9me3) is mainly associated with euchromatin and transcribed genes, although low levels of this mark are also detected at transposons and repeat sequences. Besides the evolutionarily conserved SET domain which is responsible for enzyme activity, most HKMTases also contain additional domains which enable them to respond to other PTMs or cellular signals. Here we show that the N-terminal WIYLD domain of the Arabidopsis SUVR4 HKMTase binds ubiquitin and that the SUVR4 product specificity shifts from di- to trimethylation in the presence of free ubiquitin, enabling conversion of H3K9me1 to H3K9me3 in vitro. Chromatin immunoprecipitation and immunocytological analysis showed that SUVR4 in vivo specifically converts H3K9me1 to H3K9me3 at transposons and pseudogenes and has a locus-specific repressive effect on the expression of such elements. Bisulfite sequencing indicates that this repression involves both DNA methylation–dependent and –independent mechanisms. Transcribed genes with high endogenous levels of H3K4me3, H3K9me3, and H2Bub1, but low H3K9me1, are generally unaffected by SUVR4 activity. Our results imply that SUVR4 is involved in the epigenetic defense mechanism by trimethylating H3K9 to suppress potentially harmful transposon activity. The characteristics of the diverse cell types in multicellular organisms result from differential gene expression that is dependent on the level of DNA packaging. Genes that are essential for the function of the cell are expressed; while unessential genes, and DNA elements (transposons or “jumping genes”) that can move from one position to another within a genome and potentially cause deleterious mutations, are repressed. The mechanisms evolved in eukaryotes to avoid unwanted gene expression and transposon movement include DNA methylation and specific combinations of post translational modifications (PTMs) of the histones that package DNA. Here we show that the SUVR4 enzyme binds the signaling protein ubiquitin and that ubiquitin enables the enzyme to trimethylate lysine 9 (H3K9me3) of histone H3. In contrast to other reports demonstrating an activating role on expressed genes, we show that H3K9me3 has a locus-specific repressive effect on the expression of transposons. The specificity is maintained by the communication with other PTMs on transposons and euchromatic genes, which has a stimulating or repressing effect on enzyme activity, respectively. Our results demonstrate how repression of transcription can be restricted to specific targets and demonstrate that this repression involves a context-dependent read-out of different PTMs.
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Affiliation(s)
- Silje V. Veiseth
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | | | - Kyoko L. Yap
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Andreas Fischer
- Institute of Biology, Developmental Genetics, Martin Luther University Halle, Halle, Germany
| | - Wolfgang Egge-Jacobsen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- Glyconor Mass Spectrometry, Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Gunter Reuter
- Institute of Biology, Developmental Genetics, Martin Luther University Halle, Halle, Germany
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Reidunn B. Aalen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Tage Thorstensen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
- * E-mail:
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192
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Abstract
Epigenetic control mechanisms play a key role in the regulation of embryonic development and tissue homeostasis and modulate cardiovascular diseases. Increasing evidence suggests that lineage commitment of stem/progenitor cells is tightly regulated by epigenetic mechanisms. These epigenetic control mechanisms include DNA and histone modifications, which modulate the chromatin structure thereby regulating access of transcription factors. Particularly, the modification of histone acetylation and methylation, which is controlled by families of histone acetylases/deacetylases and methyltransferases/demethylases, respectively, controls stem cell maintenance, differentiation, and function. This review article summarizes our current understanding of epigenetic mechanisms regulating the differentiation of cardiovascular cells, specifically endothelial cells and cardiac muscle lineages. In particular, the article will focus on the enzymes which modify histones and are involved in chromatin remodelling.
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Affiliation(s)
- Kisho Ohtani
- Institute of Cardiovascular Regeneration, Center for Molecular Medicine, University of Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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193
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SET/MYND Lysine Methyltransferases Regulate Gene Transcription and Protein Activity. Genes (Basel) 2011; 2:210-8. [PMID: 24710145 PMCID: PMC3924839 DOI: 10.3390/genes2010210] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 01/25/2011] [Accepted: 02/07/2011] [Indexed: 12/20/2022] Open
Abstract
The SET and MYND (SMYD) family of lysine methyltransferases is defined by a SET domain that is split into two segments by a MYND domain, followed by a cysteine-rich post-SET domain. While members of the SMYD family are important in the SET-mediated regulation of gene transcription, pathological consequences have also been associated with aberrant expression of SMYD proteins. The last decade has witnessed a rapid increase in the studies and corresponding understanding of these highly impactful enzymes. Herein, we review the current body of knowledge related to the SMYD family of lysine methyltransferases and their role in transcriptional regulation, epigenetics, and tumorigenesis.
