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Research Institute for the Biology of Farm Animals, 18196 Dummerstorf, Germany
Address all correspondence and requests for reprints to: Dr. R. Fürbass, Forschungsinstitut für die Biologie landwirtschaftlicher Nutztiere, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany. E-mail: fuerbas{at}uranus.fbn.uni-rostock.de
| Abstract |
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| Introduction |
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Until recently, in other mammalian species only transcripts starting with the 5'-UTR of exon 2 have been described. It was first discovered in cattle that transcripts with different 5'-UTR also exist in nonhuman species. Bovine placental complementary DNA (cDNA) clones revealed a previously unknown first exon that, interestingly, does not show any homology to human placental transcripts (6, 7). In the meantime, it has been demonstrated in rodents that a brain-specific first exon that is homologous to that of the human gene is present (8, 9, 10).
As Cyp19 plays an important role in the development, function, and regulation of the female reproduction cycle, we consider it to be a potential candidate gene affecting fertility performance in cattle. In this regard, we are interested in elucidating the mechanisms of its regulation and its tissue-specific expression as an approach toward understanding its physiological role in reproduction. Secondly, we are searching for gene variants that might influence fertility performance. For this purpose, detailed structural and sequence data of the cattle gene itself are an essential prerequisite. Therefore, we set about to clone the entire Cyp19 gene, to analyze its structure, and to identify its promoter sequences.
For promoter definition, we first systematically analyzed the 5'-ends of Cyp19 transcripts isolated from various tissues with the 5'-RACE (rapid amplification of complementary DNA ends) approach. We also estimated the level of Cyp19 expression by reverse transciption-PCR (RT-PCR) to elucidate the importance of transcript variants to the tissues investigated.
| Materials and Methods |
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Sequencing was performed with the PRISM Ready Reaction Dye Deoxy Terminator Cycle Sequencing Kit (Applied Biosystems, Weiterstadt, Germany). Extension products were analyzed on the Applied Biosystems model 373A DNA Sequencing System.
Long range PCR using genomic DNA as template was performed with the Expand Long Template PCR System (Boehringer Mannheim, Mannheim, Germany), as recommended by the supplier.
RNA isolation
Except for placenta, all tissues were dissected from freshly
slaughtered animals. Placental tissue was obtained from two Black Pied
cows after parturition. Adrenal glands, testicular tissue, livers, and
kidneys were dissected from 18-month-old Angus bulls, and the
hippocampus region was dissected from a 4-week-old female Galloway
calf. The tissue samples were frozen in liquid nitrogen before
processing. Granulosa cells from Black Pied cows were aspirated from
follicles after dissection of the ovaries and immediately processed for
RNA preparation.
RNA was isolated with the RNeasy kit (Qiagen, Hilden, Germany), as recommended by the supplier.
Primer extension
The antisense primer 1.1p.e. (Table 1
and Fig. 3
)
was labeled at its 5'-end using [
-32P]ATP and T4
polynucleotide kinase (11). The radiolabeled primer was annealed to 40
µg total placental RNA and subsequently extended with 200 U Moloney
mouse leukemia virus reverse transcriptase (Life Technologies,
Eggenstein, Germany) for 10 min at 20 C, 10 min at 37 C, and 30 min at
42 C. The extension products were analyzed on a 5% sequencing gel
(19:1, acrylamide-bisacrylamide-7 M urea), next to the
sequence ladder of the corresponding genomic DNA. For sequencing, the
dsDNA Cycle Sequencing System (Life Technologies) and the radiolabeled
primer were used.
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RT-PCR
RT was carried out with 2 µg of a total RNA preparation,
antisense primer 5 (Table 1
), and Moloney mouse leukemia virus reverse
transcriptase (Life Technologies) in 20 µl of the incubation buffer
provided by the supplier, supplemented with deoxy-NTPs and RNAsin
(Promega, Heidelberg, Germany), for 60 min at 37 C. Subsequently, the
cDNA was diluted with 80 µl H2O. Five microliters of the
dilution were used as template for PCR analysis.
Subsequent PCR was performed with Taq DNA polymerase
(Appligene, Heidelberg, Germany) in 50 µl of the incubation buffer
provided by the supplier, supplemented with deoxy-NTPs and sense and
antisense primers (Table 1
and Fig. 3
), for 30 reaction cycles.
We assessed the Cyp19 transcript concentrations within
different tissues, based on the quantity of PCR products after the
first and second amplifications, as estimated by ethidium
bromide-stained 4% agarose gels (see Fig. 2
).
