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Endocrinology Vol. 142, No. 8 3389-3396
Copyright © 2001 by The Endocrine Society


ARTICLES

DNA Methylation Regulates Placental Lactogen I Gene Expression

Jae-Hyeon Cho, Hiromichi Kimura, Tatsuya Minami1, Jun Ohgane, Naka Hattori, Satoshi Tanaka and Kunio Shiota

Laboratory of Cellular Biochemistry, Animal Resource Sciences/Veterinary Medical Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan

Address all correspondence and requests for reprints to: Dr. Kunio Shiota, Laboratory of Cellular Biochemistry, Animal Resource Sciences/Veterinary Medical Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. E-mail: ashiota{at}mail.ecc.u-tokyo.ac.jp


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Expression of rat placental lactogen I is specific to the placenta and never expressed in other tissues. To obtain insight into the mechanism of tissue-specific gene expression, we investigated the methylation status in 3.4 kb of the 5'-flanking region of the rat placental lactogen I gene. We found that the distal promoter region of the rat placental lactogen I gene had more potent promoter activity than that of the proximal area alone, which contains several possible cis-elements. Although there are only 17 CpGs in the promoter region, in vitro methylation of the reporter constructs caused severe suppression of reporter activity, and CpG sites in the placenta were more hypomethylated than other tissues. Coexpression of methyl-CpG-binding protein with reporter constructs elicited further suppression of the reporter activity, whereas treatment with trichostatin A, an inhibitor of histone deacetylase, reversed the suppression caused by methylation. Furthermore, treatment of rat placental lactogen I nonexpressing BRL cells with 5-aza-2'-deoxycytidine, an inhibitor of DNA methylation, or trichostatin A resulted in the de novo expression of rat placental lactogen I. These results provide evidence that change in DNA methylation is the fundamental mechanism regulating the tissue-specific expression of the rat placental lactogen I gene.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
THE PLACENTA IS a multifunctional organ essential for the survival of the mammalian embryo in utero. One of the placental functions in the rodent is achieved by expressing specific genes encoding placental hormones called placental lactogen (PL) or PRL-like protein, which are structurally related to PRL and GH. To date, more than 10 members of the placental PRL/GH family have been discovered (1, 2, 3, 4, 5). Of these, PL-I and PL-II are major placental hormones acting as luteotropic factors, and they both bind to the PRL receptor (6). The expression of PLs and PRL-like proteins is strictly controlled and is never detected in tissues except for the placenta in normal animals.

Several elements responsible for the gene expression of placental PRL family members have been identified. By analyzing the promoter region of mouse PL-I (mPL-I) and rat PL-II (rPL-II), sites for transcription factors activating protein-1 (AP1), GATA2, GATA3, and ETS have been found to be responsible for placental gene expression (7, 8, 9, 10). HAND1, previously termed Hxt, was also found to be involved in PL-I expression in trophoblast cells (11). Duckworth and colleagues (12) reported that the 5'-flanking region responsible for rPL-I expression was homologous to that of rPL-II, but there is no report to date identifying the regulatory elements of rPL-I.

The placenta is one of the tissues that strongly expresses DNA methyltransferase-1 (13). In vertebrates, methylation of DNA occurs at the 5'-position of cytosine in the CpG dinucleotides, forming 5-methylcytosine, and approximately 60–90% of the CpG in the genome of adult mammals is reported to be methylated (14, 15). An inverse correlation between DNA methylation in the promoter region and gene expression has been documented (15), and some endogenous genes are activated from their repressed status by treatment with demethylating agents such as 5-azacytidine (5-azaC) and 5-aza-2'-deoxycytidine (5-aza-dC) (16, 17). For example, treatment with 5-azaC induced expression of collagen IV in F9 teratocarcinoma cells (18) and PRL in GH3CDL cells (19). Involvement of DNA methylation in the regulation of chromatin structure has recently been postulated in view of findings indicating that the methyl-CpG-binding protein (MeCP2), which is one of the methyl-binding domain (MBD) proteins, forms a complex with proteins such as histone deacetylase 1 (HDAC1) that affects the chromatin architecture and a repressor protein (Sin3) (20, 21, 22, 23). In addition, another MBD protein (MBD1) is likely to associate with the other HDAC than HDAC1 to form a complex (24). Therefore, DNA methylation is thought to be one of the fundamental mechanisms in gene silencing (for reviews, see Ref. 25).

