301
|
Zou MX, Butcher DT, Sadikovic B, Groves TC, Yee SP, Rodenhiser DI. Characterization of functional elements in the neurofibromatosis (NF1) proximal promoter region. Oncogene 2004; 23:330-9. [PMID: 14647436 DOI: 10.1038/sj.onc.1207053] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An essential requirement to understand how genes contribute to genetic disease is the thorough knowledge of the transcriptional regulation of gene expression. Here, we have characterized transcription factor binding sites within the type 1 neurofibromatosis (NF1) proximal regulatory region, and addressed the molecular mechanisms that regulate NF1 transcription. Overlapping regions of the NF1 proximal promoter have been cloned and characterized for use in luciferase reporter assays. These assays have identified a 500 bp region displaying activities up to 80-fold higher than control reporter levels. Mutations at putative CRE and SP1-binding sites immediately 5' to the transcription start site have dramatic effects that lead to a 70-90% decrease in reporter activity in all cell lines tested. Gelshift assays confirm binding of CREB and SP1/KLF family members to their putative recognition sequences, and provide the first evidence identifying functional sites likely involved in regulating NF1 transcription. These assays have also revealed a putative repressor region within the NF1 promoter region corresponding to CCCTC-rich sequences between the transcription and translation start sites. This work provides new information concerning the transcriptional regulation of the NF1 gene, and is the most thorough attempt to date to map functionally relevant regions within the NF1 proximal promoter region.
Collapse
Affiliation(s)
- Min-Xu Zou
- London Regional Cancer Centre, University of Western Ontario, London, Ontario, Canada
| | | | | | | | | | | |
Collapse
|
302
|
Fisher O, Siman-Tov R, Ankri S. Characterization of cytosine methylated regions and 5-cytosine DNA methyltransferase (Ehmeth) in the protozoan parasite Entamoeba histolytica. Nucleic Acids Res 2004; 32:287-97. [PMID: 14715927 PMCID: PMC373271 DOI: 10.1093/nar/gkh161] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2003] [Revised: 10/24/2003] [Accepted: 11/11/2003] [Indexed: 12/29/2022] Open
Abstract
The DNA methylation status of the protozoan parasite Entamoeba histolytica was heretofore unknown. In the present study, we developed a new technique, based on the affinity of methylated DNA to 5-methylcytosine antibodies, to identify methylated DNA in this parasite. Ribosomal DNA and ribosomal DNA circles were isolated by this method and we confirmed the validity of our approach by sodium bisulfite sequencing. We also report the identification and the characterization of a gene, Ehmeth, encoding a DNA methyltransferase strongly homologous to the human DNA methyltransferase 2 (Dnmt2). Immunofluorescence microscopy using an antibody raised against a recombinant Ehmeth showed that Ehmeth is concentrated in the nuclei of trophozoites. The recombinant Ehmeth has a weak but significant methyltransferase activity when E.histolytica genomic DNA is used as substrate. 5-Azacytidine (5-AzaC), an inhibitor of DNA methyltransferase, was used to study in vivo the role of DNA methylation in E.histolytica. Genomic DNA of trophozoites grown with 5-AzaC (23 microM) was undermethylated and the ability of 5-AzaC-treated trophozoites to kill mammalian cells or to cause liver abscess in hamsters was strongly impaired.
Collapse
MESH Headings
- 5-Methylcytosine/analysis
- 5-Methylcytosine/metabolism
- Amino Acid Sequence
- Animals
- Azacitidine/pharmacology
- Base Sequence
- Blotting, Western
- CHO Cells
- Cell Nucleus/enzymology
- Chromatography, Affinity
- Cloning, Molecular
- Cricetinae
- DNA (Cytosine-5-)-Methyltransferases/antagonists & inhibitors
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/isolation & purification
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation/drug effects
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Protozoan/metabolism
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- Entamoeba histolytica/cytology
- Entamoeba histolytica/enzymology
- Entamoeba histolytica/genetics
- Entamoeba histolytica/pathogenicity
- Genome, Protozoan
- Humans
- Liver Abscess/parasitology
- Mesocricetus
- Molecular Sequence Data
- Protein Transport
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Substrate Specificity
- Virulence/drug effects
Collapse
Affiliation(s)
- Ohad Fisher
- Department of Molecular Microbiology, The Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, POB 9649, 31096 Haifa, Israel
| | | | | |
Collapse
|
303
|
Coombes MM, Briggs KL, Bone JR, Clayman GL, El-Naggar AK, Dent SYR. Resetting the histone code at CDKN2A in HNSCC by inhibition of DNA methylation. Oncogene 2004; 22:8902-11. [PMID: 14654786 DOI: 10.1038/sj.onc.1207050] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the fifth most frequent cancer in the US. Several genetic and epigenetic alterations are associated with HNSCC tumorigenesis, including inactivation of CDKN2A, which encodes the p16 tumor suppressor, in cell lines and primary tumors by DNA methylation. Reactivation of tumor suppressor genes by DNA-demethylating agents and histone deacetylase (HDAC) inhibitors shows therapeutic promise for other cancers. Therefore, we investigated the ability of these agents to reactivate p16 in Tu159 HNSCC cells. Treatment of cells with 5-aza-2'deoxycytidine (5-aza-dC) increases CDKN2A expression and slightly increases histone H3 acetylation at this gene. No reactivation of CDKN2A is observed upon treatment with the HDAC inhibitor trichostatin A (TSA), but synergistic reactivation of CDKN2A is observed upon sequential treatment of Tu159 cells with both 5-aza-dC and TSA. Silencing of CDKN2A in Tu159 cells is correlated with increased methylation of histone H3 at lysine 9 and decreased methylation at lysine 4 relative to the upstream p15 gene promoter. Interestingly, global levels of H3-K9 methylation are decreased upon treatment with 5-aza-dC. Together these data indicate that DNA methylation is a dominant epigenetic mark for silencing of CDKN2A in Tu159 tumor cells. Moreover, changes in DNA methylation can reset the histone code by impacting multiple H3 modifications.