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For amplification of the constant region of Cyp19 messenger
RNA, both antisense primers were consecutively combined with primer 2b,
which is located downstream from the splice acceptor site within exon
2. To selectively detect transcripts with different 5'-UTRs that were
identified in prior 5'-RACE experiments, specific sense primers for
each of the 5'-UTRs were designed (Table 1
and Fig. 3
). To prove their
identity, nested PCR products were purified and directly sequenced.
| Results |
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EMBL3, were screened with various bovine cDNA probes (6), revealing
six clones. A DNA stretch of 44 kilobases (kb) including exons 1.310
(Fig. 1
(13) were isolated on additional clones and were
distinguished by PCR (not shown). However, these clones were not
further analyzed.
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Isolation of tissue-specific transcripts
RNA samples from seven different tissues were screened for total
Cyp19 expression with a two-step RT-PCR. After the first
amplification with primers 2b and 3a, only cDNA samples from placenta
and granulosa cells gave rise to a clearly visible PCR product, whereas
the yield was low with cDNA templates derived from hippocampus and
testis. In adrenal gland and liver, Cyp19 transcripts could
be detected only after the second amplification with primers 2b and 3b
(Fig. 2
). In RNA preparations from kidney we could not
detect Cyp19 transcripts. Based on this analysis,
Cyp19 transcript concentrations in placenta and granulosa
cells were estimated to be high, those within hippocampus and testis
were estimated to be intermediate, and those in adrenal gland and liver
were estimated to be low. The results were reproducible in repeated
experiments with different RNA preparations.
Except for liver, we could generate specific 5'-RACE products from all
other tissues with detectable Cyp19 expression. From 42
analyzed RACE clones, 29 were derivatives from independent PCR
products. Ten clones from granulosa cells and adrenal gland included a
5'-UTR that was homologous to the region upstream from the splice
acceptor site of exon 2. They could be divided into 2 groups, based on
the transcriptional start sites: 2 clones corresponded to start site 1,
and 8 clones corresponded to start site 2 (see Fig. 5
). Both start
sites were previously described (7).
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In granulosa cells, placenta, testis, adrenal gland, and hippocampus,
we found a first exon (exon 1.1) that was homologous to that of the
major placental transcript previously described (6). However, the
5'-ends of only six RACE clones were consistent with the known
transcriptional start site (7), called start site 2 during this study.
Two longer clones started at site 1, one at site 4, and four at site 5
(Fig. 5
). Primer extension experiments with placenta RNA confirmed
these start sites. Moreover, they clearly showed the additional site 3,
thus suggesting that exon 1.1 has multiple transcriptional start sites
scattered over a DNA stretch of 99 bp. However, the extension product
corresponding to start site 2 was the most prominent, indicating the
preferential usage of this site (Fig. 4
).
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Tissue-specific distribution of transcript variants
To estimate the relative amounts of the transcripts identified
with the 5'-RACE method in different tissues, we derived primers (1.1,
1.2a, 1.3, 1.4, and 2a; see Table 1
) for all leading 5'-UTR and
performed a two-step PCR analysis by combining these primers
consecutively with the antisense primers 3a and 3b. Sequence analysis
after reamplification confirmed that all primer combinations generated
specific products. Transcripts with all different 5'-UTR were present
in granulosa cells and placenta, some of them at high concentrations.
However, in granulosa cell-derived transcripts, the 5'-UTR of exon 2
was present at a high concentration, and exon 1.1 was present at an
intermediate concentration, whereas the majority of Cyp19
transcripts in the placenta started with exon 1.1 or 1.3 (Fig. 2
). The
remaining 5'-UTR variants were found at intermediate or weak
concentrations in both tissues. In testis, all transcript variants
could be detected at low concentrations, except those including exon
1.2a. In adrenal gland only transcripts with the 5'-UTR of exon 2 were
present at low concentrations. In the hippocampus, transcripts with
exon 1.4 were represented at intermediate concentrations, other
transcript variants (1.2a and 1.3) at low levels. None of these 5'-UTR
variants could be detected in liver tissue, although Cyp19
messenger RNA was undoubtedly present.
Surprisingly, exon 1.2a-specific RT-PCR (primers 1.2a/3b) generated two
products (390 and 300 bp) when the cDNA was prepared from placenta or
granulosa cells (Fig. 2
). In contrast, when the cDNA was derived from
hippocampus, only the shorter PCR product (300 bp) was amplified.
Cloning and sequencing of the PCR fragments showed that the 390-bp
fragment was derived from transcripts with a 5'-UTR composed of exons
1.2a and 1.2b. This corresponds to our 5'-RACE clone derived from
placenta. The shorter fragment of 300 bp was derived from a transcript
with only exon 1.2a as the 5'-UTR. Thus, in the hippocampus,
Cyp19 transcripts do not include exon 1.2b, whereas in
placenta and granulosa cells, transcripts with or without exon 1.2b are
produced at comparable concentrations.