We have analyzed the methylation status of CpG islands in tissues including the placenta by restriction landmark genomic scanning, which enables us to analyze the genome-wide methylation pattern (26). We found that there are placenta-specific methylated or unmethylated loci in genomic DNA, and that the differentiation process is accompanied by changes in the methylation of CpG islands (26), implying that the formation of a DNA methylation pattern contributes to placental development, and that the establishment of a unique CpG methylation pattern in each cell is an essential event in development. Sequences in the promoter region upstream of the placental PRL/GH family members, however, contain relatively few CpG sites with a TATA box (27). In the present study we determined the methylation pattern of rPL-I promoter and provided evidence that DNA methylation is important for the tissue-specific expression of the rPL-I gene.


    Materials and Methods
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Reagents, cell culture, 5-aza-dC, and trichostatin A (TSA) treatment
All reagents, unless described otherwise, were purchased from Wako Pure Chemicals (Osaka, Japan).

Rcho-1 trophoblast cells, which were derived from a rat choriocarcinoma (28) and are capable of differentiating into trophoblast giant cells (29), were cultured in NCTC-135 medium (Sigma, St. Louis, MO) supplemented with 20% FBS, 50 µM 2-mercaptoethanol, and 1 mM sodium pyruvate (29, 30). The cells were induced to differentiate by growing to near confluence in FBS-supplemented medium and then replacing the FBS with 10% horse serum (30). BRL cells, which were derived from Buffalo rat liver (31), were maintained in DMEM supplemented with 10% FBS.

For treatment with 5-aza-dC (Sigma), cells were plated (3 x 104 cells/100-mm dish) and incubated for 24 h, and then cultured for 3 d in medium containing 10 µM 5-aza-dC. TSA, a gift from Dr. M. Yoshida, is a potent and specific inhibitor of histone deacetylase both in vivo and in vitro (32, 33). For treatment with TSA, cells were plated at 5 x 105 cells/100-mm dish, incubated for 24 h, and exposed to 400 nM TSA for 48 h.

Analysis of rPL-I expression by RT-PCR
Total RNA was prepared from cells and tissues with TRIzol reagent (Life Technologies, Inc., Gaithersburg, MD). One microgram of total RNA was subjected to first strand cDNA synthesis with oligo(deoxythymidine) primers and Superscript II reverse transcriptase (Life Technologies, Inc.). PCR was performed with forward (5'-ATGCAGCTGACTTTGACTCTT-3') and reverse (5'-TCAAAAGGTGGACACTCCA-3') primers to detect the full-length open reading frame of rPL-I cDNA under the following conditions: 94 C for 2 min, 30 cycles of 94 C (40 sec), 62 C (45 sec), and 72 C (1 min), and then 72 C for 7 min. Control detection of ß-actin was performed with forward (5'-GACAACGGCTCCGGCATGTGCAAAG-3') and reverse (5'-TTCACGGTTGGCCTTAGGGTTCAG-3') primers under the same conditions.

Identification of the 5'-flanking region of rPL-I gene
Selective amplification of the genome segment was performed by cassette ligation-mediated PCR (34), in which the 5'-flanking region of the gene can be obtained. Genomic DNA containing approximately 3.5 kb upstream of the rPL-I-coding region was cloned by this PCR-based method with the primer sets, which were designed in the first exon and intron.

Briefly, genomic DNA was digested with restriction enzymes, EcoRI, PstI, and SalI, respectively. Each digested fragment was ligated with oligonucleotide-adapters that have specific cohesive ends corresponding to the restriction enzymes described above. The constructed cassettes were amplified by a series of PCR reactions with two sets of primers. One was primer C1 (5'-GTACATATTGTCGTTAGAACGCG-3'), which was presented in all of the adapters, and primer rPL-I IntA(R) (5'-TAAATGTTTACTAAGAGGTACATG -3') corresponding to the 5'-terminal sequence in the first intron of rPL-I. The other primer set was cassette primer C2 (5'-ACGACTCACTATAGGGAGAAG-3') and specific primer rPL-I Ex 1(R) corresponding to the sequence in the rPL-I first exon (5'-AGAGCCCGAAAGAGTCAAAGTCAGCTG-3'). The resulting cassettes were cloned into pUC118 vector (Takara, Kyoto, Japan) and analyzed by sequencing.