Collapse
Affiliation(s)
- Madelene M Coombes
- Department of Biochemistry and Molecular Biology, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
| | | | | | | | | | | |
Collapse
|
304
|
Abstract
Immediate early genes (IEG) are rapidly but transiently induced directly by intracellular signaling cascades to alter patterns of gene expression. It has been proposed that histone modifications could be the key to the quick alteration of chromatin structure, as this spread occurs too rapidly to be the consequence of passage of RNA polymerase II. In this review, we will discuss the different modifications on histones and the chromatin remodeling enzymes, allowing the promoter regions of two IEGs, c-fos and c-jun, to be accessed.
Collapse
Affiliation(s)
- Judy Chia Ghee Sng
- Laboratory of Molecular Pharmacology, Kanazawa University Graduate School of Natural Science and Technology, Ishikawa, Japan
| | | | | |
Collapse
|
305
|
Bolander FF. Modifications and Conformations of DNA and Nuclear Proteins. Mol Endocrinol 2004. [DOI: 10.1016/b978-012111232-5/50014-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
306
|
Veldic M, Caruncho HJ, Liu WS, Davis J, Satta R, Grayson DR, Guidotti A, Costa E. DNA-methyltransferase 1 mRNA is selectively overexpressed in telencephalic GABAergic interneurons of schizophrenia brains. Proc Natl Acad Sci U S A 2003; 101:348-53. [PMID: 14684836 PMCID: PMC314188 DOI: 10.1073/pnas.2637013100] [Citation(s) in RCA: 213] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A down-regulation of reelin and glutamic acid decarboxylase (GAD) 67 mRNAs was detected in gamma-aminobutyric acid (GABA)ergic cortical interneurons of schizophrenia (SZ) postmortem brains (10), suggesting that the availability of GABA and reelin may be decreased in SZ cortex. In situ hybridization of the mRNA encoding for DNA-methyltransferase 1, which catalyzes the methylation of promoter CpG islands, shows that the expression of this mRNA is increased in cortical GABAergic interneurons but not in pyramidal neurons of SZ brains. Counts of reelin mRNA-positive neurons in Brodmann's area 10 of either nonpsychiatric subjects or SZ patients show that the expression of reelin mRNA is decreased in layer-I, -II, and -IV GABAergic interneurons of SZ patients. These findings are consistent with the hypothesis that the increase of DNA-methyltransferase 1 expression in telencephalic GABAergic interneurons of SZ patients causes a promoter hypermethylation of reelin and GAD(67) and perhaps of other genes expressed in these interneurons. It is difficult to decide whether this dysfunction of GABAergic neurons detected in SZ is responsible for this disease or is a consequence of this disorder. Although at present we cannot differentiate between these two alternatives, it is important to consider that so far a molecular pathology of cortical GABAergic neurons appears to be the most consistent finding associated with SZ morbidity.
Collapse
Affiliation(s)
- M Veldic
- Psychiatric Institute, Department of Psychiatry, College of Medicine, University of Illinois, 1601 West Taylor Street, Chicago, IL 60612, USA
| | | | | | | | | | | | | | | |
Collapse
|
307
|
Abstract
High-resolution structural studies of protein-DNA complexes have proven to be an invaluable means of understanding the diverse functions of proteins that manage the genome. Most of the structures determined to date represent proteins bound noncovalently to various DNA sequences or structures. Although noncovalent complexation is often adequate to study the structures of proteins that have robust, specific interactions with DNA, it is poorly suited to the study of transient intermediates in enzyme-catalyzed DNA processing reactions or of complexes that exist in multiple equilibrating forms. In recent years, strategies developed for the covalent trapping of protein-DNA complexes have begun to show promise as a window into an otherwise inaccessible world of structure.