Tissue-specific promoters of Cyp19
The potential promoter regions upstream from exons 1.1, 1.3, and 2
(designated P1.1, P1.3, and P2 in this study) were sequenced and
further examined with the computer program FACTOR of the EMBL Data Base
(Heidelberg, Germany) to identify potential cis-acting
regulatory elements.
Within a stretch of 2023 bp of the placental P1.1 region, the computer
search revealed numerous potential factor-binding sites, some of which
were of particular interest (Fig. 5
). Apparently, there is no consensus
TATA motif at an appropriate distance from any of the five
transcriptional start sites. However, a putative transcriptional
initiator region (INR) matching the consensus structure,
(Py)2CA(Py)5 (16), spans the major
transcriptional start site 2. In addition, two consensus binding motifs
for the ubiquitous upstream stimulating factor (USF) were identified,
one of them located 59 bp upstream from the transcriptional start site
2. Within the sequence studied, two potential binding sites for the
nuclear factor interleukin-6 (NF-IL6) were also recognized as well as
four CAAT transcription elements, which might be recognized by multiple
factors. A hexameric sequence motif, AGGTCA (i.e. half of an
estrogen receptor-binding site), occurs twice within P1.1. It was shown
to bind the steroidogenic transcription factor (SF1), also known as
Ad4BP (17, 18).
Of the second placental promoter, P1.3, 300 bp have been sequenced to
date (Fig. 5
). Beside the sequence AATAAA at position -27 resembling a
consensus TATA box, only a CAAT motif at position -178 was
identified.
As both promoter regions were shown to be most active within placental tissue, we compared them to the corresponding human Cyp19 promoter sequence (19, 20). This sequence comparison revealed no significant homology (<50%).
The proximal ovarian promoter region, P2, features two consensus TATA
boxes, one of them located at position -29 of the transcriptional
start site 1, and the other at position -30 of start site 2 (Fig. 5
).
In addition, three CAAT elements as well as a potential SF1 binding
hexameric motif were found within the 1176 bp sequenced to date. This
bovine promoter revealed a strong sequence similarity (80%) toward the
corresponding regions of the human Cyp19 gene (19).
| Discussion |
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Aside from those clones that could be unambiguously assigned to the pseudogene (13), no evidence emerged for the existence of additional Cyp19-related genes or isoforms recently detected in the porcine genome (21).
Our finding of 10 retroposon elements within the Cyp19 locus is consistent with the previously noted high frequency of occurrence of those elements within the bovine genome (15). There might be even more interspersed repetitive motifs in areas that have not yet been sequenced.
Expression of the Cyp19 gene
Transcripts of the Cyp19 gene could be detected in all
tissues investigated, except kidney. However, the semiquantitative
analysis, based on the two-step RT-PCR assay, revealed very different
concentrations. These were low in adrenal gland and liver, on the one
hand, and high in placenta and granulosa cells, on the other hand.
The classification into quantitative groups, of course, does not allow the determination of absolute transcript quantities, but the technique is appropriate for a rough estimate of tissue-specific differences in Cyp19 expression.
In the liver, low concentrations of Cyp19 transcripts were detected reproducibly with primers specific for a constant region of the gene, although 5'-UTR-specific RT-PCR did not yield any products. Cyp19 expression might, therefore, be driven by a yet unidentified liver-specific promoter region, resulting in a new transcript variant. However, because liver was the only tissue in which repeated 5'-RACE experiments did not generate any products, we prefer another interpretation; several promoter regions might contribute to Cyp19 expression, but the various 5'-UTR of these transcripts might be below the threshold of detection. This does not exclude a functional relevance of Cyp19 transcripts in the liver, but could also be a consequence of a leaky transcriptional regulation of Cyp19 expression.
The observed abundance of Cyp19 transcripts in granulosa cells and placenta is consistent with previous investigations demonstrating that these tissues show the highest aromatase activity and Cyp19 expression in humans and cattle (5).
Transcript variants in different tissues
From granulosa cells, placenta, testis, adrenal gland, and
hippocampus we could isolate Cyp19 transcript variants with
six different 5'-UTRs. Four of them (exon 1.2a, 1.2b, 1.3, and 1.4)
have not previously been described in cattle. In granulosa cells and
placenta, all variants were detected with RT-PCR. However, the main
transcripts were not identical in the two tissues.
The concentration of transcript variants clearly suggests that in granulosa cells the most important transcript is driven by the promoter region upstream from exon 2, P2. This is the most proximal promoter of the Cyp19 gene, and it has been described in several other species. Therefore, it was thought (5) that it is the primordial Cyp19 promoter. In cattle, our experiments as well as others (7) demonstrate two distinct transcriptional start sites in this region with two canonical TATA boxes at appropriate locations. The potentially hexameric SF1 binding motif found in P2 is also present in the promoter regions of all steroidogenic P450 genes studied to date (17, 18). It was shown to enhance transcription of those genes in a cAMP-dependent manner (22, 23, 24). As no classical cAMP-responsive element was identified, it is reasonable to assume that SF1 binding might also confer cAMP responsiveness on the bovine promoter 2.