Southern blotting
Genomic DNA from the dissected tissues was extracted as previously described (26). Genomic DNA was digested with HindIII and a methyl-sensitive enzyme, HhaI, that digests only unmethylated GCGC sites. The resulting fragments were size-fractionated on a 0.8% agarose gel, transferred to nylon filters, and hybridized with [{alpha}-32P]deoxy-CTP (Amersham Pharmacia Biotech, NJ)-labeled probes corresponding to the rPL-I 5'-flanking region. The probes used were probe A (-3407 to -2520) or probe B (-1006 to +30; Fig. 2AGo). The signals were visualized by a Fujix BAS-2000 analyzer (Fuji Photo Film Co., Ltd., Tokyo, Japan).



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Figure 2. Methylation patterns at HhaI sites (GCGC sequences) in the 5'-flanking region of the rPL-I gene. A, Schematic diagram of the upstream region of the rPL-I gene. Vertical lines on the gene show CpG dinucleotides whose numbers indicate the positions from the translation start site (+1). ORF, Open reading frame (ORF). Double headed arrows indicate fragments possibly resulting from treatment with HindIII and HhaI, which appeared in Southern hybridization. {square}, Probes. B and C, Southern blot analyses of rPL-I gene in various tissues. Genomic DNA extracted from tissues was digested by HindIII and methyl-sensitive HhaI, and then hybridized with the probes indicated. Br, Brain; Li, liver; Mu, skeletal muscle; Ov, ovary; Pit, anterior pituitary; Sp, spleen and Pl, placenta on d 12 (d12) and d 20 (d20) of pregnancy.

 
Sodium bisulfite genomic sequencing
Bisulfite sequencing was carried out as previously described (35, 36) with a slight modification. Five micrograms of genomic DNA digested with PstI were denatured by adding NaOH to a final concentration of 0.3 M and incubating for 15 min at 37 C. After the incubation, sodium metabisulfite and hydroquinone (Nacalai, Osaka, Japan) were added to final concentrations of 2.0 M and 0.5 mM, respectively, and the mixture was incubated at 55 C for 7 h. The bisulfite reaction was terminated by adding NaOH again to a final concentration of 0.3 M and incubated at 37 C for 15 min. The solution was neutralized by adding NH4OAc, and the DNA was ethanol precipitated, dried, and resuspended in water. After the bisulfite reaction, the genome was amplified by PCR with various sets of primers to cover the whole sequence of the 5'-flanking region, and each amplified fragment was sequenced to determine the methylated cytosine sites.

Reporter gene constructs
The 5'-flanking fragment of the rPL-I gene was used for generating a series of reporter constructs to evaluate the promoter activity. The fragment from -3365 to -5 was cloned into pGL2-Basic vector (Promega Corp., Madison, WI; the translation start site was designated +1) and subjected to PCR with specific forward primers and a common reverse primer (5'-GGGCTAGCAGATCCAGGACAGTGTAG-3') to generate genome fragments of various lengths. Amplified fragments were subcloned into pGL-Luciferase vector (Promega Corp.), which expresses firefly luciferase. The resultant vectors were designated according to the positions of the fragments as -3365Luc, -2445Luc, -1402Luc, -1069Luc, and -498Luc, which were generated by using each specific forward primer of the following sequencesm respectively: 5'-AGGAGCTCACAACATAAGATGCCTGA-3' (-3365 to -3340), 5'-CCGAGCTCATCTGCATAGTGATATTTTGA-3' (-2445 to -2417), 5'-TAGAGCTCAATATTCATAAGGGAAATTGG-3' (-1402 to -1374), 5'-CTGAGCTCAGCCCTGAGTTTGATTATTTC-3' (-1069 to -1061), and 5'-ACGAGCTCATTTTACAGTGTTTGTGGTTA-3' (-498 to -470; Fig. 3AGo).



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Figure 3. Promoter activity of the 5'-flanking region of the rPL-I gene. A, Schematic diagram of reporter constructs. Deletion mutants of rPL-I promoter were ligated to the expression vector of firefly luciferase. According to the length of the reporter constructs, they were termed -498Luc, -1069Luc, -1402Luc, -2445Luc, and -3365Luc. The control luciferase vector without a promoter is designated 0Luc. In the proximal region (-300 to -50), there are several cis-elements indicated that may affect rPL-I transcription. B, Promoter activity of the -498 region in Rcho-1 cells. The -498Luc construct exhibited promoter activity in Rcho-1 trophoblast cells. The activity was maximal on d 8 of differentiation. C, Promoter activity of the rPL-I upstream region was revealed by deletion promoter constructs in the differentiated Rcho-1 cells on d 8. Note that -1402Luc and -2445Luc exhibited more extensive activity than -498Luc, whereas the activity of -3365Luc was comparable to the -498Luc level. All experiments were performed twice independently, in triplicate each time.

