Methylation of an alpha-foetoprotein gene intragenic site modulates gene activity

Novel human alpha-fetoprotein mRNA isoform lacking exon 1 identified in ovarian yolk sac tumor

OBJECTIVE

Alpha-fetoprotein (AFP) is a major fetal serum protein, the biologic role of which has not been not fully elucidated. Recently, existence of a novel AFP mRNA isoform (del.1 AFP mRNA isoform), which is transcribed from the intron A (the intron between exons 1 and 2), has been reported in murine yolk sac and fetal liver. In the present study, we intended to identify the human homologue of the murine AFP mRNA isoform in the yolk sac tumor.

METHODS

To investigate the existence of the mRNA isoform (which we termed the "AFP-C mRNA isoform"), reverse transcription-polymerase chain reaction (RT-PCR) was used. Moreover, the expression analysis of the AFP-C cDNA isoform using the AFP-negative human cell line was carried out.

RESULTS

RT-PCR revealed the existence of the AFP-C mRNA isoform in the yolk sac tumor and human hepatocellular carcinoma cells. The expression analysis clarified that the molecular size of the AFP-C was approximately 65 kd, and that the protein was not secreted, in contrast to the traditional AFP.

CONCLUSION

From these results, the existence of the AFP-C mRNA isoform has been demonstrated for the first time in humans. The AFP-C located in cytoplasm possibly plays physiologic/pathogenic roles distinct from those of the traditional AFP in the yolk sac tumor and hepatocellular carcinoma.

Transcription factor interactions and chromatin modifications associated with p53-mediated, developmental repression of the alpha-fetoprotein gene

We performed chromatin immunoprecipitation (ChIP) analyses of developmentally staged solid tissues isolated from wild-type and p53-null mice to determine specific histone N-terminal modifications, histone-modifying proteins, and transcription factor interactions at the developmental repressor region (-850) and core promoter of the hepatic tumor marker alpha-fetoprotein (AFP) gene. Both repression of AFP during liver development and silencing in the brain, where AFP is never expressed, are associated with dimethylation of histone H3 lysine 9 (DiMetH3K9) and the presence of heterochromatin protein 1 (HP1). These heterochromatic markers remain localized to AFP during developmental repression but spread to the upstream albumin gene during silencing. Developmentally regulated decreases in levels of acetylated H3 (AcH3K9) and H4 (AcH4) and of di- and trimethylated H3K4 (DiMetH3K4 and TriMetH3K4) occur at both the core promoter and distal repressor regions of AFP. Hepatic expression of AFP correlates with FoxA interaction at the repressor region and the binding of RNA polymerase II and TATA-binding protein to the core promoter. p53 acts as a developmental repressor of AFP in the liver by binding to chromatin, excluding FoxA interaction and targeting mSin3A/HDAC1 to the distal repressor region. p53-null mice exhibit developmentally delayed AFP repression, concomitant with acetylation of H3K9, methylation of H3K4, and loss of DiMetH3K9, mSin3A/HDAC1, and HP1 interactions.

Identification of an enhancer and an alternative promoter in the first intron of the alpha-fetoprotein gene

In this study we have characterized a positive regulatory region located in the first intron of the alpha-fetoprotein (AFP) gene. We show that the enhancer activity of the region depends on a 44 bp sequence centered on a CACCC motif. The sequence is the target of the two zinc fingers transcription factors BKLF and YY1. The introduction of a mutation destroying the CACCC box impairs the binding of BKLF but improves that of YY1. Moreover, the mutated sequence behaves as a negative control element, suggesting that BKLF behaves as a positive factor and that YY1 is a negative one. We also demonstrate the existence of a novel, tissue-specific AFP mRNA isoform present in the yolk sac and fetal liver which initiates from an alternative promoter located approximately 100 bp downstream of the enhancer element. The transcriptional start site controlled by this new promoter (called P2), was mapped to 66 bp downstream of a TATA box. A putative AUG translation site in-frame with exon 2 of the classical gene was found 295 bp downstream of the transcription start site. Like the traditional AFP promoter (P1), the P2 promoter is active in the yolk sac and fetal liver. Embryonic stem cells with an AFP knock-in gene containing either the P2 promoter or deleted for it were isolated and comparative analysis of embryonic bodies derived from these cells suggests that the P2 promoter contributes to early expression of the AFP gene.

