Hepatocyte-Nuclear Factor 3p Gene Transcripts Generate Protein Isoforms with Different Transactivation Properties on the Glucagon Gene Jacques Philippe Department of Genetics and Microbiology Medicine Centre M6dical Universitaire 1211 Geneva 4, Switzerland and Hepatocyte-nuclear factor 36 (HNF96), a member of the HNF-3 gene family, is expressed in glucagon-producing islet cells and represses glucagon gene expression. We show here that at least three different HNF-36 transcripts that encode HNF-36 protein variants are present in glucagon-producing cells, HNF-BP,, HNF-3&., and HNF-3&. Compared with the HNF-36, cDNA, HNF-36, cDNA lacks sequences of exon 1 while exons 1 and 4 are absent from the HNF-36, cDNA. The deduced amino-acid (aa) sequence of HNF-36, and HNF-36, proteins differs from HNF-36, by a 6-aa amino-terminal extension and by the absence of the first 30 aa, respectively. HNF-BP,, HNF-3&, and HNF-3& bind to the major enhancer of the rat glucagon gene G2 with similar affinity. By contrast to HNF-36,, which represses glucagon gene expression when overexpressed in the glucagon-producing cell line InRlG9, HNF-36, and HNF-36, do not affect transcriptional activity. Furthermore, cotransfection of HNF-3P, or HNF-36, along with HNF-3& decreases the negative effects of HNF-36,. We conclude that glucagon gene expression may be regulated by the relative abundance of the three different HNF-3P variants in cu-cells. (Molecular Endocrinology 9: 366-374, 1995) INTRODUCTION ulation of the glucagon gene may thus implicate The glucagon gene is expressed in the pancreatic islets, the intestine, and the brain (1). Pancreatic-specific expression is conferred by 300 base pairs (bp) of the 5’-flanking region of the rat glucagon gene, which contains three DNA elements, the upstream promoter element G, and two enhancers, G, and G,. G, acts as a potent activator of glucagon gene expression and is only active in islet cells (2, 3). 0888-8809/95/$3.00/O Molecular Endocrmology Copyright 0 1995 by The Endocme We recently identified two major protein complexes binding to G,; whereas one complex is islet-specific and appears to act positively on glucagon gene transcription, the second complex contains hepatocytenuclear factor-36 (HNF-3P), a DNA-binding protein found in abundance in the liver (4). HNF-36 belongs to a gene family characterized by a winged-helix (WH) DNA-binding domain and is found predominantly in tissues derived from the endoderm (5, 6). Overexpression of HNF-30 in glucagon-producing cells results in a repression of glucagon transcription (4). Since different mRNAs were identified by Northern analysis using an HNF-3 P-specific probe in glucagonproducing cells, we searched for HNF36 cDNA variants. We report here the cloning of two additional HNF36 cDNA clones, HNF-36, and HNF-36,. The putative proteins they encode differ from HNF-36 (referred to now as HNF-36,) at the amino-terminal end. HNF-36,, the most abundant form has a six-amino acid (aa) amino-terminal extension whereas HNF-36, lacks the first 30 aa. Both HNF-36, and HNF-36, bind G, with a similar affinity compared with HNF-36,. However, by contrast to HNF-Sp,, they do not modify glucagon gene transcriptional activity. We hypothesize that the lack of effect of HNF-3/3, and HNF-36, on transcription results from differences in their aminoterminal ends compared with HNF-3& The aminoterminal end of HNF-36, is a transactivation domain (7) and its modification may impair its function. Reg- Society multiple element. transcription factors RESULTS AND DISCUSSION binding the G, We previously reported that two different mRNAs of 2 and 2.2 kilobases (kb) were detected in islet glucagonproducing cells with an HNF-S/3-specific probe (4). To further investigate whether multiple mRNAs encoding different HNF-36 protein isoforms were present in Regulation of Glucagon Gene Expression 369 glucagon-producing cells, we screened a mouse aTC1 cDNA library with an HNF-36 cDNA probe. We obtained 14 HNF-38 clones; IO of these contained sequences limited to exon 6 (Fig. 1). One cDNA corresponded to the originally