Heterogeneity in the 5' untranslated region of mouse cytochrome cT mRNAs leads to altered translational status of the mRNAs

DDX3X, the X homologue of AZFa gene DDX3Y, expresses a complex pattern of transcript variants only in the male germ line

DDX3X, the functional X homologue of the major AZFa gene, DDX3Y, belongs to the highly conserved PL10-subfamily of DEAD-box RNA helicase genes which are functionally conserved from yeast to man. They are mainly involved in cell cycle control and translation initiation control of gene transcripts with long 5'UTR extensions containing complex secondary structures. Interestingly, in humans both gene copies were found to be expressed at different phases of human spermatogenesis. Whereas DDX3Y transcripts are translated only in premeiotic male germ cells, the DDX3X protein is expressed only in postmeiotic spermatids. In this study, we found that the major class of DDX3X transcripts in human testis become activated first after meiosis and at a specific core promoter not active in somatic tissues and not present upstream of the DDX3Y homologue. Two alternative 5'UTR transcript lengths are subsequently produced by an additional testis-specific 5'UTR splicing event. Both transcripts are mainly processed for polyadenylation in their proximal 3'UTR. A minor transcript class starting at the same male germ line-specific core promoter produces primary transcripts with an extremely long 3'UTR (∼ 17 kb), which is subsequently spliced at distinct sites resulting in six short 3'UTR splice variants (I-VI). Comparative analyses of the DDX3X transcripts in mouse and primates revealed that this complex pattern of male germ line-specific transcript variants first evolved in primates. Our data thus suggest complex translational control mechanism(s) for the human DDX3X gene locus functioning only in the male germ line and resulting in expression of its protein only in the postmeiotic spermatids.

Evolution of 5' untranslated region length and gene expression reprogramming in yeasts

The sequences of the untranslated regions (UTRs) of mRNAs play important roles in posttranscriptional regulation, but whether a change in UTR length can significantly affect the regulation of gene expression is not clear. In this study, we examined the connection between UTR length and Expression Correlation with cytosolic ribosomal proteins (CRP) genes (ECC), which measures the level of expression similarity of a group of genes with CRP genes under various growth conditions. We used data from the aerobic fermentation yeast Saccharomyces cerevisiae and the aerobic respiration yeast Candida albicans. To reduce statistical fluctuations, we computed the ECC for the genes in a Gene Ontology (GO) functional group. We found that in both species, ECC is strongly correlated with the 5' UTR length but not with the 3' UTR length and that the 5' UTR length is evolutionarily better conserved than the 3' UTR length. Interestingly, we found 11 GO groups that have had a substantial increase in 5' UTR length in the S. cerevisiae lineage and that the length increase was associated with a substantial decrease in ECC. Moreover, 9 of the 11 GO groups of genes are involved in mitochondrial respiration function, whose expression reprogramming has been shown to be a major factor for the evolution of aerobic fermentation. Finally, we found that an increase in 5' UTR length may decrease the +1 nucleosome occupancy. This study provides a new angle to understand the role of 5' UTR in gene expression regulation and evolution.

Translational control of the AZFa gene DDX3Y by 5'UTR exon-T extension

The human DEAD-box Y (DBY) RNA helicase (aka DDX3Y) gene is thought to be the major azoospermia factor a (AZFa) gene in proximal Yq11. Although it is transcribed in many tissues, the protein is expressed only in spermatogonia. In this study, we demonstrate that this translational control mechanism is probably germ cell-specific because of its association with expression of a distinct class of DDX3Y testis transcripts present only in pre- and post-meiotic male germ cells. They are initiated from a second distal DDX3Y promoter domain at two distinct start sites in the gene's 5' untranslated region (UTR) exon-T sequence. With the aid of an EGFP-3xFLAG reporter cassette cloned downstream of DDX3Y minigenes containing exons 1-4 and two different exon-T extensions, we discovered that DDX3Y translation is influenced by the presence of several ATG triplets located in exon-T, thus upstream of the main translational ATG start codon in exon 1. Strong translational repression of the DDX3Y minigene transcripts was observed when they contained the longest exon-T sequence with five upstream ATG triplets (uATGs). The potential formation of complex distinct stem-loop structures serve here as additional repressor element. Only minor translational attenuation was seen for the DDX3Y minigene transcripts when containing the shortest exon-T sequence, that is, starting at first transcriptional start site (coined 'T-TSS-I'). It was completely released after its single uATG was abolished by mutation. As we found DDX3Y transcripts with the longest exon-T sequence predominantly in spermatids, our results suggest that the amount of DDX3Y protein in pre-meiotic germ cells and its absence in post-meiotic germ cells are tightly controlled by the different extensions of exon-T in this germ cell-specific DDX3Y transcript class.