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194
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Dudley KJ, Li X, Kobor MS, Kippin TE, Bredy TW. Epigenetic mechanisms mediating vulnerability and resilience to psychiatric disorders. Neurosci Biobehav Rev 2011; 35:1544-51. [PMID: 21251925 DOI: 10.1016/j.neubiorev.2010.12.016] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 12/13/2010] [Accepted: 12/20/2010] [Indexed: 01/22/2023]
Abstract
The impact that stressful encounters have upon long-lasting behavioural phenotypes is varied. Whereas a significant proportion of the population will develop "stress-related" conditions such as post-traumatic stress disorder or depression in later life, the majority are considered "resilient" and are able to cope with stress and avoid such psychopathologies. The reason for this heterogeneity is undoubtedly multi-factorial, involving a complex interplay between genetic and environmental factors. Both genes and environment are of critical importance when it comes to developmental processes, and it appears that subtle differences in either of these may be responsible for altering developmental trajectories that confer vulnerability or resilience. At the molecular level, developmental processes are regulated by epigenetic mechanisms, with recent clinical and pre-clinical data obtained by ourselves and others suggesting that epigenetic differences in various regions of the brain are associated with a range of psychiatric disorders, including many that are stress-related. Here we provide an overview of how these epigenetic differences, and hence susceptibility to psychiatric disorders, might arise through exposure to stress-related factors during critical periods of development.
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Affiliation(s)
- Kevin J Dudley
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia.
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195
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Abstract
Organismal aging and longevity are influenced by many complex interacting factors. Epigenetics has recently emerged as another possible determinant of aging. Here, we review some of the epigenetic pathways that contribute to cellular senescence and age-associated phenotypes. Strategies aimed to reverse age-linked epigenetic alterations may lead to the development of new therapeutic interventions to delay or alleviate some of the most debilitating age-associated diseases.
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Affiliation(s)
- Ursula Muñoz-Najar
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA.
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196
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Uchida S, Hara K, Kobayashi A, Otsuki K, Yamagata H, Hobara T, Suzuki T, Miyata N, Watanabe Y. Epigenetic Status of Gdnf in the Ventral Striatum Determines Susceptibility and Adaptation to Daily Stressful Events. Neuron 2011; 69:359-72. [DOI: 10.1016/j.neuron.2010.12.023] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2010] [Indexed: 01/16/2023]
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197
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Khare T, Pal M, Petronis A. Understanding bipolar disorder: the epigenetic perspective. Curr Top Behav Neurosci 2011; 5:31-49. [PMID: 25236548 DOI: 10.1007/7854_2010_64] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bipolar disease (BPD) is a complex major psychiatric disorder that affects between 1% and 2% of the population and exhibits ?85% heritability. This has made BPD an appealing target for genetic studies yet, despite numerous attempts, the genetic basis of this disease remains elusive. Recently, it has come to light that epigenetic factors may also influence the development of BPD. These factors act via stable but reversible modifications of DNA and chromatin structure. In this chapter, we revisit the epidemiological, clinical, and molecular findings in BPD and reanalyze them from the perspective of inherited and acquired epigenetic misregulation. Epigenetic research has great potential to enhance our understanding of the molecular basis of BPD.
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Affiliation(s)
- Tarang Khare
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario, M5T 1R8, Canada,
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198
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Sakurai T, Bai H, Konno T, Ideta A, Aoyagi Y, Godkin JD, Imakawa K. Function of a transcription factor CDX2 beyond its trophectoderm lineage specification. Endocrinology 2010; 151:5873-81. [PMID: 20962045 DOI: 10.1210/en.2010-0458] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The transcription factor caudal-related homeobox 2 (CDX2) regulates trophectoderm differentiation, but its function beyond trophectoderm differentiation is not well characterized. CDX2 was shown to regulate a trophoblast-specific gene, interferon τ (IFNT), in the ruminants. However, its regulatory mechanism has not been determined. Here, we report a new role of CDX2 in histone modifications of the IFNT gene. Chromatin immunoprecipitation assays using ovine conceptuses obtained from d 14, 16, 16.5, or 20 of pregnancy (d 0, day of mating) revealed that H3K18 acetylation was highly detectable at the upstream and open reading frame regions of the IFNT gene on d 14 and 16, when CDX2 reached its peak expression. From d 16.5, when the conceptus initiates attachment to uterine epithelial cells, histone acetylation along with CDX2 expression declines. Two candidate CDX2 binding sites (-300 to -294 bp and -293 to -287 bp) of the bovine IFNT gene promoter region were detected from chromatin immunoprecipitation and luciferase assay. When Cdx2 constructs were transfected into bovine ear-derived fibroblast cells, histone acetylation was increased, concurrent with the recruitment of cAMP response element binding protein-binding protein, which has histone acetyltransferase activity. H3K18 acetylation was seen in the proximity of the CDX2 binding region located at the IFNT gene's upstream region in CT-1 cells, but when these cells were treated with specific CDX2 small interfering RNA, H3K18 acetylation was decreased. These findings suggest that CDX2 regulates its targeted gene through cAMP response element binding protein-binding protein recruitment, which correlates with greater histone acetylation.
