Molecular mechanisms underlying the expression of the human HOX-5.1 gene

Characterization of Nrf1b, a novel isoform of the nuclear factor-erythroid-2 related transcription factor-1 that activates antioxidant response element-regulated genes

Nuclear factor E2-related factor 1 (Nrf1) is a basic leucine zipper transcription factor that plays an important role in the activation of cytoprotective genes through the antioxidant response elements. The previously characterized long isoform of Nrf1 (Nrf1a) is targeted to the endoplasmic reticulum and accumulates in the nucleus in response to activating signals. Here we characterized a novel Nrf1 protein isoform (Nrf1b) generated through an alternative promoter and first exon that lacks the ER targeting domain of Nrf1a. The 5′-flanking region of Nrf1b directed high levels of luciferase reporter expression in cells. RT-PCR and Western blotting showed Nrf1b is widely expressed in various cell lines and mouse tissues. Immunoblot analysis of subcellular fractions and imaging of green fluorescence protein (GFP)-tagged Nrf1b demonstrate Nrf1b is constitutively localized to the nucleus. Nrf1b can activate GAL4-dependent transcription when fused to the heterologous GAL4 DNA-binding domain. Gel-shift and coimmunoprecipitation experiments demonstrate that Nrf1b forms a complex with MafG, and expression of Nrf1b activates the expression of antioxidant response element containing reporters and genes in cells. These results suggest Nrf1b is targeted to the nucleus where it activates ARE-driven genes and may play a role in modulating antioxidant response elements.

Nuclear accumulation of an uncapped RNA produced by Drosha cleavage of a transcript encoding miR-10b and HOXD4

Patterning of the animal embryo's antero-posterior (AP) axis is dependent on spatially and temporally regulated Hox gene expression. The murine Hoxd4 gene has been proposed to harbour two promoters, an upstream promoter P2, and a downstream promoter P1, that lie 5.2 and 1.1 kilobase pairs (kb) upstream of the coding region respectively. The evolutionarily conserved microRNA-10b (miR-10b) gene lies in the Hoxd4 genomic locus in the intron separating the non-coding exons 4 and 5 of the P2 transcript and directly adjacent to the proposed P1 promoter. Hoxd4 transcription is regulated by a 3′ neural enhancer that harbours a retinoic acid response element (RARE). Here, we show that the expression profiles of Hoxd4 and miR-10b transcripts during neural differentiation of mouse embryonal carcinoma (EC) P19 cells are co-ordinately regulated, suggesting that both Hoxd4 and miR-10b expression is governed by the neural enhancer. Our observation that P1 transcripts are uncapped, together with the mapping of their 5′ ends, strongly suggests that they are generated by Drosha cleavage of P2 transcripts rather than by transcriptional initiation. This is supported by the colocalization of P1 and P2 transcripts to the same posterior expression domain in the mouse embryo. These uncapped P1 transcripts do not appear to possess an Internal Ribosomal Entry Site (IRES), but accumulate within multiple punctate bodies within the nucleus suggesting that they play a functional role. Finally, similar uncapped Drosha-cleaved P1-like transcripts originating from the paralogous Hoxb4/miR-10a locus were also identified. We propose that these transcripts may belong to a novel class of regulatory RNAs.

The interaction with HMG20a/b proteins suggests a potential role for beta-dystrobrevin in neuronal differentiation

alpha and beta dystrobrevins are cytoplasmic components of the dystrophin-associated protein complex that are thought to play a role as scaffold proteins in signal transduction and intracellular transport. In the search of new insights into the functions of beta-dystrobrevin, the isoform restricted to non-muscle tissues, we performed a two-hybrid screen of a mouse cDNA library to look for interacting proteins. Among the positive clones, one encodes iBRAF/HMG20a, a high mobility group (HMG)-domain protein that activates REST (RE-1 silencing transcription factor)-responsive genes, playing a key role in the initiation of neuronal differentiation. We characterized the beta-dystrobrevin-iBRAF interaction by in vitro and in vivo association assays, localized the binding region of one protein to the other, and assessed the kinetics of the interaction as one of high affinity. We also found that beta-dystrobrevin directly binds to BRAF35/HMG20b, a close homologue of iBRAF and a member of a co-repressor complex required for the repression of neural specific genes in neuronal progenitors. In vitro assays indicated that beta-dystrobrevin binds to RE-1 and represses the promoter activity of synapsin I, a REST-responsive gene that is a marker for neuronal differentiation. Altogether, our data demonstrate a direct interaction of beta-dystrobrevin with the HMG20 proteins iBRAF and BRAF35 and suggest that beta-dystrobrevin may be involved in regulating chromatin dynamics, possibly playing a role in neuronal differentiation.

Functional characterization of the HOXB13 promoter region

Homeobox (HOX) genes are crucial regulators of cell growth and differentiation. These genes initiate and control gene expression cascades that drive development. More recently, the absent or aberrant expression of HOX genes has been implicated in cancer development. Despite the observance of these expression changes, the regulation of the HOX genes in adult tissues and how these genes become deregulated in cancerous tissues still needs much investigation. We characterized the promoter region of the HOXB13 gene. A 3 kb region upstream of the HOXB13 gene, which included the 5'UTR, increased reporter gene expression in LNCaP cells by approximately 99 fold over the promoterless control construct. A highly conserved 179 base pair fragment containing only the 5'UTR of the HOXB13 gene constituted a minimal promoter in the LNCaP cell line. Strong promoter activity was seen in the presence or absence of testosterone, although testosterone exposure did decrease expression in LNCaP cells by 50%. In an androgen insensitive cell line Du145, no sensitivity to testosterone was detected and a consistent low basal level of expression was observed. Since HOXB13 expression is highly tissue specific, we investigated the ability of the promoter to drive expression in tissues other than prostate. We observed highest expression in LNCaP cells with low levels of expression in lung, retinoblastoma, and colon cancer cells and higher expression in MCF7 breast cancer cells.