Collapse
Affiliation(s)
- Gregory L Verdine
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | | |
Collapse
|
308
|
Tao Q, Robertson KD. Stealth technology: how Epstein-Barr virus utilizes DNA methylation to cloak itself from immune detection. Clin Immunol 2003; 109:53-63. [PMID: 14585276 DOI: 10.1016/s1521-6616(03)00198-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epstein-Barr virus (EBV) is a large lymphotrophic DNA virus that establishes life-long residency in the infected host and is associated with a number of human tumors. The EBV genome encodes proteins essential for persistence, an oncoprotein, and proteins that render it vulnerable to the host's immune system; therefore, EBV gene transcription is tightly regulated. One critically important regulatory mechanism utilized by EBV is DNA methylation. Methylation of cytosines within CpG dinucleotides at promoter regions is important for gene silencing and genome integrity. Although most parasitic elements are methylated in mammalian cells never to be reactivated again, EBV has evolved to utilize DNA methylation to maximize persistence and cloak itself from immune detection. EBV's reliance on DNA methylation also provides a unique therapeutic strategy for the treatment of EBV-associated tumors. DNA demethylating agents are capable of reactivating transcription of highly immunogenic viral proteins, rendering tumor cells susceptible to killing by the host immune system, and inducing the viral lytic cycle which culminates in cell lysis.
Collapse
Affiliation(s)
- Qian Tao
- Tumor Virology/Cancer Epigenetics Laboratory, Johns Hopkins Singapore, Level 5, Clinical Research Center, NUS, 10 Medical Drive, Singapore 117597
| | | |
Collapse
|
309
|
De Larco JE, Wuertz BRK, Yee D, Rickert BL, Furcht LT. Atypical methylation of the interleukin-8 gene correlates strongly with the metastatic potential of breast carcinoma cells. Proc Natl Acad Sci U S A 2003; 100:13988-93. [PMID: 14623984 PMCID: PMC283533 DOI: 10.1073/pnas.2335921100] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previously, we have shown that a strong correlation exists between the metastatic potential of breast carcinoma cell lines and their ectopic expression of IL-8. The undifferentiated, highly metastatic cell lines with high metastatic potential produce much more IL-8 than their differentiated lower metastatic counterparts. After eliminating the possibility that transcription factor activity was responsible for differences in IL-8 release, we examined the IL-8 gene for possible epigenetic modifications. Here, we report an aberrant methylation pattern that may be responsible for the differences in IL-8 release between the high and low metastatic cell lines. We determined that none of the deoxycytidylate-phosphate-deoxyguanylate (CpG) sites in the reported IL-8 promoter were methylated in either cell type. Much further upstream in the IL-8 gene, two CpG sites were identified that are differentially methylated. These two sites were fully methylated in the high metastatic cell lines, which produce large quantities of IL-8 and remain unmethylated in the low metastatic cell lines where the IL-8 gene is relatively silent. The DNA methylation results presented here differ from the common epigenetic paradigm in which methylation of promoter CpG islands silences gene expression, suggesting that there are additional epigenetic control mechanisms that as yet have not been fully appreciated or explored.
Collapse
MESH Headings
- Base Sequence
- Breast Neoplasms/genetics
- Breast Neoplasms/immunology
- Breast Neoplasms/secondary
- Cell Line, Tumor
- CpG Islands
- DNA Methylation
- DNA, Complementary/genetics
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- Female
- Gene Expression
- Gene Silencing
- Genes, Reporter
- Humans
- Interleukin-8/biosynthesis
- Interleukin-8/genetics
- Luciferases/genetics
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transfection
Collapse
Affiliation(s)
- Joseph E De Larco
- Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455, USA.
| | | | | | | | | |
Collapse
|
310
|
Rousseau E, Ruchoux MM, Scaravilli F, Chapon F, Vinchon M, De Smet C, Godfraind C, Vikkula M. CDKN2A
, CDKN2B
and p14 ARF
are frequently and differentially methylated in ependymal tumours. Neuropathol Appl Neurobiol 2003; 29:574-83. [PMID: 14636164 DOI: 10.1046/j.0305-1846.2003.00505.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Ependymal tumours are histologically and clinically varied lesions. Numerical abnormalities of chromosome 9 are frequently associated with these tumours. Nevertheless, the three important tumour suppressor genes located in this chromosome, CDKN2A, CDKN2B and p14 ARF, have not been reported to be commonly altered in them. We studied promoter methylation of these genes, an important mechanism associated with gene silencing in a series of 152 ependymal tumours of WHO grades I to III. Methylation status of the CDKN2A, CDKN2B and p14 ARF promoters was assessed by methylation-specific polymerase chain reaction and the genetic results were correlated to clinicopathological features. We observed promoter methylation for CDKN2A in 21% (26/123) of tumours, for CDKN2B in 32% (23/71) and p14 ARF in 21% (23/108). For all three genes, posterior fossa ependymomas were less frequently methylated in paediatric patients than in adults. For CDKN2B, extracranial tumours were more frequently methylated than intracranial ones. For CDKN2B and p14 ARF, methylation was more frequent in low-grade tumours; the reverse was observed for CDKN2A. CDKN2A, CDKN2B and p14 ARF promoters were methylated in 21-32% of the tumours. Frequencies of methylation varied according to clinicopathological features. This suggests a role for these genes in ependymoma tumorigenesis.