De novo methylation of the proto-oncogene, c-fos, during development occurs step-wise and directionally in the laboratory mouse

We have analyzed the ontogenic initiation and maintenance of methylation of certain Hpall (m), Hhal (H), Hincll (Hc), and Sall (SI)-specific CpG sites in the coding region of the proto-oncogene, c-fos, through testicular cells, sperm, and fetal, neonatal, and adult somatic tissues. The results show that 1) sperm-derived methylated sites get demethylated in early development. However, unlike other studied genes, they remain so at least up to day 13.5 post coitum (pc); 2) de novo methylation proceeds unidirectionally in a step-wise, site-specific manner between m5-m3 sites; 3) the mature, tissue-specific, adult methylation pattern is established between day 0 and day 20 of neonatal development; 4) the Hc and SI sites (CGTCGAC), occurring at an interval of one nucleotide, are only partially methylated in all the tissues; and 5) m3 and H1 sites, which occur close to an Sp1 motif, escape methylation in most of the tissues. The present study on the embryonic gene, c-fos, thus provides a novel pattern of de novo methylation in development. Also, it suggests that close proximity of CpGs may prevent methylation.

Comparison of effect of tumor promoter treatments on DNA methylation status and gene expression in B6C3F1 and C57BL/6 mouse liver and in B6C3F1 mouse liver tumors

The effects of different liver tumor-promoting treatments (i.e., a choline-devoid, methionine-deficient (CMD) diet, phenobarbital (PB), or both) on Ha-ras and raf methylation status and expression were determined in mouse strains with different susceptibilities to liver tumor formation: the relatively sensitive B6C3F1 and the relatively resistant C57BL/6. Additionally, B6C3F1 mouse liver tumors, spontaneous or PB induced, were assessed for alterations in global DNA methylation status and expression of Ha-ras and raf. The CMD diet led to hypomethylation of Ha-ras and raf after 12 wk of administration in B6C3F1 and C57BL/6 mice. At this early phase of tumor promotion, the frequency of increased expression of both Ha-ras and raf mRNAs was higher in the B6C3F1 but not the C57BL/6 mice. This is a mechanism that may, in part, underlie the heightened sensitivity of the B6C3F1 mouse to liver tumorigenesis. Subpopulations of B6C3F1 mouse liver tumors displayed altered global methylation status, with both hypomethylation and hypermethylation evident. Carcinomas were significantly more hypomethylated than adenomas. The level of raf mRNA was not changed in spontaneous or PB-induced B6C3F1 mouse liver tumors. Increased expression of Ha-ras was evident in some spontaneous B6C3F1 liver tumors and in most of the PB-induced liver tumors. These experiments support the concept that altered DNA methylation plays a key role in tumorigenesis and indicate that the high propensity of the B6C3F1 mice to liver tumorigenesis may be due, in part, to a decreased ability to maintain normal methylation status.

A retinoic acid/cAMP-responsive enhancer containing a cAMP responsive element is required for the activation of the mouse thrombomodulin-encoding gene in differentiating F9 cells

Activation of thrombomodulin-encoding gene (TM) transcription in murine teratocarcinoma F9 cells occurs during differentiation in response to retinoic acid (RA) and dibutyryl cAMP (dbcAMP). To define regulatory elements involved in TM activation, reporter plasmids containing various lengths of the 5' flanking region of the mouse TM promoter fused to the cat gene were examined in transfected F9 cells. Stable transfectants showed no CAT activity in undifferentiated or RA-treated cells, and only those plasmids containing a 431-bp region approximately 700 bp upstream of the transcription start point showed significant CAT activity on subsequent treatment with RA/dbcAMP. Transfer of this region to an enhancerless SV40 promoter conferred position-independent responsiveness to RA/dbcAMP. Within this region is a 46-bp domain that contains potential transcription factor binding sites, including a cAMP responsive element (CRE) and a direct repeat sequence (DR). CAT assays using reporters lacking these sites showed that both contribute to TM expression in differentiating F9 cells. Gel retardation experiments demonstrated protein binding to both the CRE and DR sequences, and suggested that the factor interacting with the DR influences binding of a factor to the CRE site. Binding of both factors disappeared in differentiated cells, suggesting they are required for induction but not continued expression of TM. The CpG methylation pattern of the TM promoter was identical in undifferentiated and differentiated F9 cells. DNase I hypersensitivity studies showed increased DNase I resistance and the loss of a hypersensitive site in differentiated F9 cells. We conclude that an enhancer-like region containing a DR sequence and CRE is necessary for the induction of TM expression in differentiating F9 cells, that methylation does not play a role in the regulation of TM, and that the RA/cAMP response is associated with specific alterations to chromatin structure.