Transcription factors GATA-1 and Fli-1 regulate human HOXA10 expression in megakaryocytic cells

HOXA10 is a member of the HOX family of regulatory genes that are involved in hematopoiesis. Its role in megakaryopoiesis has been suggested by its expression in immature megakaryocytes and by the proliferation of megakaryocyte-primitive blast colonies upon HOXA10 overexpression. We sought to understand the role of HOXA10 in megakaryopoiesis better, by investigating its transcriptional regulation. Analysis of the 5' untranslated region and transfection of promoter/plasmids into human tissue culture cell lines identified transcriptionally active sequences that contain GATA-1 and Ets-1 sites and a putative binding site for its neighboring gene, HOXA11. Gel shift assays confirmed protein-DNA interactions at these sites. Mutation of the GATA-1 and the Ets-1 motifs amplified the expression of HOXA10 in HEL and K562 cells, confirming the importance of these cis-acting elements in regulating HOXA10 expression in megakaryocytic cells. Chromatin immunoprecipitation (ChIP) and chloramphenicol acetyl transferase (CAT) assays confirm that HOXA11 binds to the putative binding site, resulting in repression of HOXA10 expression. These data taken together give insight into the regulation of HOXA10 expression in megakaryocytic differentiation.

Dynamic expression pattern of Hoxc8 during mouse early embryogenesis

The Hoxc8 expression pattern was examined in mouse embryos 7.5-12.5 days postcoitum (dpc) using whole-mount in situ hybridization and RT-PCR. The expression of Hoxc8 started between 7.5 and 8.5 dpc. A strong expression was detected in the ectoderm and mesoderm at 8.5 dpc. At 9.5 dpc, a distinct anterior boundary of Hoxc8 expression was established at the 10th and 16th somites in the neural tube and the paraxial mesoderm, respectively. This staggered expression pattern was maintained throughout the later stages. By 12.5 dpc, the forward progression of the Hoxc8 expression pattern was observed and the stain was weakened. In the ectoderm-derived neural tube, strong Hoxc8 expression was observed in the ventral horn and later in the ventral and mediolateral region of the mantle layer, indicating a possible association with the onset and progression of neural differentiation. In the case of the mesoderm-derivative cells, strong Hoxc8 expression was detected in the sclerotome on the way to the notochord and neural tube and mesonephros, suggesting a role of Hoxc8 in the formation of the vertebrae and ribs and the possible involvement in the differentiation into the kidney.

Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5'-UTR

The serine/threonine kinase pim-1 mRNA contains a long and G/C rich 5'-untranslated region (5'-UTR). Previous work suggested that the pim-1 5'-UTR harbors an internal ribosomal entry site (IRES) allowing for internal initiation of translation. However, several previously reported eukaryotic IRES elements actually contain cryptic promoter activity. To test whether an IRES or a cryptic promoter is present in the pim-1 5'-UTR, the 5'-UTR was re-examined using stringent test procedures. Our results show the presence of strong promoter activity in the DNA sequence corresponding to the pim-1 5'-UTR. Both promoterless dicistronic test and northern blot analysis show transcripts being derived from the cryptic promoter in the pim-1 5'-UTR sequence. This cryptic promoter is active in all cell types tested, including Cos-7, NIH3T3, HEK293, Jurkat and K562 cells. When a dicistronic mRNA containing the pim-1 5'-UTR was translated in vitro or in vivo, no IRES activity could be detected. However, the control IRESs from both human rhinovirus and encephalomyocarditis virus exhibited strong IRES activities. In addition, both the RNase protection assay and the 5'-RACE assay detected endogenous pim-1 transcripts with shorter 5'-UTRs. Our data strongly suggest that the IRES activity reported earlier for the pim-1 5'-UTR sequence is due to cryptic promoter activity.

Expression of homeobox genes in cervical cancer

OBJECTIVE

Members of the homeobox (HB) gene superfamily encode transcription factors crucial for development and may be associated with tumorigenesis. In this study, we aimed to develop a procedure to survey the expression of the dispersed-type HB genes in cervical cancer cells.

METHODS

Nineteen sets of degenerate primers were designed based on conserved homeodomains of known dispersed-type HB genes. A cDNA library derived from HeLa, a cervical cancer cell line, was used. Two successive rounds of PCR were performed using a combination of the HB degenerate primers and a primer recognizing the flanking sequence of the vector used in the cDNA library construction.

RESULTS

On cloning and sequence analysis of the PCR fragments generated, 10 known and 3 putative novel HB genes were detected in HeLa. RT-PCR expression analysis further showed that HOXD9 and ATBF1 were differentially expressed in cancer cells and not in normal cervix.

CONCLUSIONS

Our data demonstrate the feasibility of using degenerate primers in PCR experiments in a collective analysis of complex gene families. Our data indicate that HOXD9 and ATBF1 are expressed in cervical cancer, but not in normal cervix.

Translational activation and repression by distinct elements within the 5'-UTR of ENaC alpha-subunit mRNA

The rat amiloride-sensitive epithelial Na(+) channel (rENaC), the rate-limiting step in epithelial Na(+) transport, consists of three subunits, alpha, beta, and gamma. We hypothesized that alpha-rENaC translation is regulated via its 5'-untranslated region (UTR). Transient transfections of alpha-rENaC promoter-reporter constructs in representative epithelial cell lines demonstrated up to fivefold differences in activity among constructs containing different amounts of the alpha-rENaC 5'-UTR sequence. Differences in reporter protein activity did not parallel differences in reporter mRNA, demonstrating that 5'-UTR regulation must be at the level of translation. Specifically, translation was enhanced by a region extending from +53 to +211 bp downstream from the transcription start site and repressed by the region between +367 and +499 bp. Examination of the 5'-UTR sequence revealed an out-of-frame initiation codon within the repressive region, 43 bp upstream from the start of the alpha-rENaC open reading frame. Mutational analysis of this upstream start codon indicated that it plays, at most, a minor role in impeding translation both in vitro and in vivo, suggesting that additional mechanisms of translational regulation are operative.