Novel testis-expressed profilin IV associated with acrosome biogenesis and spermatid elongation

A novel profilin, named profilin IV, was cloned and characterized as a testicular isoform, distinct from the previously described testis-specific profilin III. Profilin IV showed only 30% amino acid identity with the other mammalian profilins; nevertheless, database searches produced significant alignments with the conserved profilin domain. Northern blot analysis and in situ transcript hybridization suggested that profilin IV, like profilin III, is transcribed in the germ cells. However, the timing of their expression during post-natal development of rat testis and in the rat spermatogenetic cycle was distinct. In the human testis, profilin IV mRNA expression correlates with the presence of germ cells suggesting that it may be a suitable molecular diagnostic parameter to supplement conventional histopathological diagnostics in the assessment of testicular biopsies. The predicted profilin IV protein was verified employing an anti-oligopeptide antibody. Western blot analysis detected an immunorelated testicular protein of approximately 14 kDa. Immunohistochemistry revealed an intracellular protein of the rat, the mouse and the human testis accumulating asymmetrically in the cytoplasm of round and elongating spermatids with its perinuclear location coinciding with the position of the developing acrosome-acroplaxome and the manchette. Profilin IV thus may regulate testicular actin cytoskeleton dynamics and play a role in acrosome generation and spermatid nuclear shaping.

A possible meiotic function of the peculiar patterns of gene expression in mammalian spermatogenic cells

This review focuses on the striking differences in the patterns of transcription and translation in somatic and spermatogenic cells in mammals. In early haploid cells, mRNA translation evidently functions to restrict the synthesis of certain proteins, notably protamines, to transcriptionally inert late haploid cells. However, this does not explain why a substantial proportion of virtually all mRNA species are sequestered in translationally inactive free-messenger ribonucleoprotein particles (free-mRNPs) in meiotic cells, since most mRNAs undergo little or no increase in translational activity in transcriptionally active early haploid cells. In addition, most mRNAs in meiotic cells appear to be overexpressed because they are never fully loaded on polysomes and the levels of the corresponding protein are often much lower than the mRNA and are sometimes undetectable. A large number of genes are expressed at grossly higher levels in meiotic and/or early haploid spermatogenic cells than in somatic cells, yet they too are translated inefficiently. Many genes utilize alternative promoters in somatic and spermatogenic cells. Some of the resulting spermatogenic cell-altered transcripts (SCATs) encode proteins with novel functions, while others contain features in their 5'-UTRs, secondary structure or upstream reading frames, that are predicted to inhibit translation. This review proposes that the transcriptional machinery is modified to provide access to specific DNA sequences during meiosis, which leads to mRNA overexpression and creates a need for translational fine-tuning to prevent deleterious consequences of overproducing proteins.

Parathyroid hormone/parathyroid hormone-related peptide type 1 receptor in human bone