Collapse
Affiliation(s)
- E Rousseau
- Laboratory of Neuropathology, Université Catholique de Louvain, Brussels, Belgium
| | | | | | | | | | | | | | | |
Collapse
|
311
|
Tang LY, Reddy MN, Rasheva V, Lee TL, Lin MJ, Hung MS, Shen CKJ. The eukaryotic DNMT2 genes encode a new class of cytosine-5 DNA methyltransferases. J Biol Chem 2003; 278:33613-6. [PMID: 12819212 DOI: 10.1074/jbc.c300255200] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNMT2 is a subgroup of the eukaryotic cytosine-5 DNA methyltransferase gene family. Unlike the other family members, proteins encoded by DNMT2 genes were not known before to possess DNA methyltransferase activities. Most recently, we have shown that the genome of Drosophila S2 cells stably expressing an exogenous Drosophila dDNMT2 cDNA became anomalously methylated at the 5'-positions of cytosines (Reddy, M. N., Tang, L. Y., Lee, T. L., and Shen, C.-K. J. (2003) Oncogene, in press). We present evidence here that the genomes of transgenic flies overexpressing the dDnmt2 protein also became hypermethylated at specific regions. Furthermore, transient transfection studies in combination with sodium bisulfite sequencing demonstrated that dDnmt2 as well as its mouse ortholog, mDnmt2, are capable of methylating a cotransfected plasmid DNA. These data provide solid evidence that the fly and mouse DNMT2 gene products are genuine cytosine-5 DNA methyltransferases.
Collapse
Affiliation(s)
- Lin-Ya Tang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, Republic of China
| | | | | | | | | | | | | |
Collapse
|
312
|
Archer GS, Dindot S, Friend TH, Walker S, Zaunbrecher G, Lawhorn B, Piedrahita JA. Hierarchical phenotypic and epigenetic variation in cloned swine. Biol Reprod 2003; 69:430-6. [PMID: 12700187 PMCID: PMC2637358 DOI: 10.1095/biolreprod.103.016147] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Cloning by somatic cell nuclear transfer can result in the birth of animals with phenotypic and gene expression abnormalities. We compared adult cloned pigs and adult pigs from naturally bred control females using a series of physiological and genetic parameters, including detailed methylation profiles of selected genomic regions. Phenotypic and genetic analyses indicated that there are two classes of traits, one in which the cloned pigs have less variation than controls and another characterized by variation that is equally high in cloned and control pigs. Although cloning creates animals within the normal phenotypic range, it increases the variability associated with some traits. This finding is contrary to the expectation that cloning can be used to reduce the size of groups involved in animal experimentation and to reproduce an animal, including a pet, with a homogenous set of desired traits.
Collapse
Affiliation(s)
- Greg S. Archer
- Department of Animal Sciences, Texas A&M University, College Station, Texas 77843
| | - Scott Dindot
- Department of Veterinary Anatomy and Public Health, Texas A&M University, College Station, Texas 77843
| | - Ted H. Friend
- Department of Animal Sciences, Texas A&M University, College Station, Texas 77843
| | - Shawn Walker
- Department of Veterinary Anatomy and Public Health, Texas A&M University, College Station, Texas 77843
| | - Gretchen Zaunbrecher
- Department of Veterinary Anatomy and Public Health, Texas A&M University, College Station, Texas 77843
| | - Bruce Lawhorn
- Department of Large Animal Medicine, Texas A&M University, College Station, Texas 77843
| | - Jorge A. Piedrahita
- Department of Animal Sciences, Texas A&M University, College Station, Texas 77843
- Correspondence: Jorge A. Piedrahita, Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606. FAX: 919 515 4237; e-mail: jorge
| |
Collapse
|
313
|
Horikawa I, Barrett JC. Transcriptional regulation of the telomerase hTERT gene as a target for cellular and viral oncogenic mechanisms. Carcinogenesis 2003; 24:1167-76. [PMID: 12807729 DOI: 10.1093/carcin/bgg085] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Malignant transformation from mortal, normal cells to immortal, cancer cells is generally associated with activation of telomerase and subsequent telomere maintenance. A major mechanism to regulate telomerase activity in human cells is transcriptional control of the telomerase catalytic subunit gene, human telomerase reverse transcriptase (hTERT). Several transcription factors, including oncogene products (e.g. c-Myc) and tumor suppressor gene products (e.g. WT1 and p53), are able to control hTERT transcription when over-expressed, although it remains to be determined whether a cancer-associated alteration of these factors is primarily responsible for the hTERT activation during carcinogenic processes. Microcell-mediated chromosome transfer experiments have provided evidence for endogenous factors that function to repress the telomerase activity in normal cells and are inactivated in cancer cells. At least one of those endogenous telomerase repressors, which is encoded by a putative tumor suppressor gene on chromosome 3p, acts through transcriptional repression of the hTERT gene. The hTERT gene is also a target site for viruses frequently associated with human cancers, such as human papillomavirus (HPV) and hepatitis B virus (HBV). HPV E6 protein contributes to keratinocyte immortalization and carcinogenesis through trans-activation of the hTERT gene transcription. In at least some hepatocellular carcinomas, the hTERT gene is a non-random integration site of HBV genome, which activates in cis the hTERT transcription. Thus, a variety of cellular and viral oncogenic mechanisms converge on transcriptional control of the hTERT gene. Regulation of chromatin structure through the modification of nucleosomal histones may mediate the action of these cellular and viral mechanisms. Further elucidation of the hTERT transcriptional regulation, including identification and characterization of the endogenous repressor proteins, should lead to better understanding of the complex regulation of human telomerase in normal and cancer cells and may open up new strategies for anticancer therapy.