Distinct mRNAs that encode La autoantigen are differentially expressed and contain internal ribosome entry sites

Analysis by reverse transcription-polymerase chain reaction has suggested the existence of at least two La autoantigen-encoding mRNAs that contain different 5' noncoding regions (NCRs) linked to the same La coding region (Troster, H., Metzger, T. E., Semsei, I., Schwemmle, M., Winterpacht, A., Zabel, B., and Bachmann, M. (1994) J. Exp. Med. 180, 2059-2067). La-encoding transcripts La1 and La1' contain 115- and 483-nucleotide 5' NCRs, respectively. To determine whether the various La transcripts are functional mRNAs, the expression and polysomal association of natural La1 and La1' RNAs were examined. Although La1 transcripts were ubiquitously expressed in human tissues, La1' transcripts were predominantly expressed in peripheral blood leukocytes, especially in B, T, and natural killer cells. Both La1 and La1' transcripts associated with polysomes in natural killer cells, suggesting that these transcripts were functional mRNAs. Upon activation of B cells with the mitogens phorbol 12-myristate 13-acetate and ionomycin, the amount of La1' mRNA, but not La1, declined. In contrast, after chemical activation of T cells, the amount of La 1 mRNA, but not La1', declined. The mechanism by which the La1 and La1' 5' NCRs initiate translation initiation was tested in cultured human HeLa cells and in two different in vitro translation systems. It was found that both 5' NCRs can mediate translation initiation by internal initiation. These findings indicate that the constitutive expression of La1 mRNA and the tissue-specific expression of La1' mRNA can both allow La protein synthesis under conditions when cap-dependent translation is compromised, such as inflammation, apoptosis, or certain viral infections.

Murine hoxd4 expression in the CNS requires multiple elements including a retinoic acid response element

We have identified a retinoic acid response element (RARE) within a neural enhancer located 3' to the Hoxd4 gene. This RARE is required for the initiation and maintenance of Hoxd4 transgene expression in neurectoderm, and for full anteriorized expression upon retinoic acid (RA) treatment. Mutations within the sequence TTTTCTG, located 2 bp downstream of the RARE, posteriorized transgene activity. However, the onset of transgene expression and its response to RA were indistinguishable from wild type. While the TTTTCTG motif resembles a CDX binding site, human CDX1 protein did not interact with this element in vitro. Three additional regions were also shown to control transgene expression in neurectoderm, establishing that multiple elements constitute the Hoxd4 neural enhancer.

Investigation of expression of HOX 2C and HOX 4B homeobox genes in human colorectal cancer by using an RT-PCR method

Investigation of expression of both HOX 2C and HOX 4B homeobox genes in the same patient with colorectal cancer was proposed by using an RT-PCR method. In order to conduct this investigation, PCR products of 445 bp of HOX 2C and 301 bp of HOX 4B were amplified in both tumor and normal samples of ten patients. Expressions of HOX 2C gene were observed in both tumor and normal samples of four patients and in only a tumor sample of one patient, while the expression was not observed in both tumor and normal samples of five patients. Expressions of HOX 4B gene were not observed in both tumor and normal samples of ten patients. In the present study, it was found that individuality seems to be important. The results of these two genes, observed in patients with colorectal cancer, should be taken into consideration for further researches.

Endothelial cells express a novel, tumor necrosis factor-alpha-regulated variant of HOXA9

The expression of the class 1 homeobox (HOX) family of "master control" transcription factors has been studied principally in embryogenesis and neoplasia in which HOX genes play a critical role in cell proliferation, migration, and differentiation. We wished to test whether HOX family members were also involved in a differentiation-like process occurring in normal, diploid adult cells, that is, cytokine-induced activation of endothelial cells (EC). Screening of a human EC cDNA library yielded several members of the A and B groups of HOX transcription factors. One clone represented a novel, alternatively spliced variant of the human HOXA9 gene containing a new exon and the expression of which was driven by a novel promoter. This variant termed HOXA9EC appeared restricted to cells of endothelial lineage, i.e. expressed by human EC from multiple sources, but not by fibroblasts, smooth muscle cells, or several transformed cell lines. HOXA9EC mRNA was rapidly down-regulated in EC in response to tumor necrosis factor-alpha due to an apparent reduction in transcriptional rate. Reporter construct studies showed that the 400 base pairs of genomic DNA directly 5' to the transcription initiation site of HOXA9EC contained the information required for both up-regulation in response to cotransfection with a HOXA9EC expression vector and tumor necrosis factor-alpha-dependent down-regulation of this gene. These results provide evidence of a novel HOX family member that may participate in either the suppression or the genesis of EC activation.

A differentially expressed prion gene mRNA is found in prion-infected mouse brains and in N2A cells but not in uninfected mice

The transmissible spongiform encephalopathies comprise a group of fatal neurodegenerative diseases that are characterized by the conversion of the normal host cellular prion protein (PrPC) to the abnormal protease-resistant isoform PrPSC. Distinct alterations of transcriptional regulation during disease progression could not be observed. The regulation of transcription 5' and 3' to the previously described cap sites of the prion gene mRNA as well as usage of internal short ORF's was investigated. We identified a mRNA species which is expressed differentially in prion-infected mice and in N2A cells. This mRNA is detectable neither in uninfected mice nor in early stages of the disease. The novel mRNA contains two short open reading frames which encode two small peptides with a calculated molecular weight of 2.1 kDA and 0.7 kDa. These peptides were also found to be expressed in vitro and in vivo.