described HNF-36 sequence, HNF-38, (5, 8, 9), and three additional cDNAs contained sequences at the 5’-end potentially encoding two different HNF-38 isoforms, HNF3& and HNF-36,. The major differences between HNF-Sp,, HNF-3&, and HNF-36, cDNAs are the absence of exon 1 in p2 and of exons 1 and 4 in &; in addition, p2 and p3 cDNAs contain exons 3 and 5, respectively (Fig. 1, A and B). These transcripts result from alternative splicing mechanisms of the HNF-36 gene, which contains 6 exons (10, 11). Interestingly, an in-frame stop codon is present in the V-untranslated sequences of both HNF-36, and p2 cDNAs (Fig. 1A). The HNF-38, cDNA contains a single large open reading frame that would encode a protein of 465 aa. The initiator methi- Fig. 1. Structure and Sequence of the HNF-36 cDNA Variants A, Y-Ends of the HNF-38,, &, and &, cDNAs and the predicted aa sequence of the encoded proteins. The initiator ATGs are in bold letters; it is preceded by an in-frame termination codon in the HNF-36, and p2 cDNA. The sequence underlined represents the Y-primers (a, b, and c) used to amplify the respective cDNAs. The arrow indicates the boundary of exon 6. B, Structure of the HNF-3 gene (16-l 8) and of the HNF-36 variant cDNAs. Exons (E) of the HNF-3 gene are represented by boxes and introns by lines. Each cDNA is schematized by the juxtaposition of the exons it contains. The expected size of each HNF-36 protein isoform is indicated on the right. onine conforms well to the consensus for eukaryotic initiation (12). Comparison of the aa sequence with that of HNF-38, indicates that both proteins only differ by the presence of six additional aa at the aminoterminal end of HNF-36,. The HNF-38, cDNA contains a shorter open reading frame of 429 aa which lacks the 30 first amino-terminal aa of HNF-36,; except for the absence of these 30 aa, the coding sequences of HNF-36, are identical to that of HNF-38,. An additional potential ATG is present in the rat HNF-36, cDNA 234 bp upstream of the initiator ATG (11). It is, however, not conserved in the mouse cDNA. To examine whether the two different mRNAs observed on Northern analysis correspond to the cloned cDNAs (Fig. 2, lane l), we used DNA fragments specific for each cDNA for hybridization. Whereas probes specific for HNF-36, and & hybridized to the 2.2 kb mRNA (Fig. 2, lane 2 and 3, respectively), no signal was seen with the HNF-38, probe, indicating that mRNA encoding HNF-38, is less abundant than those fiNF30 B El E3 Et E2 AT6 GENE E5 cDNAs E6 protefns HNF 381 459 m h El E4 E6 E3 E4 E6 AT6 i HNF3E2 465 m HW363 429 m MOL 370 END0 . 1995 Fig. 2. Northern Blot Analysis of HNF-36 mRNAs Total RNA extracted from the glucagon-producing cell line RIN 56 A was hybridized with 32P-labeled rat HNF-36, cDNA probe (lane l), exon 1 of the rat HNF-36 gene (16) (lane 2), or the ?-untranslated sequence of the mouse HNF36, cDNA along with the rat glucagon cDNA (lane 3). -I indicates the 2.0 kb and 2.2 bands and -1-indicates glucagon mRNA. coding for HNF-36, and p2 (data not shown). No hybridization to the relatively abundant 2.0-kb message was detected. The same results were obtained from Northern analyses with total RNA extracted from the three glucagon producing cell lines RIN 56A (Fig. 2), OirCl , and InRl G9 (data not shown). To investigate whether an additional variant HNFS cDNA that was not represented in our 14 original clones was present in (uTC1, RIN 56 A, or lnRlG9 cells, we performed reverse transcription (RT) from cytoplasmic RNA extracted from these cell lines and amplified by polymerase chain reaction (PCR) most of exon 6 se- Fig. 3. RNase Protection Analysis of HNF-36 mRNAs A, A 590-bp fragment containing the Y-end (534 bp) of the rat HNF-36, cDNA and 56 bp of unrelated sequences was transcribed by the T7 polymerase into a ‘“P-labeled riboprobe that was used for RNase protection analysis with 30 pg RIN 56 A cytoplasmic RNA. M indicates markers whose sizes are indicated on the left: arrows point to the expected protected fragments of 534 bases (HNF-Sp,), 243 bases (HNF-36,) and 173 bases (HNF363). B, Schematic