Collapse
Affiliation(s)
- Izumi Horikawa
- Laboratory of Biosystems and Cancer, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 9000 Rockville Pike, Building 37, Room 5046, MSC-4264, Bethesda, MD 20892, USA.
| | | |
Collapse
|
314
|
Rombauts S, Florquin K, Lescot M, Marchal K, Rouzé P, van de Peer Y. Computational approaches to identify promoters and cis-regulatory elements in plant genomes. PLANT PHYSIOLOGY 2003; 132:1162-76. [PMID: 12857799 PMCID: PMC167057 DOI: 10.1104/pp.102.017715] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2002] [Revised: 01/10/2003] [Accepted: 03/17/2003] [Indexed: 05/19/2023]
Abstract
The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different approaches have been developed to detect conserved motifs in a set of genes that are either coregulated or orthologous. However, although recent approaches seem promising, in general, unambiguous identification of regulatory elements is not straightforward. The delineation of promoters is even harder, due to its complex nature, and in silico promoter prediction is still in its infancy. Here, we review the different approaches that have been developed for identifying promoters and their regulatory elements. We discuss the detection of cis-acting regulatory elements using word-counting or probabilistic methods (so-called "search by signal" methods) and the delineation of promoters by considering both sequence content and structural features ("search by content" methods). As an example of search by content, we explored in greater detail the association of promoters with CpG islands. However, due to differences in sequence content, the parameters used to detect CpG islands in humans and other vertebrates cannot be used for plants. Therefore, a preliminary attempt was made to define parameters that could possibly define CpG and CpNpG islands in Arabidopsis, by exploring the compositional landscape around the transcriptional start site. To this end, a data set of more than 5,000 gene sequences was built, including the promoter region, the 5'-untranslated region, and the first introns and coding exons. Preliminary analysis shows that promoter location based on the detection of potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. Nevertheless, because the landscape of CpG/CpNpG islands differs considerably between promoters and introns on the one side and exons (whether coding or not) on the other, more sophisticated approaches can probably be developed for the successful detection of "putative" CpG and CpNpG islands in plants.
Collapse
Affiliation(s)
- Stephane Rombauts
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9000 Gent, Belgium
| | | | | | | | | | | |
Collapse
|
315
|
Werner T, Fessele S, Maier H, Nelson PJ. Computer modeling of promoter organization as a tool to study transcriptional coregulation. FASEB J 2003; 17:1228-37. [PMID: 12832287 DOI: 10.1096/fj.02-0955rev] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Understanding how the regulation of gene networks is orchestrated is an important challenge for characterizing complex biological processes. Gene transcription is regulated in part by nuclear factors that recognize short DNA sequence motifs, called transcription factor binding sites, in most cases located upstream of the gene coding sequence in promoter and enhancer regions. Genes expressed in the same tissue under similar conditions often share a common organization of at least some of these regulatory binding elements. In this way the organization of promoter motifs represents a "footprint" of the transcriptional regulatory mechanisms at work in a specific biologic context and thus provides information about signal and tissue specific control of expression. Analysis of promoters for organizational features as demonstrated here provides a crucial link between the static nucleotide sequence of the genome and the dynamic aspects of gene regulation and expression.