 
In vitro methylation of plasmid DNA
Reporter constructs of the rPL-I promoter were methylated in vitro with 3 U SssI methylase (New England Biolabs, Inc., Beverly, MA) for each microgram of DNA in the presence of 160 µM S-adenosylmethionine at 37 C for 3 h. We confirmed by HhaI restriction enzyme digestion followed by electrophoresis and bisulfite sequencing that methylation at all CpG sites in the promoter region were completed (data not shown).

Luciferase assays
Luciferase assays were carried out according to the method described previously (37) with a slight modification. Rcho-I cells (4 x 104) were transfected with 430 nmol reporter constructs with Lipofectamine (Life Technologies, Inc.) on d 0 (undifferentiated state), 4, and 8 of differentiation, and cells were harvested after 48 h. To normalize the luciferase activity driven by the rPL-I promoters, 21.5 nmol (34 ng) control plasmid expressing Renilla luciferase, which requires a different substrate from firefly luciferase, were cointroduced to cells, and the activities of both luciferases were determined by means of a Dual-Luciferase Reporter System (Promega Corp.).

To examine the function of the MeCP2 in promoter activity in the rPL-I 5'-flanking region, full-length rat MeCP2 cDNA was cloned by PCR according to a previous report (38) and subcloned into pFLAG-CMV-2 expression vector (Sigma). We confirmed the protein expression with the MeCP2 expression construct by Western blotting (data not shown). A mixture of the promoter constructs containing luciferase reporters and 2 µg MeCP2 expression vectors was cotransfected into Rcho-I cells. To analyze the action of TSA on the reporters, 50 nM TSA was added to the medium at 3 h after transfection, and the cells were incubated for 45 h. All luciferase assay experiments were performed twice independently in triplicate. All results are shown as the mean ± SE.


    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Tissue-specific expression of rPL-I mRNA
It is well documented that the expression of rPL-I is specific to the placenta (1, 39). To confirm the strict repression of rPL-I in tissues other than the placenta, the presence of rPL-I mRNA was examined by RT-PCR, which enables us to detect trace amounts of transcript (40). As shown in Fig. 1Go, a single PCR fragment corresponding to the rPL-I open reading frame was detected only in the placenta. The PCR product was confirmed to be derived from rPL-I mRNA by nucleotide sequencing (data not shown) and Southern blotting of the PCR products (Fig. 1Go, lower panel). RT-PCR products corresponding to rPL-I were not detected in any of the other tissues examined (brain, heart, kidney, liver, skeletal muscle, ovary, pituitary, and spleen; Fig. 1Go). These results indicate that the expression of rPL-I mRNA was restricted to the placenta and severely suppressed in all other tissues.



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Figure 1. Placenta-specific expression of rPL-I mRNA. RT-PCR was performed to survey the expression of rPL-I mRNA in various tissues. PCR primers were designed to amplify a full-length ORF (690 bp) of rPL-I cDNA. The ß-actin gene was used as an internal control in the same RT-PCR reaction. All PCR products were analyzed by 1.5% agarose gel electrophoresis and stained with ethidium bromide (upper panel). Southern blot analysis of the PCR products was performed with rPL-I probe (lower panel). Br, Brain; H, heart; K, kidney; Li, liver; Mu, skeletal muscle; Ov, ovary; Pit, anterior pituitary; Sp, spleen; Pl, placenta on d 12 of pregnancy.

 
Methylation status of the 5'-flanking region of rPL-I gene
Methylation in the promoter region is one of the possible ways to control the expression of rPL-I. We isolated and sequenced 3.4 kb of the 5'-flanking region of the rPL-I gene including the TATA box and the putative binding sites for the transcription factors (AP1, GATA, and HAND1) within 500 bp upstream of the translation start site (Figs. 2AGo and 3AGo). We found 17 CpG dinucleotides that are potential targets of cytosine methylation in the 3.4-kb rPL-I upstream region (Fig. 2AGo). There is no region of the clustered CpG dinucleotides characteristic of a CpG island.