The parathyroid hormone/parathyroid hormone-related peptide (PTH/PTHrP) receptor (denoted as PTH-1R) is a key signaling factor through which calcium-regulating hormones PTH and PTHrP exert their effects on bone. There are contradictory reports regarding the capability of osteoclasts to express PTH-1R. To address this issue in humans, bone biopsy specimen samples from 9 normal controls and 16 patients with moderate to severe secondary renal hyperparathyroid bone disease (2 degrees HPT) with elevated PTH levels were studied to determine whether osteoclasts in the bone microenvironment express PTH-1R messenger RNA (mRNA) and protein. We report that osteoclasts express the PTH-1R mRNA but the protein is detected only in patients with 2 degrees HPT. The PTH-1R mRNA and protein also were found in osteoblasts, osteocytes, and bone marrow cells. Receptor expression was higher in osteoclasts and osteoblasts of patients with 2 degrees HPT than normal controls (98.0 +/- 1.1% vs. 65.7 +/- 14.3% and 65.8 +/- 3.4% vs. 39.1 +/- 6.2%; p < 0.01, respectively). Approximately half of osteoclasts found in bone of patients with 2 degrees HPT have the PTH-1R protein. In patients with 2 degrees HPT, a positive relationship exists between erosion depth, a parameter of osteoclastic activity, and the percentage of osteoclasts with PTH-1R protein (r = 0.58; p < 0.05). In normal controls, an inverse relationship exists between the percentage of osteoblasts with receptor mRNA, mRNA signals/cell, and serum PTH levels (r = -0.82 and p < 0.05 and r = -0.78 and p < 0.01, respectively). The results provide the novel evidence of PTH-1R in human osteoclasts and suggest a functional role for the receptors in 2 degrees HPT.

Calcitonin and calcitonin receptors: bone and beyond

Calcitonin (CT), a 32 amino acid peptide hormone produced primarily by the thyroid, and its receptor (CTR) are well known for their ability to regulate osteoclast mediated bone resorption and enhance Ca2+ excretion by the kidney. However, recent studies now suggest that CT and CTRs may play an important role in a variety of processes as wide ranging as embryonic/foetal development and sperm function/physiology. In this review article, CT and CTR gene transcription, signal transduction and function are addressed. The effects of CT on the physiology of a variety of organ systems are discussed and the relationship between polymorphisms in the CTR gene and bone mineral density (BMD)/osteoporosis is examined. Recent studies demonstrating the ability of receptor activity modifying proteins (RAMPs) to post-translationally modify the calcitonin receptor-like receptor (CRLR) are detailed and studies employing transgenic mouse technology to determine the temporal and tissue specific transcriptional activity of the CTR gene in vivo are discussed.

Expression of lactate dehydrogenases A and B during chicken spermatogenesis: characterization of testis specific transcripts

The substrates required for glycolysis change markedly at successive stages of spermatogenesis suggesting a considerable plasticity in the expression of glycolytic enzymes. Lactate dehydrogenase (LDH) isoenzymes, LDH-A and LDH-B, are expressed in premeiotic, meiotic cells, and early spermatids, both in avian and mammalian spermatogenesis. Highly polyadenylated forms, particularly of LDH-A, were detected in chicken testis. While mammals and columbid birds express the testis specific LDH-C gene in meiotic and postmeiotic cells, several LDH-B testis specific transcripts were detected in the corresponding cells during chicken spermatogenesis. These testis specific transcripts and the mRNA of mammalian LDH-C show several properties in common, such as temporal correlation of expression, mRNA stability, and repression of premature translation. These observations suggest that the testis specific transcripts could perform during chicken spermatogenesis the functions of the LDH-C mRNA in mammalian testis.

Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals

PHTF1 (putative homeodomain transcriptional factor; HGMW-approved symbol PHTF1) is a putative homeobox gene located at band 1p11-p13 of the human genome. We report here the cloning and sequencing of its mouse and Drosophila orthologs. The conservation between mouse and human proteins extends over the entire protein and is localized at the putative homeodomain and at the N- and C-terminal regions of Drosophila protein sequence. Blast searches allowed us to identify another member of the PHTF family, PHTF2, located at 7q11.23-q21 of the human genome. The strongest homologies between human PHTF1 and PHTF2 are localized to the domains that we already described in Drosophila, i.e., the putative homeodomain and the N- and C-terminal regions. The human and mouse genes display 98% similarity to one another, 56% similarity with the Drosophila gene, and 67% similarity with PHTF2, suggesting that phtf might define a novel gene family of highly divergent homeobox genes. Finally, Northern blot analysis showed that while PHTF1 is expressed mainly in testis, PHTF2 is predominantly expressed in muscle, suggesting that these two genes may have acquired different functions after their duplication and divergence.