representation of the RNA probe used in the RNase protection assays and of the respective expected fragments from HNF-36,, P2, and p3 mRNAs. Vol 9 No. 3 quences. A single 1 .l kb band was obtained from each RT-PCR, indicating that no additional cDNA results from exon 6 splice variants (data not shown). In addition, when we looked for the presence of the HNF-36,, &, and p3 cDNAs in different cells by RT-PCR, we only obtained a single amplification product with each set of oligonucleotides (see below). To assess the relative abundance of the HNF-36,, HNF-3&, and HNF-3& mRNAs, we performed RNase protection assays with 30 pg cytoplasmic RNA from RIN 56 A and a riboprobe of 590 bases corresponding to 534 bases of the 5’-end of the rat HNF-36, cDNA and 56 bases of unrelated sequences. As shown in Fig. 3, three different bands were detected at 534,243, and 173 bases, corresponding to the expected protected fragments from HNF-36,, P2, and &, respectively. The most abundant mRNA corresponded to that encoding HNF-36,. The same relative distribution was observed in the insulin-producing cell line RIN 38 (data not shown). We also investigated whether HNF-36,, p2, and p3 were present in the glucagon-producing cell lines aTC1 and InRl G9 and in primary rat islets by RT-PCR using 5’-primers specific for each cDNA (Fig. 1A) and a common 3’-primer. Expected amplification products for HNF-36,, &, and p3 were of 232, 218, and 184 bp, respectively. As shown in Fig. 4, all three products were obtained using primary rat islet cDNA; the same profile was also observed when using glucagon- ((uTC~ and InRl G9) and insulin-producing cell line (RIN 38 and HIT-15) cDNAs (data not shown). We recently showed that HNF-36, binds to the major enhancer G, of the rat glucagon gene, and its overexpression by transient transfection assays leads to a decrease in G,-mediated chloramphenicol acetyltransferase (CAT) activity. We thus assessed whether HNF-36, and p3 could bind G, and affect its activating properties. We inserted HNF-36,, &, and p3 cDNAs Regulation of Glucagon Gene Expression 371 into an expression vector driven by the cytomegalovirus (CMV) promoter (5) and transfected these constructs into BHK-21 cells, a fibroblast cell line that does not normally synthesize HNFB proteins. We prepared nuclear extracts from DNA- and sham-transfected cells 48 h later. No G, binding activity was detected in nuclear extracts from sham-transfected BHK-21 cells (Fig. 5 A); by contrast, a complex comigrating with HNF38 from InRl G9 cells (the same pattern was obtained with 56 A and crTC1 nuclear extracts) was observed in nuclear extracts from cell lines transfected with HNF36, (Fig. 5A, lane 2), p2 (lane 3), and p3 (lane 4). HNF-36, was consistently more abundant than HNF-38, and p3 despite the fact that similar amounts of total proteins were assayed (all nuclear extracts were verified for their ability to bind the octamer sequence). Formal proof that HNF-38, with its amino-terminal extension is, in fact, synthesized awaits, however, the availability of specific antibodies. Of note, HNF-3&, the smallest protein in size, migrated slightly faster than HNF-38, and & (Fig. 5). To investigate the relative affinity of HNF-36,, &,, and p3 for G,, we added increasing amounts of unlabeled G, oligonucleotide competitor. Competition efficiency by G, was found to be similar for all three proteins 123M .267 0184 0124 Fig. 4. PC!? Amplification of the HNF-36 cDNA Variants from Rat Islets Total RNA was isolated from rat islets and reverse transcribed with random hexamers. PCR amplification of the Y-end of the HNF-36, 3p2, and p3 was performed with an oligonucleotide specific for each cDNA (Y-primer, see Materials and Methods) and a common 3’-oligonucleotide annealing to the exon 3 sequences. PCR reactions were run on a 2.5% agarose gel. The identity of the reaction products was verified by Southern analysis using a 32P-labeled HNF-38, cDNA as a probe. Lane 1 corresponds to a 184-bp amplification product of the HNF-38, cDNA, whereas lanes 2 and 3 contain the products of the HNF-38, (218 bp) and 8, (232 