Collapse
Affiliation(s)
- Thomas Werner
- GSF-National Research Center for Environment and Health, Institute of Experimental Genetics, Neuherberg, Germany
| | | | | | | |
Collapse
|
316
|
Saito Y, Kanai Y, Nakagawa T, Sakamoto M, Saito H, Ishii H, Hirohashi S. Increased protein expression of DNA methyltransferase (DNMT) 1 is significantly correlated with the malignant potential and poor prognosis of human hepatocellular carcinomas. Int J Cancer 2003; 105:527-32. [PMID: 12712445 DOI: 10.1002/ijc.11127] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alteration of DNA methylation is one of the most consistent epigenetic changes in human cancers. DNA methyltransferase (DNMT) 1 is a major enzyme involved in establishing genomic methylation patterns. Most of the studies concerning DNMT1 expression in human cancers have been performed only at the mRNA level. To directly examine DNMT1 protein expression levels during human hepatocarcinogenesis, 16 histologically normal liver tissues, 51 noncancerous liver tissues exhibiting chronic hepatitis or cirrhosis, which are considered to be precancerous conditions, and 53 hepatocellular carcinomas (HCCs) were subjected to immunohistochemic examination. If more than 20% of the cells exhibited nuclear DNMT1 staining, the tissue sample was considered to be DNMT1-positive. DNMT1 immunoreactivity was observed in 23 (43%) of the HCCs, but in none (0%) of the histologically normal liver or noncancerous liver tissues exhibiting chronic hepatitis or cirrhosis. The incidence of increased DNMT1 protein expression in HCCs correlated significantly with poor tumor differentiation (p = 0.0006) and portal vein involvement (p = 0.0002). Moreover, the recurrence-free (p = 0.0001) and overall (p < 0.0001) survival rates of patients with HCCs exhibiting increased DNMT1 protein expression were significantly lower than those of patients with HCCs that did not exhibit increased expression. Increased DNMT1 protein expression may play a critical role in the malignant progression of HCCs and be a biologic predictor of both HCC recurrence and a poor prognosis in HCC patients.
Collapse
Affiliation(s)
- Yoshimasa Saito
- Pathology Division, National Cancer Center Research Institute, Tokyo, Japan
| | | | | | | | | | | | | |
Collapse
|
317
|
Kim TY, Jong HS, Song SH, Dimtchev A, Jeong SJ, Lee JW, Kim TY, Kim NK, Jung M, Bang YJ. Transcriptional silencing of the DLC-1 tumor suppressor gene by epigenetic mechanism in gastric cancer cells. Oncogene 2003; 22:3943-51. [PMID: 12813468 DOI: 10.1038/sj.onc.1206573] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DLC-1 (deleted in liver cancer) gene is frequently deleted in hepatocellular carcinoma. However, little is known about the genetic status and the expression of this gene in gastric cancer. In this study, Northern and Southern analysis showed that seven of nine human gastric cancer cell lines did not express DLC-1 mRNA, but contained the DLC-1 gene. To identify the mechanism of the loss of DLC-1 mRNA expression in these cell lines, we investigated the methylation status of DLC-1 gene by using methylation-specific PCR (MSP) and Southern blot, and found that five of seven DLC-1 nonexpressing gastric cancer cell lines were methylated in the DLC-1 CpG island. Treatment with 5-aza-2'-deoxycytidine (5-Aza-dC) induced DLC-1 mRNA expression in the gastric cancer cell lines that have the methylated alleles. Studies using SNU-601 cell line with methylated DLC-1 alleles revealed that nearly all CpG sites within DLC-1 CpG island were methylated, and that the in vitro methylation of the DLC-1 promoter region is enough to repress DLC-1 mRNA expression, regardless of the presence of transcription factors capable of inducing this gene. In all, 29 of 97 (30%) primary gastric cancers were also shown to be methylated, demonstrating that methylation of the DLC-1 CpG island is not uncommon in gastric cancer. In addition, we demonstrated that DLC-1 mRNA expression was induced, and an increase in the level of acetylated H3 and H4 was detected by the treatment with trichostatin A (TSA) in two DLC-1 nonexpressing cell lines that have the unmethylated alleles. Taken together, the results of our study suggest that the transcriptional silencing of DLC-1, by epigenetic mechanism, may be involved in gastric carcinogenesis.
Collapse
MESH Headings
- Acetylation/drug effects
- Acetyltransferases/antagonists & inhibitors
- Alleles
- Azacitidine/analogs & derivatives
- Azacitidine/pharmacology
- Blotting, Northern
- Blotting, Southern
- CpG Islands
- DNA Methylation/drug effects
- Decitabine
- Enzyme Inhibitors/pharmacology
- GTPase-Activating Proteins
- Gene Expression Regulation, Neoplastic/physiology
- Gene Silencing/physiology
- Genes, Tumor Suppressor
- Histone Acetyltransferases
- Histones/metabolism
- Humans
- Hydroxamic Acids/pharmacology
- Neoplasm Proteins/genetics
- Protein Processing, Post-Translational/drug effects
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Neoplasm/biosynthesis
- RNA, Neoplasm/genetics
- Saccharomyces cerevisiae Proteins/antagonists & inhibitors
- Stomach Neoplasms/genetics
- Stomach Neoplasms/metabolism
- Tumor Cells, Cultured/metabolism
- Tumor Suppressor Proteins/genetics
Collapse
Affiliation(s)
- Tai Young Kim
- National Research Laboratory for Cancer Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul 110-744, Korea
| | | | | | | | | | | | | | | | | | | |
Collapse
|
318
|
Rascle A, Johnston JA, Amati B. Deacetylase activity is required for recruitment of the basal transcription machinery and transactivation by STAT5. Mol Cell Biol 2003; 23:4162-73. [PMID: 12773560 PMCID: PMC156147 DOI: 10.1128/mcb.23.12.4162-4173.2003] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The signal transducer and activator of transcription STAT5 plays a major role in the cellular response to cytokines, but the mechanism by which it activates transcription remains poorly understood. We show here that deacetylase inhibitors (trichostatin A, suberoylanilide hydroxamic acid, and sodium butyrate) prevent induction of endogenous STAT5 target genes, implying that a deacetylase activity is required for that process. Microarray analyses revealed that this requirement is common to all STAT5 target genes. Using chromatin immunoprecipitation, we show that, following STAT5 DNA binding, deacetylase inhibitors block transcription initiation by preventing recruitment of the basal transcription machinery. This inhibition is not due to effects on histone H3 and H4 acetylation or chromatin remodeling within the promoter region. This novel mechanism of transactivation by STAT5 provides a rationale for the use of deacetylase inhibitors for therapeutic intervention in STAT5-associated cancers.