Expression of the gene for mitoribosomal protein S12 is controlled in human cells at the levels of transcription, RNA splicing, and translation

The human gene RPMS12 encodes a protein similar to bacterial ribosomal protein S12 and is proposed to represent the human mitochondrial orthologue. RPMS12 reporter gene expression in cultured human cells supports the idea that the gene product is mitochondrial and is localized to the inner membrane. Human cells contain at least four structurally distinct RPMS12 mRNAs that differ in their 5'-untranslated region (5'-UTR) as a result of alternate splicing and of 5' end heterogeneity. All of them encode the same polypeptide. The full 5'-UTR contains two types of sequence element implicated elsewhere in translational regulation as follows: a short upstream open reading frame and an oligopyrimidine tract similar to that found at the 5' end of mRNAs encoding other growth-regulated proteins, including those of cytosolic ribosomes. The fully spliced (short) mRNA is the predominant form in all cell types studied and is translationally down-regulated in cultured cells in response to serum starvation, even though it lacks both of the putative translational regulatory elements. By contrast, other splice variants containing one or both of these elements are not translationally regulated by growth status but are translated poorly in both growing and non-growing cells. Reporter analysis identified a 26-nucleotide tract of the 5'-UTR of the short mRNA that is essential for translational down-regulation in growth-inhibited cells. Such experiments also confirmed that the 5'-UTR of the longer mRNA variants contains negative regulatory elements for translation. Tissue representation of RPMS12 mRNA is highly variable, following a typical mitochondrial pattern, but the relative levels of the different splice variants are similar in different tissues. These findings indicate a complex, multilevel regulation of RPMS12 gene expression in response to signals mediating growth, tissue specialization, and probably metabolic needs.

A novel calcitonin receptor gene in human osteoclasts from normal bone marrow

The calcitonin receptor (CTR) gene in human osteoclasts formed in a human bone marrow cell culture system was examined by reverse transcription-polymerase chain reaction (RT-PCR). The RT-PCR results indicated that the 5'-untranslated region (5'UTR) was different between CTR mRNAs in human osteoclasts and in a mammary tumor cell line, MCF-7 cells. We isolated the 5'UTR of the CTR gene from human osteoclasts, whose sequence had only 28.6% identity with that of other CTR genes reported until now. In a radioligand binding assay, COS-1 cells transfected with the osteoclast CTR gene bound to [125I]human CT (hCT). These results provided evidence that the CTR gene cloned from human osteoclasts was expressed functionally and its coding protein was identical to MCF-7 cell CTR.

The mouse Tsx gene is expressed in Sertoli cells of the adult testis and transiently in premeiotic germ cells during puberty

Tsx is a gene of unknown function that was previously shown to be expressed specifically in the testis. In order to gain insight into the function of Tsx its pattern of expression was characterized with regard to both timing and cell type in the testis. Northern blot analysis of early postnatal testes showed not only that Tsx message was detectable shortly after birth, but that it increased substantially between 7 and 12 days postpartum (dpp), roughly coincident with the onset of meiosis in the mouse. Alternative Tsx transcripts, detected by RT-PCR, included a spliced form that first appeared at around 12 dpp. In situ hybridization revealed Tsx signal in the somatic Sertoli cells of the adult testis. Consistent with the data from Northern blots, in situ hybridization signal was first detectable in normal pubertal testes at 12 dpp. An anti-Tsx polyclonal antiserum specifically stained premeiotic germ cells in addition to Sertoli cells of pubertal testes at 16, 19, and 27 dpp. Tsx immunostaining in germ cells was nuclear, while Sertoli cells displayed signal throughout the cytoplasm and nucleus. In the adult, Tsx was detected exclusively in Sertoli cells. In contrast, in the adult testis of the oligotriche (olt) mutant, where spermatogenesis is blocked after meiosis, Tsx protein was still present in the spermatogonial nuclei of a subset of tubules. Taken together, these results demonstrate that Tsx expression is induced in both premeiotic germ cells and Sertoli cells during the first wave of spermatogenesis, but that expression is maintained at a detectable level only in Sertoli cells of the normal adult. The persistence of Tsx expression seen in spermatogonia of the adult olt mutant supports the hypothesis that during the first wave of normal spermatogenesis, the advent of a late-stage cell type, either elongating spermatid or spermatozoan, is responsible for extinguishing expression in spermatogonia in normal adult testis. To our knowledge, Tsx is the first gene to show a pattern of germ cell expression that is apparently specific to the pubertal testis.