bp) cDNAs, respectively. %2345 6 Fig. 5. Binding 1 2 3 4 5 6 7 8 9 10 11 12 13 C 1 2 3 4 5 6 7 a 9 19 II 12 13 of the HNF-38 Protein lsoforms on G, Gel retardation assays were performed with a 3”P-labeled oligonucleotide containing the G2 binding site (4) and 2 pg InRlG9 or 6 pg BHK-21 nuclear extracts. BHK-21 cells were transfected by the calcium phosphate precipitation method with expression vector alone or containing the respective HNF-38 cDNAs. BHK-21 nuclear extracts were then obtained. A, Nuclear extracts from InRl G9 cells (lane l), BHK-21 cells transfected with expression vector containing, respectively, the HNF-38, (lane 2), HNF-38, (lane 3) HNF-38, (lane 4) cDNAs or expression vector alone (lane 5) were incubated with 32p-labeled G,. B, Nuclear extracts from lnRlG9 cells (lane 1) or cells expressing either HNF-38, (lanes 2-5), HNF-36, (lanes 6 to 9), or HNF-36, (lanes 10 to 13). Comp indicates the addition of G, oligonucleotides as competitors in a molar excess of 10 (lanes 3, 7, and 1 l), 25 (lanes 4, 8, and 14), and 50 (lanes 5, 9, and 13). C, Same as for panel A except that the competitor oligonucleotide contains the HNF-3 binding site of the lTR gene (7). Arrow indicates the HNF-36 complex and dots indicate nonspecific complexes. MOL 372 END0 1995 (Fig. 5B); similar results were obtained with the HNF3 binding site of the lTR gene (Fig. 5C). These results indicate that the three HNF3P isoforms can bind G, with similar affinities. To examine whether HNF-S/3,, P2, and p3 affect glucagon gene expression differently, we cotransfected their respective cDNAs inserted into a CMVdriven expression vector with a reporter plasmid containing G, linked to the glucagon gene promoter and the CAT gene. HNF-3/3,, &, and p3 appeared to be overexpressed in these experiments as nuclear extracts prepared from transfected cells showed a relative increase in the HNF-36 complex (data not shown). Whereas we observed a dose-dependent negative effect with HNF-36,) no change in transcriptional activity was seen with HNF-3P, and p3, indicating that the latter isoforms, although capable of binding G,, do not affect transcription (Fig. 6). Titration studies were performed with different ratios of reporter to expression vector (3 Kg/O.1 pg, 3 pgIO.5 Fg, 3 pgll pg, 1 pg/l pg, 1 pg/2.5 pg, and 1 pg/5 Fg). Although these ratios of reporter/HNF-30, expression vector resulted in quantitative differences on transcriptional activity, they consistently led to a decreased activity. The negative effects of HNF-36, could be reduced by cotransfection of both HNF-3& or p3 cDNAs (Fig. 6). HNF-3 Fig. 6. Effects of HNF-36 lsoforms on G,-Mediated Transcriptional Activity lnRlG9 cells were cotransfected with 1 wg of a reporter plasmid containing wild type or mutated G, or G, and the glucagon gene promoter linked to the CAT gene (G,-136 CAT, G,M,-136 CAT, and G,-136 CAT, respectively), 1.25 or 5 pg HNF-36 cDNAs subcloned into a CMV-driven expression vector, and 1 pg of a control plasmid, pSV,Apap (28) to assess transfection efficiency. The increasing amounts of expression vector or HNF-36 cDNAs cotransfected with the reporter plasmids are indicated as molar ratios (l/l, 2.5/l, 5/l or 2.5 + 2.5/l). CAT activities were measured 48 h after transfection and expressed as a percentage of the activity obtained with the reporter plasmids and expression vector alone. Results are corrected for the amount of proteins and the alkaline phosphatase activities and represent the mean t- ssM of six experiments. Vol 9 No. 3 p2 and p3 may thus compete with HNF-3& for the G,-binding site and their respective abundance in glucagon-producing cells along with that of the uncharacterized activator A, (4) may determine the activation potential of G,. Overexpression of HNF-36, did not modify the transcriptional activity obtained with G, or a mutant of G, (G,M,) which binds HNF-36, poorly (4). HNF-3 proteins were first identified in the liver and shown to be important for liver-specific gene expression (5, 13, 14); they belong to a family of proteins characterized by a highly conserved DNA-binding domain of 