We performed Southern blot analysis to study the methylation status of the rPL-I gene in the various tissues (placenta, brain, liver, muscle, ovary, pituitary, and spleen) by using methylation-sensitive (HhaI) and insensitive (HindIII) enzymes. There are two HhaI sites identified at -1279 and -2543 in the rPL-I gene (Fig. 2AGo). We used two probes (probe A from -3407 to -2450 and probe B from -1006 to +30) to study the methylation status of these HhaI sites (Fig. 2AGo). With probe A, we obtained two resulting bands by HindIII digestion at 3.9 and 0.2 kb in all tissues examined (Fig. 2BGo, left panel). When the genomic DNA was digested by HhaI in addition to HindIII, a novel band appeared at 2.0 kb in all tissues (Fig. 2BGo, right panel). When the resulting bands were normalized by the 0.2-kb band in each tissue from both methylated and unmethylated DNA, the relative densities of bands at 2.0 kb in the brain, liver, skeletal muscle, ovary, pituitary, spleen, and d 12 and 20 of placenta were 0.33, 0.20, 0.38, 0.32, 0.15, 0.43, 1.46, and 1.55, respectively. In the placenta, the 2.0-kb band was much more intense than those in any other tissues, including anterior pituitary and liver, suggesting that the HhaI site at -1279 was hypomethylated in the placenta. Similarly with probe B, a band generated by HhaI digestion at 1.9 kb was the most intense in the placenta (Fig. 2CGo, right panel), whereas digestion with HindIII alone resulted in a single band at 3.9 kb in all tissues (Fig. 2CGo, left panel). We did not obtain the resulting fragments of a HhaI digestion at -2543 in all tissues. These data indicated that the 5'-flanking region in the rPL-I gene is hypomethylated at the HhaI site at -1279 in the placenta, whereas the HhaI site at -2543 is hypermethylated in all tissues.

Promoter activity of the 5'-flanking region of rPL-I gene
It was previously reported that some transcription factors, such as GATA2, GATA3, AP1, and HAND1, seemed to be implicated in PL-I expression in the mouse (7, 8, 9, 10, 11). The proximal region upstream of the ATG site of the rPL-I gene is homologous to that of mPL-I (data not shown), in which cis-acting sites for these transcription factors exist (Fig. 3AGo). Nevertheless, the result of Southern blot analysis showed that the methylation status at the more distal region around the -1279 HhaI site was different in the placenta. To assess the possibility that the differentially methylated region is involved in the regulation of rPL-I expression, we constructed a series of reporter plasmids, each containing various lengths of the 5'-flanking region of rPL-I (Fig. 3AGo). We confirmed the promoter activity of -498Luc construct, which contained cis-elements for the transcription factors described above, in the trophoblastic cell line, Rcho-1 (Fig. 3BGo). In Rcho-1 cells on d 8 of differentiation, the -498Luc construct demonstrated an activity approximately 8 times as potent as in the no promoter control, 0Luc (Fig. 3CGo). We further analyzed the activity of the distal region of the promoter and found that -1402Luc and -2445Luc reporters had higher activity than -498Luc, whereas -1069Luc had comparable activity to -498Luc. The activity of -2445Luc was approximately 20 times as potent as that of the control (Fig. 3CGo). These data suggest that the 5'-flanking region between -1069 and -2445 may contain cis-acting elements that positively regulate rPL-I transcription in addition to those reported previously. The hypomethylated HhaI site in the placenta is located in this region, implying that methylation in the rPL-I 5'-flanking region is involved in the regulation of rPL-I transcription. The promoter activity of -3365Luc declined from the level of -2445Luc to that of -498Luc, suggesting that the region from -3365 to -2445 may contain negative regulatory elements for rPL-I transcription.

Differences in the methylation of CpG sites among the tissues revealed by bisulfite sequencing
We further analyzed all CpG sites between -2545 and -189 (12 CpG sites) by the bisulfite sequencing method in the placenta, pituitary, and liver and compared the total methylation status of these tissues (Fig. 4Go).



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Figure 4. Methylation status in the 5'-flanking region of rPL-I revealed by bisulfite sequencing. Genomic DNA extracted from the placenta on d 12 and 20 of pregnancy, the anterior pituitary and the liver were subjected to bisulfite reaction and then nucleotide sequencing to reveal the total methylation status within 2.6 kb of the rPL-I promoter region. At the top of the figure, a diagram of the rPL-I promoter region with the positions of CpG dinucleotides and HhaI sites are indicated. The unmethylated ({square}) and the methylated status ({blacksquare}) is represented at each CpG site. All data were calculated from the results for 10–12 independent genomic DNA clones.