Distal V beta promoters transcribe novel T-cell receptor-beta transcripts in early development

The transcriptional activation of germline T-cell receptor (TCR) and immunoglobulin (Ig) genes has been proposed to promote the rearrangement of these genes. Here we report the identification of distal TCR promoters (PDs), located upstream of the previously characterized promoters in the mouse V beta 5.1 and V beta 8.1 gene segments, that are active in germline TCR genes in fetal thymus and liver in vivo. We also identified an immature T-cell clone, SL12.4, that expresses both endogenous and transfected PDs in a regulated manner in vitro. We propose that the transcription of these distal promoters in germline TCR genes may be important for inducing TCR gene rearrangements during T-cell development. Northern blot, RNase protection and reverse transcription-polymerase chain reaction (RT-PCR) analyses demonstrated that PDs are also transcribed from fully rearranged TCR genes in adult thymus, lymph node, and spleen. Although the functional significance of this expression is not known, our sequence analysis of the 5' leader in PD-derived V beta 5.1 and V beta 8.1 transcripts revealed the presence of several open reading frames (ORFs) that may encode novel polypeptides or regulate the efficiency of TCR beta translation.

Control of the translational efficiency of beta-F1-ATPase mRNA depends on the regulation of a protein that binds the 3' untranslated region of the mRNA

The expression of the nucleus-encoded beta-F1-ATPase gene of oxidative phosphorylation is developmentally regulated in the liver at both the transcriptional and posttranscriptional levels. In this study we have analyzed the potential mechanisms that control the cytoplasmic expression of beta-F1-ATPase mRNA during liver development. Remarkably, a full-length 3' untranslated region (UTR) of the transcript is required for its efficient in vitro translation. When the 3' UTR of beta-F1-ATPase mRNA is placed downstream of a reporter construct, it functions as a translational enhancer. In vitro translation experiments with full-length beta-F1-ATPase mRNA and with a chimeric reporter construct containing the 3' UTR of beta-F1-ATPase mRNA suggested the existence of an inhibitor of beta-F1-ATPase mRNA translation in the fetal liver. Electrophoretic mobility shift assays and UV cross-linking experiments allowed the identification of an acutely regulated protein (3'betaFBP) of the liver that binds at the 3' UTR of beta-F1-ATPase mRNA. The developmental profile of 3'betaFBP parallels the reported changes in the translational efficiency of beta-F1-ATPase mRNA during development. Fractionation of fetal liver extracts revealed that the inhibitory activity of beta-F1-ATPase mRNA translation cofractionates with 3'-UTR band-shifting activity. Compared to other tissues of the adult rat, kidney and spleen extracts showed very high expression levels of 3'betaFBP. Translation of beta-F1-ATPase mRNA in the presence of kidney and spleen extracts further supported a translational inhibitory role for 3'betaFBP. Mapping experiments and a deletion mutant of the 3' UTR revealed that the cis-acting element for binding 3'betaFBP is located within a highly conserved region of the 3' UTR of mammalian beta-F1-ATPase mRNAs. Overall, we have identified a mechanism of translational control that regulates the rapid postnatal differentiation of liver mitochondria.

Cloning and characterization of the promoter regions of the human parathyroid hormone (PTH)/PTH-related peptide receptor gene: analysis of deoxyribonucleic acid from normal subjects and patients with pseudohypoparathyroidism type 1b