The promoter adjacent to exon 1.1, P1.1, might also have a functional role in granulosa cells, because transcripts comprising this 5'-UTR variant were found at intermediate concentrations. The importance of the remaining transcript variants is unclear, as they were present at considerably lower levels.
In the placenta we detected two major Cyp19 transcript variants. One variant, comprising exon 1.1, has previously been suggested to represent the major placental transcript (6, 7). The other, harboring exon 1.3, a yet undescribed 5'-UTR, was also found at high concentration. Surprisingly, we found that multiple transcriptional start sites are used within exon 1.1, being scattered over a range of 99 bp. This could be confirmed with two independent experimental strategies (5'-RACE and primer extension). One explanation for this kind of "fuzzy" transcription initiation could be the apparent lack of consensus TATA elements within promoter 1.1. However, start site 2 is obviously preferred, probably due to the potential transcriptional INR spanning this area. It has been shown by others (25), that such elements can substitute for a missing TATA box. In this regard, the putative binding sites for the USF are interesting, as it has been demonstrated that USF can cooperatively interact with an INR-bound factor (26). In addition, USF was shown to mediate the interaction of the transcription factor IID with a TATA-deficient promoter (27). Interestingly, although the major placenta-specific promoters in human and cattle (PI.1 and P1.1) are unrelated, as demonstrated by sequence analysis, both contain consensus binding motifs for the NF-IL6, a member of the CCAAT/enhancer-binding protein family. This motif seems to be of functional importance for Cyp19 expression in the placenta, as Toda et al. (28) demonstrated that NF-IL6 interacts with the placenta-specific promoter of the human Cyp19 gene. Transcript variants with a leading exon 1.2a were found in the placenta at intermediate concentrations. Surprisingly, these transcripts vary in length depending upon whether they include exon 1.2b. Thus, the promoter region adjacent to exon 1.2a can initiate two different transcript variants as the result of alternative splicing.
In several areas of the mammalian brain, among them the hippocampus as a part of the limbic system, considerable Cyp19 transcript concentrations and aromatase activity have been demonstrated (2, 29). For this reason and because of its well defined morphology, we choose the hippocampus to represent the brain. Exon 1.4 clearly was the most prominent first exon variant in the hippocampus. Intermediate concentrations of this specific transcript were estimated. The nucleotide sequence of exon 1.4 is homologous to brain-specific transcripts in primates and rodents (8, 10, 30). This suggests that brain-specific Cyp19 expression driven by the promoter upstream from exon 1.4 is of functional importance. Our observation that none of the transcripts with a leading exon 1.2a that were detected in the hippocampus included exon 1.2b, in contrast to those found in granulosa cells and placenta, clearly demonstrates tissue-specific alternative splicing.
As expected from other investigations (31), we found Cyp19 expression in testis, but at a lower level than in the ovary and placenta tissues. No predominant first exon was detected, although others (32) claim promoter 2 to be the most active one in the human testis from fetal to adult life. This discrepancy might be due to the low expression level in our tissue sample at the limit of detection rather than to functional differences between human and cattle.
In the adrenal gland, we found low transcript concentrations. Cyp19 expression was also reported in the porcine adrenal gland (4). The majority of 5'-RACE clones included the 5'-UTR of exon 2. With RT-PCR analysis, no other 5'-UTR could be detected within adrenal gland samples.
During this study we demonstrate six transcript variants of the bovine Cyp19 gene with clearly preferred sites of expression. This suggests that in cattle, various promoter regions also direct the expression of the Cyp19 gene to specific tissues, as described for the human gene (5). The occurrence of transcript variants with different 5'-UTR linked to an identical coding region might, therefore, be considered the result of mere tissue-specific transcriptional regulation without further relevance for the regulation of gene expression. However, our observation that transcripts starting with exon 1.2a are alternatively spliced demonstrates that 5'-UTR variants are generated even after transcription initiation from the same promoter region. This suggests that 5'-UTR variants may play a role for the regulation of downstream processes. The presence or absence of exon 1.2b in transcripts that start with exon 1.2a might result in different secondary structures of the 5'-UTR, which could affect the binding of ribosomes or other protein factors influencing the efficiency of translation (33). Also, they might influence the stability of the messenger RNA (34). Although experimental evidence is still missing, posttranscriptional regulation of gene expression on the RNA level could contribute to the complex expression pattern of the Cyp19 gene.
| Acknowledgments |
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EMBL libraries. | Footnotes |
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Received December 12, 1996.
| References |
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