 
In the genomic DNA of all tissues examined including placenta, the HhaI site at -2543 was hypermethylated, which is consistent with the results of Southern blot analyses. In contrast, the CpG site at -1279 (CpG-1279), which is in the other HhaI recognition sequence, was hypermethylated in tissues other than placenta. It was 90% methylated in the anterior pituitary and 60% in the liver, but was hypomethylated (40%) in the placenta, which also confirmed the Southern blotting results.

Among the 12 CpG sites in the rPL-I 5'-flanking region, the ratios of methylated CpGs were less than 50% at 7 sites (CpG-2309, CpG-1807, CpG-1790, CpG-1309, CpG-1279, CpG-1181, and CpG-189) in the placenta (d 12 and 20), whereas the methylation score at these sites was more than 60% in anterior pituitary and liver, indicating that these 7 CpG dinucleotides might be involved in the repression of rPL-I transcription. Taken together with the results of the promoter activity assay, it is likely that hypomethylation at 7 CpG sites is important for rPL-I transcription.

The methylation pattern in the placenta was almost the same on d 12 and 20 of pregnancy, which is in agreement with the results of Southern blotting. This suggests that the methylation pattern of rPL-I 5'-flanking region is maintained in the placenta throughout gestation.

Repression of PL-I promoter activity by DNA methylation
To investigate the possibility that rPL-I transcription is repressed by methylation of the 5'-flanking region, we applied in vitro methylation to the reporter constructs for the luciferase assay. Methylation of the -498Luc reporter did not show a significant decrease in rPL-I promoter activity compared with the unmethylated reporter (Fig. 5AGo), suggesting that methylation does not have an inhibitory effect on luciferase activity itself (24). In contrast, methylation of -2445Luc and -3365Luc dramatically decreased their promoter activities in Rcho-1 cells (Fig. 5AGo), indicating that methylation of the rPL-I regulatory region can contribute to the repression of rPL-I transcription.



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Figure 5. Expression of rPL-I regulated by methylation and chromatin remodeling events. A, Promoter activity of rPL-I was suppressed by in vitro methylation with SssI. The fragments containing rPL-I promoters were methylated in vitro with SssI methylase and transfected into Rcho-I cells. Methylation had a negligible effect on the activity of the -498Luc reporter construct. However, methylation of -2245Luc and -3365Luc significantly reduced the promoter activity. B, The inhibitory effect of methylation on the rPL-I promoter activity was enhanced by MeCP2. Methylated reporter constructs were transfected into Rcho-I cells with or without the MeCP2 expression vector. C, Involvement of histone deacetylase (HDAC) in rPL-I promoter activity. The reporter-transfected Rcho-I cells were treated with the HDAC inhibitor TSA as described in Materials and Methods. TSA could cancel the suppressive effect of both methylation and MeCP2 on rPL-I promoter activity. All data in A–C are the mean ± SE for two independent experiments performed in triplicate. D, Inhibition of either DNA methylation or HDAC activity elicits the expression of rPL-I mRNA in a nonexpressing cell line. The expression of rPL-I mRNA was determined by RT-PCR in BRL cells exposed to 5-aza-dC (10 µM) for 72 h or to TSA (400 nM) for 48 h or mock-exposed to the same volume of methanol or PBS. The expression was observed only in 5-aza-dC- or TSA-treated BRL cells.

 
We further examined the effect of methylation by transfecting the MeCP2 expression vector together with the luciferase reporters, because MeCP2 is thought to be a key molecule to elicit the gene suppression by methylation (20, 41, 42). The expression of MeCP2 with methylated rPL-I promoter-luciferase reporters enhanced the inhibitory effect of methylation in all reporter constructs including -498Luc (Fig. 5BGo). We also investigated the effect of the histone deacetylase inhibitor, TSA. Recent studies have indicated that in gene silencing a relationship may exist between methylation and chromatin remodeling through histone deacetylation (43, 44). In the present experiment the treatment of Rcho-1 cells with TSA restored the reporter activity to 50% of unmethylated -2445Luc activity (Fig. 5CGo), suggesting that the inhibitory effect of methylation occurs through such chromatin remodeling mechanisms. It is to be noted that MeCP2 itself could interfere with the promoter activity without methylation of the reporter (Fig. 5CGo). This effect of MeCP2 could also be relieved by TSA treatment. Because it was reported that MeCP2 has an ability of DNA binding distinct from that of the MBD and binds weakly to nonmethylated DNA (45), it is possible that MeCP2, which was expressed with a relatively excess amount due to the transfection, might cause a nonspecific effect without methylation at the transfected reporters.