Expression of the PTH/PTH-related peptide (PTHrP) receptor (PTHR) in the mouse is controlled by at least two promoters. The downstream promoter (P2) is ubiquitously expressed, whereas expression of the upstream promoter (P1) is largely restricted to kidney. These observations may provide a genetic basis for a human PTH resistance syndrome, pseudohypoparathyroidism type 1b (PHP1b), in which renal, but not osseous, signaling by PTH is defective. We, therefore, cloned and characterized the 5'-end of the human PTHR gene and found that its organization is very similar to that of the mouse. Transcription initiation sites of human P1 and P2 promoters are in similar, but not identical, positions to those of the mouse gene. The identification of a human P2 promoter is significant because no P2-specific human PTHR complementary DNAs have been isolated to date. Southern analysis of genomic DNA from seven PHP1b patients did not reveal any rearrangements in proximal promoter regions or exons encoding 5'-untranslated region sequences. No significant sequence differences were found in clones of normal and patient DNAs encompassing proximal promoter sequences, and untranslated region and signal sequence exons. Thus, in the seven PHP1b patients analyzed, no defects were identified that would influence initiation site selection, stability, or splicing of renal PTHR transcripts. These data indicate that the genetic defect(s) in PHP1b in these patients lies in distal enhancer elements of the gene, in an essential transcriptional regulator, or in some as yet unidentified cofactor required for renal PTH signaling.

Heat-shock inducible polyubiquitin gene UbI undergoes alternative initiation and alternative splicing in mature chicken testes

Ubiquitin, a heat-shock protein highly expressed during spermatogenesis, plays an essential role in the differentiation of the germinal cells, particularly in the structural changes of chromatin taking place at the end of the process. To shed light on the mechanisms that modulate transcriptional activity of the heat-shock inducible polyubiquitin gene UbI during spermatogenesis and stabilize the message when transcription is not longer active, we have compared the characteristics of UbI transcripts in mature and immature testes and somatic cells. In mature chicken testes, transcription starts at a site placed closer to the heat-shock promoters than in somatic tissues. This site is upstream from the TATA box used in somatic cells. In addition, UbI transcript undergoes an alternative splicing that produces a longer 5' untranslated region in mature testis. These findings may provide a basis for the observed increase in expression of UbI in mature chicken testes and for the stability of the message when transcription ceases at the end of spermatogenesis.

The Pem homeobox gene. Androgen-dependent and -independent promoters and tissue-specific alternative RNA splicing

The Pem gene encodes an atypical homeodomain protein, distantly related to Prd/Pax family members, that we demonstrate is regulated in a complex transcriptional and post-transcriptional manner. We show that the rat Pem genomic structure includes three 5'-untranslated (5'-UT) exons and four coding exons, three of which encode the homeodomain. Several alternatively spliced transcripts were identified, including one that skips an internal coding exon, enabling this mRNA to express a novel form of the Pem protein. Other alternatively spliced mRNAs were characterized that possess different 5'-UT regions, including a muscle-specific transcript. The different 5'-UT termini present in Pem transcripts conferred different levels of translatability in vitro. Two promoters containing multiple transcription initiation sites were identified: a distal promoter (Pd) in the first 5'-UT exon and a proximal promoter (Pp) located in the "intron" upstream of the first coding exon. The Pd was active in placenta, ovary, tumor cell lines, and to a lesser extent in skeletal muscle. In contrast, transcripts from the Pp were only detectable in testis and epididymis and were only expressed in epididymis in the presence of testosterone. To our knowledge no transcription factors have previously been identified that exhibit androgen-dependent expression in the epididymis.

Regulation of gene expression for translation initiation factor eIF-2 alpha: importance of the 3' untranslated region

Gene expression of the alpha-subunit of eukaryotic initiation factor-2 (eIF-2 alpha), involves transcriptional and post-transcriptional mechanisms. eIF-2 alpha is a single-copy gene expressing two mRNAs, 1.6 and 4.2 kb in size. Cloning and sequencing of the cDNA for the 4.2 kb mRNA revealed that it is the result of alternative polyadenylation site selection. Four polyadenylation sites were identified within the 3' untranslated region (UTR) of eIF-2 alpha, only two of which are normally utilized in human and mouse tissues. A functional role for the extended 3' UTR was assessed by comparing the translatability and stability of the 1.6 and 4.2 kb mRNAs. Both the 1.6 and 4.2 kb transcripts could be translated in vitro and were identified in vivo as being distributed on large polyribosomes. This indicates that both mRNAs are efficiently translated. Stability studies showed that in activated T-cells the 4.2 kb mRNA was more stable than the 1.6 kb mRNA. Polyadenylation site selection and mRNA stability differ for the two mRNAs of eIF-2 alpha. These activities might be modulated by sequence elements contained within the untranslated regions of the eIF-2 alpha gene.