Developmentally regulated Xist promoter switch mediates initiation of X inactivation

Developmental regulation of the mouse Xist gene at the onset of X chromosome inactivation is mediated by RNA stabilization. Here, we show that alternate promoter usage gives rise to distinct stable and unstable RNA isoforms. Unstable Xist transcript initiates at a novel upstream promoter, whereas stable Xist RNA is transcribed from the previously identified promoter and from a novel downstream promoter. Analysis of cells undergoing X inactivation indicates that a developmentally regulated promoter switch mediates stabilization and accumulation of Xist RNA on the inactive X chromosome.

Characterization and retinoic acid responsiveness of the murine Hoxd4 transcription unit

We have characterized the transcription unit of a murine Hox gene in the fourth paralogous group, Hoxd4. We have identified two Hoxd4 transcription start sites by S1 analysis. The upstream promoter (P2) is 5.2 kilobase pairs upstream from the coding region, while the downstream promoter (P1) is 1.1 kilobase pairs distant. Both promoters bear a cluster of start sites. Multiple transcripts were identified by Northern blot, originating from both promoters and multiple polyadenylation signals. Expression of P1 transcripts in the neural tube shows an anterior border at the rhombomere 6/7 boundary, corresponding to previous reports (Gaunt, S. J., Krumlauf, R., and Duboule, D. (1989) Development 107, 131-141; Morrison, A., Moroni, M. C., Ariza-McNaughton, L., Krumlauf, R., and Mavilio, F. (1996) Development 122, 1895-1907). A more posterior boundary in the central nervous system was observed for P2 transcripts. We observed strong expression up to somite 6 and weak expression in somite 5, correlating with the phenotype of Hoxd4 null mutant mice (Horan, G. S. B., Nagy Kovàcs, E., Behringer, R. R., and Featherstone, M. S. (1995) Dev. Biol. 169, 359-372). In response to retinoic acid, expression from P1 in the hindbrain was anteriorized after 4 or 24 h of treatment. P2 transcripts seemed to be less responsive and/or to have an indirect response to retinoic acid. The long 5'-untranslated region found in all Hoxd4 transcripts suggests that translation does not occur by a classical ribosome scanning mechanism.

HOXD4 and regulation of the group 4 paralog genes

From an evolutionary perspective, it is important to understand the degree of conservation of cis-regulatory mechanisms between paralogous Hox genes. In this study, we have used transgenic analysis of the human HOXD4 locus to identify one neural and two mesodermal 3′ enhancers that are capable of mediating the proper anterior limits of expression in the hindbrain and paraxial mesoderm (somites), respectively. In addition to directing expression in the central nervous system (CNS) up to the correct rhombomere 6/7 boundary in the hindbrain, the neural enhancer also mediates a three rhombomere anterior shift from this boundary in response to retinoic acid (RA), mimicking the endogenous Hoxd4 response. We have extended the transgenic analysis to Hoxa4 identifying mesodermal, neural and retinoid responsive components in the 3′ flanking region of that gene, which reflect aspects of endogenous Hoxa4 expression. Comparative analysis of the retinoid responses of Hoxd4, Hoxa4 and Hoxb4 reveals that, while they can be rapidly induced by RA, there is a window of competence for this response, which is different to that of more 3′ Hox genes. Mesodermal regulation involves multiple regions with overlapping or related activity and is complex, but with respect to neural regulation and response to RA, Hoxb4 and Hoxd4 appear to be more closely related to each other than Hoxa4. These results illustrate that much of the general positioning of 5′ and 3′ flanking regulatory regions has been conserved between three of the group 4 paralogs during vertebrate evolution, which most likely reflects the original positioning of regulatory regions in the ancestral Hox complex.

A conserved cluster of homeodomain binding sites in the mouse Hoxa-4 intron functions in Drosophila embryos as an enhancer that is directly regulated by Ultrabithorax

The evolutionary conservation of the homeodomains suggests that their in vivo DNA binding sites may also be conserved between vertebrates and invertebrates. The regulatory function of the mouse Hoxa-4 and Hoxb-4 introns were analyzed in Drosophila since they both contain a cluster of three homeodomain binding sites, the HB1 element, which was also found in the introns of other Hox genes ranging from fish to humans as well as in the Ultrabithorax (Ubx) and decapentaplegic (dpp) genes of Drosophila. The enhancer of the Hoxa-4 intron was found to respond to several homeobox genes activating a lacZ reporter gene in particular cells of the epidermis in Drosophila embryos. The enhancer activity was found to be similar to previously described autoregulatory elements of Deformed (Dfd), the Drosophila homolog of Hoxa-4, but additional expression was observed in more posterior segments activated by Ubx and repressed by abdominal-A (abd-A). Point mutations in the homeodomain binding sites in HB1 abolished the enhancer activity. A second site suppression experiment showed that UBX interacts directly with the HB1 element. When the HB1 element in the Hoxa-4 intron was replaced by that of the mesodermal enhancer of dpp, which was previously shown to be directly controlled by Ubx, Ubx-dependent activation was retained, but repression by abd-A was lost. The same result was obtained when the third binding site of HB1 was altered, suggesting that this site is responsible for abd-A-dependent repression. Finally, deletion of potential cofactor binding sites flanking the HB1 element that are also conserved in the medaka, chicken, and mouse genes revealed that they are important for enhancer function in Drosophila and that the Dfd-dependent and the Ubx-dependent expression requires different sites. The evolutionary and functional conservation of the HB1 elements indicates that not only the homeodomains but also some of their in vivo binding sites are conserved between vertebrates and invertebrates.