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Affiliation(s)
- Toshihiro Sakurai
- Laboratory of Animal Breeding, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
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199
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Sahr T, Adam T, Fizames C, Maurel C, Santoni V. O-carboxyl- and N-methyltransferases active on plant aquaporins. PLANT & CELL PHYSIOLOGY 2010; 51:2092-2104. [PMID: 21062871 DOI: 10.1093/pcp/pcq171] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Methylation of biologically active molecules is achieved by methyltransferases (MTases). MTases can act on proteins through N- or O-carboxylmethylation reactions. Methylation of lysine and glutamic acid residues was recently described on the N-terminal tail of AtPIP2;1, a plasma membrane aquaporin of plants. In this study, we combine a bioinformatic and a biochemical screen and identify two MTases of Arabidopsis thaliana, SDG7 (At2g44150) and OMTF3 (At3g61990), as acting on the N-terminal tail of AtPIP2;1, at Lys3 and Glu6, respectively. Confocal microscopy imaging showed the two enzymes to be associated with the endoplasmic reticulum. An in vitro assay using various AtPIP2;1 N-terminal peptides as a bait allowed characterization of the enzymatic properties of recombinant SDG7 and OMTF3. The two enzymes showed minimal apparent K(m) values for their substrates, S-adenosylmethionine and peptide, in the range of 5-8 and 2-9 μM, respectively. SDG7 was shown to almost exclusively mono- or di-methylate Lys3. In contrast, OMTF3 specifically methylated Glu6, this methylation being dependent on the methylation profile of the neighboring Lys3 residue. In conclusion, this study allows the characterization of the first MTases able to methylate plant transmembrane proteins and provides the first identification of a glutamate-MTase in eukaryotes.
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Affiliation(s)
- Tobias Sahr
- Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des plantes, UMR 5004 CNRS/UMR 0386 INRA/Montpellier SupAgro/Université Montpellier 2, F-34060 Montpellier Cedex 2, France
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200
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Bártová E, Stixová L, Galiová G, Harničarová Horáková A, Legartová S, Kozubek S. Mutant genetic background affects the functional rearrangement and kinetic properties of JMJD2b histone demethylase. J Mol Biol 2010; 405:679-95. [PMID: 21073875 DOI: 10.1016/j.jmb.2010.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 11/02/2010] [Indexed: 01/04/2023]
Abstract
We have studied JMJD2b histone demethylase, which antagonizes H3K9me3 in the pericentromeric heterochromatin. In cells with a deficiency in the histone methyltransferase SUV39h, the level of full-length JMJD2b (JMJD2b-GFP-1086) at chromocenters was reduced, corresponding to a global decrease in JMJD2b and H3K9me3. In wild-type fibroblasts, the chromatin of ribosomal genes, which is dense with H3K9 methylation, lacked JMJD2b-GFP-1086, while mutant and truncated forms of JMJD2b densely occupied the nucleolar compartment. This implies that the PHD Zn-fingers and Tudor domains, which were removed in truncated JMJD2b, are responsible for the aberrant JMJD2b function. Intriguingly, the JMJD2b-GFP-1086 level was significantly higher in tumor cell nucleoli. The kinetic properties of JMJD2b-GFP-1086 in the nucleoli and nucleoplasm of normal and tumor cells were similar; ∼50% recovery of prebleached intensity was reached after <1 s. However, the mobile fraction of JMJD2b-GFP-1086 was increased in SUV39h-deficient cells. Similarly, the mobile fractions of mutant JMJD2b(1-424)H189A-GFP and truncated JMJD2b(1-424)GFP were greater than that measured for the full-length protein. We suggest that nucleoli are the site of an aberrant function of JMJD2b, the kinetic properties of which can be influenced by a mutant genetic background.
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Affiliation(s)
- Eva Bártová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic.
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