100 aa referred to as the WH motif (6). It is now becoming apparent that distinct WH proteins are distributed in most tissues with patterns of expression that are developmentally and spatially restricted. We recently reported the presence of HNF36 in all islet cell phenotypes and its effect on glucagon gene expression (4). We show here that HNF-36 consists of at least three isoforms, p,, &, and &. Compared with p,, p2 is characterized by an amino-terminal extension of six aa, a feature also found for another WH member, XFKHl (15, 16). &, by contrast, lacks the first 30 aa. Whether additional HNF-36 forms are present in islet cells is still unclear; this is suggested by the presence of a 2.0 kb mRNA that hybridizes with an HNF-36specific probe, but neither our cloning nor our PCR attempts were successful in identification of cDNAs corresponding to the 2.0-kb mRNA. The HNF-3 p2 and p3 cDNAs have recently been reported to be expressed in the adult liver and the notochord and midline neural plate cells of mammalian embryos (10, 11). HNF-36 proteins may thus serve as critical factors of endoderm differentiation and floor plate development (11, 17); their respective role and importance in these processes are undetermined, however. Although HNF-3 p2 and p3 both bind G, with a similar affinity compared with p,, they do not affect,in contrast to p,, the transcriptional activity conferred by G,. One potential explanation lies in the difference between the amino terminus of the three isoforms. HNF-36, has indeed two transcriptional activation domains, one of which is located within the 50 aminoterminal aa, is rich in serine, and contains two putative casein kinase I phosphorylation sites (7). Deletion of the amino-terminal activation domain of HNF-36, results in a 50% loss in the ability to activate transcription from the lTR promoter. The first 30 aa in HNF-36, could thus be critical in the negative transcriptional effects on glucagon gene expression. How the aminoterminal extension of HNF-36, abolishes the effects observed with 6, is less clearly apparent; however, three of the six aa are serines and potential sites of phosphorylation. Changes in the phosphorylation state of HNF-3& may result in different negative activation potential. Alternative splicing of transcripts from a single gene is often used to generate protein isoforms with different functions. Many genes coding for transcription factors are subject to alternative splicing, a mecha- Regulation of Glucagon Gene Expression nism directly responsible for the generation of transcription factors with distinct or opposite activities (18-25). Our results suggest that the three HNF-3P proteins play different roles on glucagon gene expression and may compete for the G, binding site. Several questions, however, are raised by our data. How is the synthesis of the different HNF-3/3 isoforms regulated? Are different promoters under the control of different transcription factors responsible for the generation of all three transcripts? What are the physiological roles of the HNF-3 isoforms in the developmental regulation of the glucagon gene? Their role may not be limited to glucagon gene expression inasmuch as these proteins are present in the different islet cell phenotypes; identification of genes regulated by HNF-3fl may help to understand islet development. Further work will be needed to better define the structure of the HNF-3P gene and the function and regulation of its protein products. MATERIALS Plasmids AND METHODS and Oligonucleotides Oligonucleotides containing G, [nucleotides (nt) -201 to -1651. G,M, (4). or G, (nt -274 to -234) with BamHl compatible ends’were ins&t& into a BamHl site 5’ the glucagon 373 plasmid; 1, 2.5, or 5 Fg effector plasmid (expression vector containing the HNF-3/3,, -p2 or -p3 cDNAs), and 1 pg of the plasmid pSV,Apap to monitor transfection efficiency. pSV,Apap is a plasmid containing the human alkaline phosphatase gene driven by the simian virus 40 long terminal repeat (30). Cell extracts were prepared 48 h after transfection and analyzed for CAT and alkaline