A sequence conserved in vertebrate Hox gene introns functions as an enhancer regulated by posterior homeotic genes in Drosophila imaginal discs

The intron of the mouse Hoxa-4 gene acts as a strong homeotic response element in Drosophila melanogaster leg imaginal discs. This activity depends on homeodomain binding sites present within a 30 bp conserved element, HB1, in the intron. A similar arrangement of homeodomain binding sites is found in many other potential homeotic target genes. HB1 activity in Drosophila imaginal discs is activated by Antennapedia and more posterior homeotic genes, but is not activated by more anterior genes. Testing a reporter gene construct with mutated binding sites in mouse embryos shows that HB1 is also active in the expression domains of posterior Hox genes in the mouse neural tube.

Improvement of the specific infectivity of the rubella virus (RUB) infectious clone: determinants of cytopathogenicity induced by RUB map to the nonstructural proteins

A plasmid, Robo102, which contains a cDNA copy of the rubella virus (RUB) genomic RNA from which infectious transcripts can be synthesized in vitro, was recently developed (C. Y. Wang, G. Dominguez, and T. K. Frey, J. Virol. 68:3550-3557, 1994). To increase the specific infectivity of Robo102 transcripts (approximately 5 plaques/10 microg of transcripts), a modified reverse transcription-PCR method was used to amplify nearly 90% of the RUB genome in three fragments, which were then used to replace the corresponding fragments in Robo102. Replacement of a fragment covering nucleotides (nt) 5352 to 9759 of the RUB genome yielded a construct, Robo202, which produced highly infectious transcripts (10(4) plaques/microg), indicating the presence of an unrecognized deleterious mutation (or mutations) in this region of the Robo102 cDNA. Robo102 was based on the w-Therien strain of RUB, which forms opaque plaques in Vero cells, while the PCR replacement fragments were generated from a variant, f-Therien, which produces clear plaques in Vero cells. Although Robo202 contains over 4,000 nt from f-Therien, Robo202 virus produces opaque plaques. However, when the other two PCR fragments amplified from f-Therien (nt 1 to 1723 and nt 2800 to 5352) were introduced into Robo202, the resulting construct, Robo302, yielded transcripts that produced a virus that formed clear plaques. This indicates that the determinants of plaque morphology map to the regions of the genome covered by these two fragments, both of which are in the nonstructural open reading frame. Generation of Robo202/302 chimeras indicated that the most 5' terminal fragment (nt. 1 to 1723) had the greatest effect on plaque morphology. The plaque morphology was correlated with the ability of the viruses to kill infected cells. The only difference at the molecular level detected among the viruses was that the more cytopathic viruses produced more nonstructural proteins than did the less cytopathic viruses. This finding, as well as the mapping of the genetic determinants to the region of the genome encoding these proteins, indicates that the nonstructural proteins can mediate cell killing.

Intron of the mouse Hoxa-7 gene contains conserved homeodomain binding sites that can function as an enhancer element in Drosophila

The 5' flanking sequences and the intron of the mouse Hoxa-7 gene were searched for regulatory elements that can function in Drosophila. Only the intron is able to activate a lacZ fusion gene in various tissues of Drosophila embryos. This enhancer function requires a cluster of three homeodomain binding sites (HB1-element) that are also found in the introns of other Hox genes as well as in a putative autoregulatory element of Ultrabithorax (Ubx), the Drosophila homolog of Hoxa-7. If a single binding site in the autoregulatory element of fushi tarazu (ftz) is replaced by the HB1-element of Hoxa-7, the expression pattern is altered and newly controlled by the homeotic gene caudal (cad). These data suggest that HB1 is a potential target for different homeodomain proteins of both vertebrates and invertebrates.

In vitro and transgenic analysis of a human HOXD4 retinoid-responsive enhancer

Expression of vertebrate Hox genes is regulated by retinoids in cell culture and in early embryonic development. We have identified a 185-bp retinoid-responsive transcriptional enhancer 5′ of the human HOXD4 gene, which regulates inducibility of the gene in embryonal carcinoma cells through a pattern of DNA-protein interaction on at least two distinct elements. One of these elements contains a direct repeat mediating ligand-dependent interaction with retinoic acid receptors, and is necessary though not sufficient for the enhancer function. The HOXD4 enhancer directs expression of a lacZ reporter gene in the neural tube of transgenic mouse embryos in a time-regulated and regionally restricted fashion, reproducing part of the anterior neuroectodermal expression pattern of the endogenous Hoxd-4 gene. Administration of retinoic acid to developing embryos causes alterations in the spatial restriction of the transgene expression domain, indicating that the HOXD4 enhancer is also a retinoid-responsive element in vivo. The timing of the retinoic acid response differs from that seen with more 3′ Hox genes, in that it occurs much later. This shows that the temporal window of competence in the ability to respond to retinoic acid differs between Hox genes and can be linked to specific enhancers. Mutations in the direct repeat or in a second element in the enhancer affect both retinoid response in culture and developmental regulation in embryos, suggesting that co-operative interactions between different factors mediate the enhancer activity. These data provide further support for a role of endogenous retinoids in regulation and spatial restriction of Hox gene expression in the central nervous system.

Characterization of the 3' untranslated region of the mouse homeobox gene HoxB5

The mouse pre-B cell line, 70Z/3, expresses multiple transcripts of the homeobox gene, HoxB5. We show here that this heterogeneity is due, at least in part, to the usage of alternative poly-A addition sites in the 3' untranslated region (UT) of the primary HoxB5 transcript. Furthermore, upon analysis of the subcellular distribution of the different HoxB5 RNA species, we found that the transcripts are present mainly in the nucleus, with two-to-five-fold less RNA present in the cytoplasm. These studies suggest that multiple post-transcriptional regulatory mechanisms are involved in the expression of HoxB5 RNA.