Activation of rPL-I transcription by the treatment with 5-aza-dC or TSA in a nonexpressing cell line
We treated BRL cells, which do not express rPL-I, with the reagent for DNA demethylation (5-aza-dC) or inhibitor for histone deacetylation (TSA) to investigate whether the repression of rPL-I could be relieved in non-rPL-I-expressing cells. In BRL cells, the expression of rPL-I mRNA could not be detected by RT-PCR under nontreated conditions (Fig. 5DGo), confirming that rPL-I is inactive in this cell line. It is striking that 5-aza-dC treatment of BRL cells elicited de novo expression of rPL-I mRNA (Fig. 5DGo). The conversion of methylcytosine to unmodified cytosine seemed to cause the release of rPL-I silencing in BRL cells. Activation of rPL-I expression was also observed in BRL cells treated with TSA. These results strongly support our hypothesis that expression of the rPL-I gene is regulated by methylation and chromatin remodeling. The level of rPL-I mRNA evoked by treatment with 5-aza-dC or TSA was not high compared with that in Rcho-1 cells, which suggests that some transcription factors required for maximal rPL-I expression, such as HAND1, are lacking or insufficient in BRL cells.


    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Expression of the rPL-I gene is strictly regulated so that this gene is silent in most tissues. The aim of this study was to determine whether the DNA methylation system is involved in the mechanisms underlying gene silencing of rPL-I. We previously demonstrated that the DNA methylation status of CpG islands differs among tissues and that the change in the methylation status was associated with differentiation of the trophoblast cell lineage (26). Here we report that 1) treatment of BRL cells with 5-aza-dC or TSA reactivates rPL-I gene expression; 2) the 5'-flanking region of rPL-I is hypomethylated in the placenta, and the methylation status of the region inversely correlates with the expression among tissues; 3) methylation of the rPL-I promoter-reporter construct represses the reporter activity; 4) overexpression of MeCP2 causes further suppression of methylated reporters; and 5) the treatment with TSA overcomes the repression of the reporter activity. These data obtained by independent and complementary analyses clearly showed that the expression of rPL-I is regulated by DNA methylation.

The sequence within the Orange to -300 bp upstream region of the rPL-I gene contains cis-elements for AP1, GATA2, GATA3, and HAND1, which had been found to be important in the regulation of mPL-I and rPL-II genes (7, 8, 9, 10, 11). These elements were also found in the 5'-flanking region of rPL-I, and the -498 Luc reporter gene containing these elements had considerable promoter activity in the present study, supporting the possibility that these cis-elements are involved in rPL-I expression in the placenta. As a further increase in reporter activity was observed in the -2445Luc construct, there should be additional important regions responsible for rPL-I transcription within the region between -2445 and -1402 of the 5'-flanking region. In addition to the enhancer elements, there may be a negative regulatory element(s) between -2445 and -3365 of the rPL-I gene. Taken together, multiple elements for rPL-I transcription are located within 3.4 kb in the 5'-flanking region and seem to be coordinated in transcriptional regulation of the rPL-I gene.

In the region spanning the rPL-I promoter, the density of CpG dinucleotides is lower than 1 CpG/220 nucleotides, which was found to be the minimally required density for repression by MeCP2 (38, 45, 46). As the methylation of -498Luc did not affect the promoter activity, CpG-189, which is close to the AP1 element, is unlikely to be involved in the DNA methylation-mediated repression of rPL-I gene expression. The methylation of the -2445Luc construct, however, severely repressed the reporter gene activity. Several mechanisms for methylation-mediated repression of gene expression have been postulated. Methylation of CpG interferes with the binding of transcription factors to their recognition sequences by modifying cytosine nucleotides, or the binding of specific proteins, such as MeCP2, to the methylated DNA physically blocks basal transcription machinery to access the region (47). Moreover, recent studies have indicated that MeCP2 interacts with methylated DNA to recruit HDAC, which functions to close the chromatin structure and renders transcriptional machineries unable to associate with genes (25). In the present study coexpression of MeCP2 repressed the reporter activity, whereas TSA could recover reporter activity to up to 50% of the unmethylated control. In addition, the treatment of BRL cells with TSA resulted in rPL-I gene expression, implying that the mechanism for rPL-I repression is likely to involve deacetylation of histones. Considering our findings and previous reports, DNA methylation-mediated silencing of rPL-I requires MeCP2 and may be linked to the alteration of the chromatin structure through the process of histone deacetylation.