phosphatase activities as described previously (31). BHK-21 cells were grown in the same medium as the islet cell lines and transfected by the calcium phosphate precipitation technique. Cell Extracts Nuclear Schreiber performed and Gel Retardation extracts were et al. (32). as previously Assays prepared by Gel retardation described (31). the method of assays were RT and PCR Total RNA was extracted from whole rat islets and cytoplasmic RNA was obtained from mouse, rat, and hamster glucagon-producing cell lines by standard procedures (33). RNA was reverse-transcribed into cDNA with random hexamers by Moloney murine leukemia virus reverse transcriptase (Superscript, Bethesda Research Laboratories, Rockville, MD) and 100 ng of cDNA were used for 30 cycles of PCR amplification (1 min at 94 C, 1 min at 58 C, and 1 min at 72 C). The different HNF-38 cDNA variants were amplified with oligonucleotides a and d (232 bp of HNF-36,) b and d (218 bp of HNF-36,) and c and d (184 bp of HNF-38,). PCR amplification products were run on a 2.5% low melt agarose gel. The nature of the amplification products was confirmed by Southern analysis. promoter (nt -136 to +51) (4). HNF-38,, &. and p3 cDNAs were inserted into a CMV-driven expression vector (5). The HNF-3 binding site from the transthyretin gene promoter (7) was generously given by M. Raymondjean (Hopital Cochin, Paris). Sequences of oligonucleotides (5’-3’) used in the PCR were as follows (see Fig. 1A): a) TCTGGAGCAGCGGCCAGCGAG [nt 162 to 182 from 8, (26)]; b) GCACTCGGCTTCCAGTATGCT (representing the sequence encoding the six aminoterminal aa of ._. 8,); c) GAGCTCAGCCTAGGTGCTAACCTG; d) ACATAGGATGACATGTTCATGGAG [nt 372 to 395 from 8, (26)l: e) TATTGGCTGCAGCTAAGCGG fnt 10 to 29 from &, ‘[26)]; 9 GTTACAGTTAAGTCCCAGGGA [nt 130 to 150 from 6, (26)]. The rat HNF-38, cDNA was generously provided by Dr. E. Lai (Memorial Sloan-Kettering Cancer Center, New York). Northern blots were performed with total RNA as previously described (27). HNF-B&-specific probe was represented by exon 1, which was amplified from rat genomic DNA by oligonucleotides e and f; HNF-36, and &-specific probes were the 5’-untranslated sequences of the respective cDNA clones. HNF-38,, p2, and p3 transcripts were assayed in cytoplasmic RNA (30 kg) from the RIN 56 A cell line by RNase protection analysis (33). A rat HNF-381 probe was used and obtained by cloning a 534 bp EcoRI-Aval fragment of the HNF-38, cDNA (26) along with 56 bp of unrelated sequence into Bluescript. HNF-3p Acknowledgments cDNA Cloning Polyadenylated mRNA was isolated by the Poly A tract mRNA isolation kit (Promega, Madison, WI). A random and oligo (dT) primed cDNA library was made from 5 pg poly A+-selected RNA from the mouse glucagon-producing cell line, LY TCl which was generously provided by Dr. D. Hanahan (University of California, San Francisco, CA). After addition of EcoRl (Notl) adaptors, cDNAs were ligated into the Agt 11 vector. The cDNA library was screened with a random-primed 32Plabeled HNF-3 p-specific DNA fragment corresponding to the first 340 bp of the HNF-38, cDNA (4) according to standard procedures. The isolated cDNA clones were inserted into Bluescript (Stratagene, La Jolla, CA) for sequence analysis. Cell Culture and Transfection Northern We thank de Peyer and RNase Protection Isabel Pacheco for expert for typing the manuscript. Analyses technical help and Marie Received September 20, 1994. Revision received November 7, 1994. Accepted December 6, 1994. Address requests for reprints to: Jacques Philippe, M.D., Department of Genetics and Microbiology, Centre Medical Universitaire, 9, avenue de Champel, 1211 Geneva 4, Switzerland. This work was supported by the Swiss National Science Foundation. Studies The glucagon-producing cell lines RIN 56A (rat) (27) (rTC 1 (mouse) (28), and InRl G9 (hamster) (29) were grown in RPM1 1640 medium containing 5% fetal calf serum and 5% newborn calf serum. InRl G9 cells were transfected in suspension by the diethylaminoethyl-dextran method with 1 kg reporter REFERENCES 1. 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