Multiple positive and negative regulatory elements in the promoter of the mouse homeobox gene Hoxb-4

Mouse Hoxb-4 (Hox-2.6) is a homeobox gene that belongs to a family which also includes Hoxa-4, Hoxc-4, and Hoxd-4 and that is related to the Deformed gene in Drosophila melanogaster. We have determined the sequence of 1.2 kb of 5' flanking DNA of mouse Hoxb-4 and by nuclease S1 and primer extension experiments identified two transcription start sites, P1 and P2, 285 and 207 nucleotides upstream of the ATG initiator codon, respectively. We have shown that this region harbors two independent promoters which drive CAT expression in several different cell lines with various efficiencies, suggesting that they are subject to cell-type-specific regulation. Through detailed mutational analysis, we have identified several cis-regulatory elements, located upstream and downstream of the transcription start sites. They include two cell-type-specific negative regulatory elements, which are more active in F9 embryonal carcinoma cells than in neuroblastoma cells (regions a and d at -226 to -186 and +169 to +205, respectively). An additional negative regulatory element has been delimited (region b between +22 and +113). Positive regulation is achieved by binding of HoxTF, a previously unknown factor, to the sequence GCCATTGG (+148 to +155) that is essential for efficient Hoxb-4 expression. We have also defined the minimal promoter sequences and found that they include two 12-bp initiator elements centered around each transcription start site. The complex architecture of the Hoxb-4 promoter provides the framework for fine-tuned transcriptional regulation during embryonic development.

Multiple positive and negative regulatory elements in the promoter of the mouse homeobox gene Hoxb-4

Mouse Hoxb-4 (Hox-2.6) is a homeobox gene that belongs to a family which also includes Hoxa-4, Hoxc-4, and Hoxd-4 and that is related to the Deformed gene in Drosophila melanogaster. We have determined the sequence of 1.2 kb of 5' flanking DNA of mouse Hoxb-4 and by nuclease S1 and primer extension experiments identified two transcription start sites, P1 and P2, 285 and 207 nucleotides upstream of the ATG initiator codon, respectively. We have shown that this region harbors two independent promoters which drive CAT expression in several different cell lines with various efficiencies, suggesting that they are subject to cell-type-specific regulation. Through detailed mutational analysis, we have identified several cis-regulatory elements, located upstream and downstream of the transcription start sites. They include two cell-type-specific negative regulatory elements, which are more active in F9 embryonal carcinoma cells than in neuroblastoma cells (regions a and d at -226 to -186 and +169 to +205, respectively). An additional negative regulatory element has been delimited (region b between +22 and +113). Positive regulation is achieved by binding of HoxTF, a previously unknown factor, to the sequence GCCATTGG (+148 to +155) that is essential for efficient Hoxb-4 expression. We have also defined the minimal promoter sequences and found that they include two 12-bp initiator elements centered around each transcription start site. The complex architecture of the Hoxb-4 promoter provides the framework for fine-tuned transcriptional regulation during embryonic development.

Construction of rubella virus genome-length cDNA clones and synthesis of infectious RNA transcripts

Plasmids containing a complete cDNA copy of the rubella virus (RUB) genomic RNA were constructed. Transfection into cell culture of genome-length RNA transcribed in vitro from one of these cDNA clones, Robo102, resulted in the production of virus which preserved the genetic and phenotypic characteristics of the parental virus from which the cDNA clone was derived. Prior to construction of the RUB genome-length cDNA clones, the 5'-terminal sequence of the RUB genomic RNA was determined to be 5'CAAUGG...3' following the cap structure. Analysis of the specific infectivity of RUB genomic RNA isolated from virions revealed that in Vero cells, the specific infectivity of RUB genomic RNA is roughly equivalent to that of Sindbis virus genomic RNA. In RUB virion RNA preparations, the subgenomic RNA was detected. It was demonstrated that subgenomic RNA was packaged into RUB virions; however, the presence of the subgenomic RNA was not essential for infectivity of the genomic RNA.

A proline-rich transcriptional activation domain in murine HOXD-4 (HOX-4.2)

The product of the murine Hoxd-4 (Hox-4.2) gene is a transcription factor that acts upon an autoregulatory element in Hoxd-4 upstream sequences (1). Using this activity as an assay in transient transfections of P19 embryonal carcinoma (EC) cells, we performed a mutational analysis to map functional domains in the HOXD-4 protein. The importance of the homeodomain was shown by a single amino acid change in this region that abolished activity. Deletion analysis revealed that many evolutionarily conserved regions outside of the homeodomain were dispensable for activation in our assay. Fusions to the GAL4 DNA-binding domain mapped a transcriptional activation function to the HOXD-4 proline-rich N-terminus. The proline-rich transcription factor AP2 squelched activation by HOXD-4 and by GAL4/HOXD-4 N-terminus fusion proteins. Together, these results suggest that HOXD-4 harbors a transcriptional activation domain of the proline-rich type.

Structure and differential expression of two distinct genes encoding the chloroplast elongation factor Tu in tobacco

We have isolated two nuclear genes, tufA and tufB, encoding chloroplast EF-Tu from a tobacco (Nicotiana sylvestris) genomic library. The tufA gene encodes a polypeptide of 478 amino-acid residues, consisting of a putative transit peptide of 70 residues and a mature EF-TuA of 408 residues. The tufB gene codes for a precursor proteins of 485 residues, containing a transit peptide of 77 residues and a mature EF-TuB of 408 residues. No introns were found in either gene. The sequence similarity within the coding regions of the two genes is 84.3% for nucleotides and 89.7% for amino acids. Multiple 5' ends of transcripts were observed for both tuf genes. Northern analysis revealed that the EF-Tu mRNA accumulated at least 30-fold more in leaf than in root tissue. Ribonuclease protection assays using gene-specific probes showed that the level of tufB mRNA is three-fold higher than that of tufA mRNA in leaves but in roots the tufB mRNA levels is less than half that of tufA mRNA. The relative amount of tufB mRNA is 30-fold higher in leaves than in roots whereas tufA messages are only five-fold higher in leaves. These data suggest that expression of both tuf genes is differentially regulated according to tissue and plastid type.