Collapse
Affiliation(s)
- Anne Rascle
- Department of Discovery Research, DNAX Research Inc, Palo Alto, California 94304, USA
| | | | | |
Collapse
|
319
|
|
320
|
Wang S, Zhu J. Evidence for a relief of repression mechanism for activation of the human telomerase reverse transcriptase promoter. J Biol Chem 2003; 278:18842-50. [PMID: 12611896 DOI: 10.1074/jbc.m209544200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcriptional activation of human telomerase reverse transcriptase (hTERT) is an important step during cellular immortalization and tumorigenesis. To study how this activation occurs during immortalization, we have established a set of genetically related pre-crisis cells and their immortal progeny. As expected, hTERT mRNA was detected in our telomerase-positive immortal cells but not in pre-crisis cells or telomerase-negative immortal cells. However, transiently transfected luciferase reporters controlled by hTERT promoter sequences exhibited similar levels of luciferase activity in both telomerase-positive and -negative cells, suggesting that the endogenous chromatin context is likely required for hTERT regulation. Analysis of chromatin susceptibility to DNase I digestion consistently identified a DNase I hypersensitivity site (DHS) near the hTERT transcription initiation site in telomerase-positive cells. In addition, the histone deacetylase inhibitor trichostatin A (TSA) induced hTERT transcription and also a general increase in chromatin sensitivity to DNase treatment in telomerase-negative cells. The TSA-induced hTERT transcription in pre-crisis cells was accompanied by the formation of a DHS at the hTERT promoter. Furthermore, the TSA-induced hTERT transcription and chromatin alterations were not blocked by cycloheximide, suggesting that this induction does not require de novo protein synthesis and that TSA induces hTERT expression through the inhibition of histone deacetylation at the hTERT promoter. Taken together, our results suggest that the endogenous chromatin environment plays a critical role in the regulation of hTERT expression during cellular immortalization.
Collapse
Affiliation(s)
- Shuwen Wang
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
| | | |
Collapse
|
321
|
Ishida C, Ura K, Hirao A, Sasaki H, Toyoda A, Sakaki Y, Niwa H, Li E, Kaneda Y. Genomic organization and promoter analysis of the Dnmt3b gene. Gene 2003; 310:151-9. [PMID: 12801642 DOI: 10.1016/s0378-1119(03)00545-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Dnmt3b gene encodes a de novo DNA methyltransferase that is essential for normal mouse development. It is highly expressed in early embryos and embryonic stem (ES) cells but downregulated in most adult somatic tissues. To gain insight into the regulation of Dnmt3b, we have isolated a mouse genomic bacterial artificial chromosome clone that contains the Dnmt3b gene. Complete sequence analysis of the clone demonstrated that Dnmt3b consists of at least 24 exons and spans 38 kilobases. S1 nuclease analysis identified two adjacent transcriptional start sites located downstream of a unique TATA-like element in a CpG island. There was an unknown gene which we named mU(3) 17 kb upstream of the Dnmt3b locus, and it was transcribed ubiquitously and in the opposite direction of Dnmt3b. Transfection analysis revealed that the minimal promoter region containing an Sp1 site was active even in somatic cells, and that there were several repressor elements within 7.9 kb upstream of Dnmt3b downregulated this gene specifically in somatic cells but not in ES cells. These findings provide a basis for future detailed studies of the mechanisms controlling Dnmt3b expression.