MyoD1 promoter autoregulation is mediated by two proximal E-boxes

We show that in mouse myoblasts the MyoD1 promoter is highly stimulated by MyoD1 expression, suggesting that it is controlled by a positive feedback loop. Using deletion and mutation analyses, we identified the targets for MyoD1 promoter autoregulation as the two proximal E-boxes located close to the MyoD1 core promoter. Gel mobility shift competition assays with MyoD1 antibodies as competitor suggest that the MyoD1 protein is binding directly to these E-boxes. Autoregulation did not occur in fibroblasts cotransfected with the expression vector of MyoD1. It is assumed that autoregulation is controlled by the stoichiometry between the MyoD1 protein and negatively regulatory proteins like Id, which is known to be highly expressed in fibroblasts. When the MyoD1 promoter was methylated, autoregulation only occurred when the density of methylated sites was low. The density of DNA methylation, therefore, can determine the accessibility of the MyoD1 promoter to transcription factors and interfere with the auto- and crossregulatory loop. The MyoD1 promoter in vivo was found to be only partially methylated in all tissues tested except in skeletal muscle where it was demethylated. We propose that high level expression of the MyoD1 gene is a result of release from constraints such as negative regulatory factors and/or DNA methylation interfering with MyoD1 autoregulation.

The expression of liver-specific genes within rat embryonic hepatocytes is a discontinuous process

The onset of transcription and mRNA accumulation of two liver-specific genes, carbamoylphosphate synthase (CPS) and phosphoenolpyruvate carboxykinase (PEPCK) in individual embryonic rat hepatocytes was investigated with in situ hybridization. In vitro CPS and PEPCK mRNAs can be induced prematurely in monolayer cultures of embryonic rat hepatocytes by glucocorticosteroids and cyclic AMP, i.e. the hormones that also regulate the expression of these genes in vivo. Upon exposure to hormones the cultures showed an interhepatocyte heterogeneity in CPS and PEPCK mRNA content. The pattern of accumulation of nuclear CPS mRNA-precursors indicates that this heterogeneity is generated by intercellular differences in the timing of the onset of transcription. However, under induced steady-state conditions the heterogeneity in the hepatocyte population persisted. The degree of heterogeneity is inversely related to the half life of the gene product (i.e. higher for PEPCK than for CPS and higher for mRNAs than for the respective proteins) and to the concentrations of inducing hormones. Accordingly, the interhepatocyte heterogeneity was most pronounced for the nuclear CPS mRNA-precursor. In contrast, no intercellular differences in the rate of degradation of the mRNAs were seen. These observations reveal that although all hepatocytes can and do express the genes, transcription of a gene in a particular cell is a discontinuous process.

Alterations in the methylation status and expression of the raf oncogene in phenobarbital-induced and spontaneous B6C3F1 mouse liver tumors

The liver tumor-prone B6C3F1 mouse (C57Bl/6 female x C3H/He male), in conjunction with the more susceptible C3H/He paternal strain and the resistant C57BL/6 maternal strain, is an excellent model for studying the mechanisms involved in carcinogenesis. The study reported here indicated that the B6C3F1 mouse inherited a maternal raf allele containing a methylated site not present in the paternal allele. Seven days after partial hepatectomy or after administration of a promoting dose of phenobarbital (PB) for 14 d; raf in B6C3F1 mouse liver was hypomethylated. The additional methylated site in the allele inherited from C57BL/6 was not maintained. The methylation status of raf in the liver of the C57BL/6 mouse was not affected by PB treatment. This indicates that the B6C3F1 mouse is less capable of maintaining methylation of raf than the C57BL/6 strain is. In both PB-induced and spontaneous B6C3F1 liver tumors, raf was hypomethylated in a nonrandom fashion. The level of raf mRNA increased in seven of 10 PB-induced tumors but in only one of five spontaneous tumors, whereas the level of Ha-ras mRNA increased in nine of 10 PB-induced tumors and in four of five spontaneous tumors. The results of our investigation (a) support the hypothesis that hypomethylation of DNA is a nongenotoxic mechanism involved in tumorigenesis, (b) support the notion that PB promotes liver tumors that develop along a pathway different from that leading to spontaneous tumors, and (c) indicate that differences in DNA methylation between C57BL/6 and B6C3F1 mice could, in part, account for the unusually high tendency of the latter strain to develop liver tumors.

Effects of DNA methylation on DNA-binding proteins and gene expression

DNA methyltransferase is needed for normal development, perhaps because DNA methylation plays a part in the control of gene activity. It is clear that the methylation of promoters often leads to repression of transcription. Studies of the mechanism suggest that repression may either result from the direct effects of methylation on transcription factors, or may be indirectly caused by repressor proteins that bind to methylated DNA. Current evidence suggests that both mechanisms can be involved.