Regulation of the human HOXD4 gene by retinoids

Hox genes are developmentally regulated in mammalian embryogenesis, according to temporally and spatially restricted patterns which are affected by retinoids, vitamin A derivatives which have a function as, or at least mimic the action of, axis-specifying morphogens. In the human embryonal carcinoma cell line NT2/D1, HOX gene clusters are activated by at least two retinoids, all-trans- and 9-cis-retinoic acid (RA), in a 3' to 5' sequential cascade which reproduces the activation pattern observed in early embryogenesis. We have studied the regulation of the early activated HOXD4 gene, which is expressed in human embryogenesis in multiple transcripts generated by the developmentally controlled use of alternative transcription start sites and polyadenylation signals. Transfection of a 2.9 kb HOXD4 upstream genomic region linked to a reporter gene in NT2/D1 cells, allowed the identification of two different promoters and a distal enhancer element necessary for RA-dependent gene activation. This element confers to a heterologous promoter the ability to be induced by RA in NT2/D1 cells, and transactivated by alpha, beta and gamma retinoic acid receptors (RARs), but not retinoid X receptor (RXR), in COS-7 cells. DNase I footprinting analysis allowed the identification of four sequences which bind nuclear factors from both RA-induced NT2/D1 cells and embryonic tissues with similar patterns. The use of specific antibodies allowed the identification of at least RAR beta in some of the DNA-protein complexes, although the four sequences bind single RARs transfected in COS cells much less efficiently, or not at all, when compared to a canonical RAR responsive element. Induction of the HOXD4 promoter-enhancer in the presence of a selective RAR alpha antagonist indicated that the RAR alpha-dependent RAR beta activation is nevertheless a necessary step in HOX gene activation. Our results indicate that the ligand-dependent activity of RARs upon specific, cis-acting regulatory elements may have a key role in the induction of early activated HOX genes in response to retinoids. However, RARs represent only a fraction of the transcription factors interacting with the RA-responsive HOXD4 enhancer, which appears to be a complex element requiring specific combinations of nuclear factors for its proper function.

Identification of a retinoic acid response element upstream of the murine Hox-4.2 gene

Hox genes play an important role in the process of vertebrate pattern formation, and their expression is intricately regulated both temporally and spatially. All-trans-retinoic acid (RA), a physiologically active metabolite of vitamin A, affects the expression of a large number of Hox genes in vitro and in vivo. However, the regulatory mechanisms underlying the RA response of these genes have not been extensively studied, and no response element for RA receptors (RARs) has been characterized in a Hox regulatory region. The expression of murine Hox-4.2 and its human homolog, HOX4B, is increased in embryonal carcinoma (EC) cell lines upon RA treatment (M. S. Featherstone, A. Baron, S. J. Gaunt, M.-G. Mattei, and D. Duboule, Proc. Natl. Acad. Sci. USA 85:4760-4764, 1988; A. Simeone, D. Acampora, V. Nigro, A. Faiella, M. D'Esposito, A. Stornaiuolo, F. Mavilio, and E. Boncinelli, Mech. Dev. 33:215-228, 1991). Using transient expression assays, we showed that luciferase reporter gene constructs carrying genomic sequences located upstream of Hox-4.2 responded to RA in murine P19 EC cells. A 402-bp NcoI fragment was necessary for the RA responsiveness of reporter constructs. This fragment contained a regulatory element, 5'-AGGTGA(N)5AGGTCA-3', that closely resembles the consensus sequence for an RA response element. The Hox-4.2 RA response element was critical for the RA induction and specifically bound RARs. In addition, the response to RA could be inhibited by expressing a dominant negative form of RAR alpha in transfected P19 EC cells. These results suggested that Hox-4.2 is a target for RAR-mediated regulation by RA.

Expression of homeobox-containing genes in primary and metastatic colorectal cancer

Homeobox genes are a network of genes encoding nuclear proteins functioning as transcriptional regulators. Human and murine homeobox genes of the HOX family are organised in four clusters on different chromosomes. Gene order within each cluster is highly conserved, perhaps in direct relation to their expression. Homeobox genes have recently been involved in normal development and oncogenesis. We have analysed HOX gene expression in normal human colon and in primary and metastatic colorectal carcinomas. The majority of HOX genes are active in normal adult colon and their overall expression pattern is characteristic of this organ. Furthermore, the expression of some HOX genes is identical in normal and neoplastic colon indicating that these genes may exert an organ-specific function. In contrast, other HOX genes exhibit altered expression in primary colon cancers and their hepatic metastases which may suggest an association with colon cancer progression.

Identification of a retinoic acid response element upstream of the murine Hox-4.2 gene

Hox genes play an important role in the process of vertebrate pattern formation, and their expression is intricately regulated both temporally and spatially. All-trans-retinoic acid (RA), a physiologically active metabolite of vitamin A, affects the expression of a large number of Hox genes in vitro and in vivo. However, the regulatory mechanisms underlying the RA response of these genes have not been extensively studied, and no response element for RA receptors (RARs) has been characterized in a Hox regulatory region. The expression of murine Hox-4.2 and its human homolog, HOX4B, is increased in embryonal carcinoma (EC) cell lines upon RA treatment (M. S. Featherstone, A. Baron, S. J. Gaunt, M.-G. Mattei, and D. Duboule, Proc. Natl. Acad. Sci. USA 85:4760-4764, 1988; A. Simeone, D. Acampora, V. Nigro, A. Faiella, M. D'Esposito, A. Stornaiuolo, F. Mavilio, and E. Boncinelli, Mech. Dev. 33:215-228, 1991). Using transient expression assays, we showed that luciferase reporter gene constructs carrying genomic sequences located upstream of Hox-4.2 responded to RA in murine P19 EC cells. A 402-bp NcoI fragment was necessary for the RA responsiveness of reporter constructs. This fragment contained a regulatory element, 5'-AGGTGA(N)5AGGTCA-3', that closely resembles the consensus sequence for an RA response element. The Hox-4.2 RA response element was critical for the RA induction and specifically bound RARs. In addition, the response to RA could be inhibited by expressing a dominant negative form of RAR alpha in transfected P19 EC cells. These results suggested that Hox-4.2 is a target for RAR-mediated regulation by RA.