Collapse
Affiliation(s)
- Chisaki Ishida
- Division of Gene Therapy Science, Osaka University School of Medicine, 2-2 Yamada-oka, Suita, 565-0870, Osaka, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
322
|
Liu K, Wang YF, Cantemir C, Muller MT. Endogenous assays of DNA methyltransferases: Evidence for differential activities of DNMT1, DNMT2, and DNMT3 in mammalian cells in vivo. Mol Cell Biol 2003; 23:2709-19. [PMID: 12665573 PMCID: PMC152572 DOI: 10.1128/mcb.23.8.2709-2719.2003] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
While CpG methylation can be readily analyzed at the DNA sequence level in wild-type and mutant cells, the actual DNA (cytosine-5) methyltransferases (DNMTs) responsible for in vivo methylation on genomic DNA are less tractable. We used an antibody-based method to identify specific endogenous DNMTs (DNMT1, DNMT1b, DNMT2, DNMT3a, and DNMT3b) that stably and selectively bind to genomic DNA containing 5-aza-2'-deoxycytidine (aza-dC) in vivo. Selective binding to aza-dC-containing DNA suggests that the engaged DNMT is catalytically active in the cell. DNMT1b is a splice variant of the predominant maintenance activity DNMT1, while DNMT2 is a well-conserved protein with homologs in plants, yeast, Drosophila, humans, and mice. Despite the presence of motifs essential for transmethylation activity, catalytic activity of DNMT2 has never been reported. The data here suggest that DNMT2 is active in vivo when the endogenous genome is the target, both in human and mouse cell lines. We quantified relative global genomic activity of DNMT1, -2, -3a, and -3b in a mouse teratocarcinoma cell line. DNMT1 and -3b displayed the greatest in vivo binding avidity for aza-dC-containing genomic DNA in these cells. This study demonstrates that individual DNMTs can be tracked and that their binding to genomic DNA can be quantified in mammalian cells in vivo. The different DNMTs display a wide spectrum of genomic DNA-directed activity. The use of an antibody-based tracking method will allow specific DNMTs and their DNA targets to be recovered and analyzed in a physiological setting in chromatin.
Collapse
Affiliation(s)
- Kui Liu
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210, USA
| | | | | | | |
Collapse
|
323
|
Di Croce L, Pelicci PG. Tumour-associated hypermethylation: silencing E-cadherin expression enhances invasion and metastasis. Eur J Cancer 2003; 39:413-4. [PMID: 12751369 DOI: 10.1016/s0959-8049(02)00815-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
324
|
Tremolizzo L, Carboni G, Ruzicka WB, Mitchell CP, Sugaya I, Tueting P, Sharma R, Grayson DR, Costa E, Guidotti A. An epigenetic mouse model for molecular and behavioral neuropathologies related to schizophrenia vulnerability. Proc Natl Acad Sci U S A 2002; 99:17095-100. [PMID: 12481028 PMCID: PMC139275 DOI: 10.1073/pnas.262658999] [Citation(s) in RCA: 285] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2002] [Indexed: 12/14/2022] Open
Abstract
Reelin and glutamic acid decarboxylase (GAD)67 expressed by cortical gamma-aminobutyric acid-ergic interneurons are down-regulated in schizophrenia. Because epidemiological studies of schizophrenia fail to support candidate gene haploinsufficiency of Mendelian origin, we hypothesize that epigenetic mechanisms (i.e., cytosine hypermethylation of CpG islands present in the promoter of these genes) may be responsible for this down-regulation. Protracted l-methionine (6.6 mmolkg for 15 days, twice a day) treatment in mice elicited in brain an increase of S-adenosyl-homocysteine, the processing product of the methyl donor S-adenosyl-methionine, and a marked decrease of reelin and GAD67 mRNAs in both WT and heterozygous reeler mice. This effect of l-methionine was associated with an increase in the number of methylated cytosines in the CpG island of the reelin promoter region. This effect was not observed for GAD65 or neuronal-specific enolase and was not replicated by glycine doses 2-fold greater than those of l-methionine. Prepulse inhibition of startle declined at a faster rate as the prepulsestartle interval increased in mice receiving l-methionine. Valproic acid (2 mmolkg for 15 days, twice a day) reverted l-methionine-induced down-regulation of reelin and GAD67 in both WT and heterozygous reeler mice, suggesting an epigenetic action through the inhibition of histone deacetylases. The same dose of valproate increased acetylation of histone H3 in mouse brain nearly 4-fold. This epigenetic mouse model may be useful in evaluating drug efficacy on schizophrenia vulnerability. Hence the inhibition of histone deacetylases could represent a pharmacological intervention mitigating epigenetically induced vulnerability to schizophrenia in individuals at risk.
Collapse
Affiliation(s)
- L Tremolizzo
- Department of Psychiatry, Psychiatric Institute, College of Medicine, University of Illinois, Chicago, IL 60612, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
325
|
Kioussis D, Ellmeier W. Chromatin and CD4, CD8A and CD8B gene expression during thymic differentiation. Nat Rev Immunol 2002; 2:909-19. [PMID: 12461564 DOI: 10.1038/nri952] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The regulation of gene expression during thymocyte development provides an ideal experimental system to study lineage-commitment processes. In particular, expression of the CD4, CD8A and CD8B genes seems to correlate well with the cell-fate decisions that are taken by thymocytes, and elucidating the molecular mechanisms that underlie the differential expression of these genes could reveal key events in differentiation processes. Here, we review examples of how gene cis elements (such as promoters, enhancers and locus control regions) and trans elements (such as transcription factors, chromatin-remodelling complexes and histone-modification enzymes) come together to orchestrate a finely tuned sequence of events that results in the complex pattern of CD4, CD8A and CD8B gene expression that is observed during thymocyte development.
Collapse
Affiliation(s)
- Dimitris Kioussis
- Division of Molecular Immunology, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.
| | | |
Collapse
|