To date, most data on methylation-mediated gene repression concern TATA-less and GC-rich promoters that are associated with the CpG islands (48, 49). It is striking that the expression of rPL-I seems to be controlled by DNA methylation even though there are only 17 CpG sites in the 5'-flanking region of the rPL-I gene. Similarly, there are only 14 CpG sites within 3.6 kb of the 5'-flanking region of the rPL-II gene, in which enhancer elements for expression exist within the region from -2828 to -1729 and negative regulatory elements between -3031 and -2838 (10), indicating that rPL-I and rPL-II share a common feature of gene regulation characterized by the location of enhancer and repressor elements. Placental PRL/GH genes are thought to have evolved from common ancestor genes (50), and PL/PRL genes are localized as a gene cluster in the genome. It was reported that a specific methylation pattern in the promoter regions of rGH and rPRL was implicated in the gene expression and that DNA methylation was inversely correlated with gene expression (19, 27), so that PL/PRL genes as well as the GH gene, which are characterized by possessing TATA boxes and poor CpG sites in their promoters, are likely to be good models for analysis of the methylation-mediated gene silencing mechanism.

In the PRL gene, methylation of CpG dinucleotides in the proximal region of the promoter decreases the activities of transcription factors such as cAMP response element-binding protein/activating transcription factor and AP2 (27). In the mPL-I and rPL-I gene, cis-elements for AP1, GATA2, and GATA3, which have been previously determined in the proximal promoter regions, do not contain any CpG sequences. Taken together with comparison of the methylation status within -2545 by bisulfite sequencing, only six of these CpGs (CpG-2309, CpG-1807, CpG-1790, CpG-1309, CpG-1279, and CpG-1181) are thought to be responsible for the repression of gene expression. Although the tissue-specific expression of rPL-I is likely to involve the change in chromatin structure as mentioned above, we cannot eliminate the possibility that the modification of CpG sites in a limited domain by methylation inhibits specialized functions of the DNA sequence by directly preventing the binding of particular transcription factors. In this context, the sequences close to the six CpG sites mentioned above will be useful in determining the gene control region in the near future.

The extraembryonic lineage develops into multiple placental cell types. Because the expression of the placental PRL/GH family is quite specific to the trophoblast cell lineage, analyses of the expression of these genes have been performed to characterize the genetic elements involved in the coordinated program of trophoblast gene expression and cellular differentiation. The rPL-I gene is predominantly expressed in midpregnancy around d 10–12 of gestation and declines toward the end of pregnancy, whereas rPL-II is mainly expressed in late pregnancy (6). Bisulfite sequencing analysis demonstrated that the methylation status in the 5'-flanking region of the rPL-I gene was similar on d 12 and 20 of pregnancy. Considering these results, it is likely that the methylation pattern of the rPL-I gene is established at an early stage of development, and once it is established, it does not change during the course of pregnancy. Considering that expression of the rPL-I gene is restricted to the trophoblast cells and that there is no leakage of expression in other tissues, DNA methylation may ensure the silencing of the rPL-I gene in nonexpressing cells, whereas a defined combination of transcription factors in trophoblast cells may dictate the stage specificity of rPL-I expression.


    Acknowledgments
 
We thank Dr. M. Yoshida for TSA, and Mr. T. Kunath for the helpful discussion and proofreading.


    Footnotes
 
This work was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences.

1 Present address: Meiji Seika Kaisha Ltd., 760 Morooka-cho, Kohoku-ku, Yokohama 222-8567, Japan. Back

Abbreviations: AP1, Activating protein-1; 5-azaC, 5-aza-2'-deoxycytidine; 5-aza-dC, 5-aza-2'-deoxycytidine; MBD, methyl-binding domain; MeCP2, methyl-CpG-binding protein; mPL-II, mouse placental lactogen I; rPL-II, rat placental lactogen I; PL, placental lactogen; TSA, trichostatin A.

Received January 30, 2001.

Accepted for publication April 27, 2001.


    References
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

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