Differential DNA binding properties of three human homeodomain proteins

The products of three human homeobox containing (HOX) genes, 2C, 3C and 4B, were produced in insect cells using the Baculovirus expression system and purified to near homogeneity. In this system we observed that the DNA binding forms of the three proteins are not glycosylated. HOX 3C and 4B are phosphorylated in insect cells, while HOX 2C is not. The three HOX proteins bind to a DNA sequence known to be a target site for Antennapedia protein with a very similar affinity (Kd = 1-2 x 10(-9) M). We then measured their binding properties to four human sequences present in the HOX 3D, 4C, 1C and 4B promoters. Two of these sequences have been reported to be binding sites for HOX proteins. HOX 2C, 3C and 4B behaved quite differently, showing low affinity for promoters of genes located upstream from their own gene in the HOX clusters and a higher affinity for regulatory sequences of their own gene and downstream HOX genes.

HOX gene expression in normal and neoplastic human kidney

As a consequence of transformation, cancer cells generally lose some of their differentiative properties. Thus, alterations interfering with the genetic mechanisms required to maintain embryonic determination could lead to tumorigenesis. Homeobox genes are a network of genes encoding nuclear proteins containing DNA-binding homeodomains that are highly conserved throughout evolution. They are expressed in a stage-related fashion in the developing embryo and, in adult life, in normal tissues. In mice and humans, homeobox genes of the HOX family are organized in 4 clusters on different chromosomes which have presumably evolved by duplication of a primordial gene cluster. Strikingly, the order of genes within each cluster is also highly conserved throughout evolution, suggesting that the physical organization of HOX genes might be essential for their expression. Recent reports indicate that homeobox mutant mice display morphological abnormalities or show neoplastic alterations, and that growth factors can turn on homeobox genes. We have studied the expression of the Antennapedia-like HOX genes in normal human kidney and in renal carcinomas. The great majority of the HOX genes analyzed are expressed in a peculiar manner in normal kidney: blocks of genes, even entire HOX loci, are coordinately regulated. Alterations in HOX gene expression in renal carcinoma can be observed in 2 genes of the HOX-2 locus, HOX-2A and HOX-2E, which are actively expressed in normal kidney and silent in cancer biopsies. The HOX-3H gene is not expressed in normal kidney whereas the HOX-3H transcripts are present in renal carcinomas. Homeobox genes within the 4 HOX loci can be aligned on the basis of the maximal sequence homology of their homeodomains: this alignment defines 13 paralogous gene groups. In renal carcinomas, genes of group 10 (HOX-1D, 2F, 3E, 4B) display a marked difference in their transcript classes when compared to those of normal kidney. Our findings suggest an association between altered HOX gene expression and kidney cancer.

A human HOX4B regulatory element provides head-specific expression in Drosophila embryos

Like other homeobox genes of the Antennapedia and bithorax complexes (collectively called the HOM complex), the Drosophila Deformed (Dfd) gene has structural homologues in the Hox/HOX complexes of mouse and humans, one of which is human HOX4B (refs 3, 4). Previous experiments indicated that HOX4B protein can specifically activate the expression of the endogenous Dfd transcription unit in Drosophila embryos and larvae. We therefore asked whether HOX4B cis-regulatory elements could mimic the function of a Dfd autoregulatory element in Drosophila embryos. Here we show that a HOX4B upstream element can surprisingly provide expression in a posterior head segment of Drosophila. One possible mechanism for the axial position-specificity of the human element may involve the conservation of a Dfd-specific autoregulatory circuit in both arthropod and chordate lineages. This possibility is supported by the finding that a Drosophila Dfd autoregulatory element supplies spatially localized expression in the hindbrain of mouse embryos.

An analysis of vertebrate mRNA sequences: intimations of translational control

Five structural features in mRNAs have been found to contribute to the fidelity and efficiency of initiation by eukaryotic ribosomes. Scrutiny of vertebrate cDNA sequences in light of these criteria reveals a set of transcripts--encoding oncoproteins, growth factors, transcription factors, and other regulatory proteins--that seem designed to be translated poorly. Thus, throttling at the level of translation may be a critical component of gene regulation in vertebrates. An alternative interpretation is that some (perhaps many) cDNAs with encumbered 5' noncoding sequences represent mRNA precursors, which would imply extensive regulation at a posttranscriptional step that precedes translation.

Involvement of the Chox-4 chicken homeobox genes in determination of anteroposterior axial polarity during limb development

We have isolated and identified four chicken homeobox genes in the upstream region of the Chox-4 complex. The Chox-4g and -4f genes, at the 5' extremity of the complex, were expressed locally in the vicinity of the zone of polarizing activity (ZPA) at early stages of limb development, substantiating the involvement of the genes in anteroposterior axis determination. To confirm their function, we implanted a bead containing retinoic acid, or the ZPA itself, in the anterior margin of the limb bud, leading to formation of mirror-image duplicated digits, and observed the resultant change in gene expression. Expression of the Chox-4g and -4f genes was induced in the new digit-forming region. Those results suggest that positional information assigned by a ZPA morphogen is imprinted on cellular memory by expression of the Chox-4 genes to maintain positional signaling along the anteroposterior axis in the limb field.