Alternative 3' processing of Xenopus alpha-tubulin mRNAs; efficient use of a CAUAAA polyadenylation signal

Modeling of Genome-Wide Polyadenylation Signals in Xenopus tropicalis

Alternative polyadenylation (APA) is an important post-transcriptional modification event to process messenger RNA (mRNA) for transcriptional termination, transport, and translation. In the present study, we characterized poly(A) signals in Xenopus tropicalis using 70,918 highly confident poly(A) sites derived from 16,511 protein-coding genes to understand their roles in the regulation of embryo development and gender difference. We examined potential factors, including the gene length, the number of introns in a gene, and the intron length, that may affect the prevalence of APA. We observed 12 prominent poly(A) signal patterns, which accounted for approximately 92% of total APA sites in Xenopus tropicalis. Among them, three patterns are specific to X. tropicalis, so they are absent in other animals such as humans or mice. We catalogued APA sites based on their genomic regions and developed a bioinformatics pipeline to identify over-represented signal patterns for each class. Then the schema of cis elements for APA sites in each genomic region was proposed. More importantly, APA usage is dramatically dynamic in embryos along five developmental stages and well-coordinated with the maternal-to-zygotic transition event. We used an entropy-based method to identify developmental stage-specific APA sites and identified significant signal patterns around specific sites and constitutive sites. We found that the APA frequency in different genomic regions varies with developmental stages and that those sites located in intron or coding sequence regions contribute most to the dynamics of gene expression during developmental stages. This study deciphers the characteristics and poly(A) signal patterns for both canonical APA sites and non-canonical APA sites across different developmental stages and gender dimorphisms in X. tropicalis, providing new insights into the dynamic regulation of distal and proximal APA.

Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis

RNA alternative polyadenylation contributes to the complexity of information transfer from genome to phenome, thus amplifying gene function. Here, we report the first X. tropicalis resource with 127,914 alternative polyadenylation (APA) sites derived from embryos and adults. Overall, APA networks play central roles in coordinating the maternal-zygotic transition (MZT) in embryos, sexual dimorphism in adults and longitudinal growth from embryos to adults. APA sites coordinate reprogramming in embryos before the MZT, but developmental events after the MZT due to zygotic genome activation. The APA transcriptomes of young adults are more variable than growing adults and male frog APA transcriptomes are more divergent than females. The APA profiles of young females were similar to embryos before the MZT. Enriched pathways in developing embryos were distinct across the MZT and noticeably segregated from adults. Briefly, our results suggest that the minimal functional units in genomes are alternative transcripts as opposed to genes.

Regulatory role of the 3' untranslated region (3'UTR) of rat 5' deiodinase (D1). effects on messenger RNA translation and stability

The previous findings that both a long and a short type 1 deiodinase (D1) mRNA are present in different tissues and that the D1 gene contains two potential polyA signals suggest that the two mRNAs result from differential polyA signal usage. In this study, we examined the properties of the two D1 mRNAs generated in HEK 293 cells by the alternative use of each of the poly A signals in order to ascertain the potential regulatory role of the 3'UTR of this gene. Our results showed that the long mRNA is less stable, but that it is translated more efficiently than the short mRNA. The net result of these differences is a higher D1 activity with the long message. These data suggest that the D1 3'UTR may play an important role in regulating the stability and translational efficiency of the D1 mRNA, both of which could be physiologically relevant when the demand for D1 activity is high.

Myxobolus cerebralis: identification of a cathepsin Z-like protease gene (MyxCP-1) expressed during parasite development in rainbow trout, Oncorhynchus mykiss

Cysteine proteases are essential to the biological function of parasitic organisms and are gaining interest as the target of chemotherapeutics aimed at their control. We report a cysteine protease gene from the myxozoan Myxobolus cerebralis, the cause of whirling disease in salmonid fish. The mature gene (MyxCP-1) encodes a 248-amino acid polypeptide that includes catalytic residues similar to the papain family of cysteine proteases. MyxCP-1 features a propeptide region and sequence insertions that are characteristics of cathepsin Z proteases. Phylogenetic comparisons of M. cerebralis to other eukaryotes based on full-length cathepsin-like genes show that MyxCP-1 is the earliest lineage in the cathepsin Z group and separated from cathepsin L, B, and C-like proteases. Using TaqMan PCR differential levels of transcription of the cathepsin Z-like protease were found in earlier and later developmental stages of the parasite in experimentally infected rainbow trout (Oncorhynchus mykiss).

Patterns of variant polyadenylation signal usage in human genes

The formation of mature mRNAs in vertebrates involves the cleavage and polyadenylation of the pre-mRNA, 10-30 nt downstream of an AAUAAA or AUUAAA signal sequence. The extensive cDNA data now available shows that these hexamers are not strictly conserved. In order to identify variant polyadenylation signals on a large scale, we compared over 8700 human 3' untranslated sequences to 157,775 polyadenylated expressed sequence tags (ESTs), used as markers of actual mRNA 3' ends. About 5600 EST-supported putative mRNA 3' ends were collected and analyzed for significant hexameric sequences. Known polyadenylation signals were found in only 73% of the 3' fragments. Ten single-base variants of the AAUAAA sequence were identified with a highly significant occurrence rate, potentially representing 14.9% of the actual polyadenylation signals. Of the mRNAs, 28.6% displayed two or more polyadenylation sites. In these mRNAs, the poly(A) sites proximal to the coding sequence tend to use variant signals more often, while the 3'-most site tends to use a canonical signal. The average number of ESTs associated with each signal type suggests that variant signals (including the common AUUAAA) are processed less efficiently than the canonical signal and could therefore be selected for regulatory purposes. However, the position of the site in the untranslated region may also play a role in polyadenylation rate.

Cloning and characterization of Gallus and Xenopus ferrochelatases: presence of the [2Fe-2S] cluster in nonmammalian ferrochelatase

Ferrochelatase (EC 4.99.1.1) catalyzes the insertion of ferrous iron into protoporphyrin IX to form protoheme IX. This membrane-bound enzyme has been cloned from a variety of bacteria, plants, mammals, and yeast. Interestingly, only in mammals has the enzyme been found to contain a [2Fe-2S] cluster. Since the presence of this feature only in mammals would have significant evolutionary implications and because there have been no nonmammalian animal ferrochelatases cloned, expressed, and characterized, we report here the cloning and characterization of ferrochelatase from chicken (Gallus gallus) and an amphibian (Xenopus laevis). The cDNAs for both of these ferrochelatases were cloned by complementation of an Escherichia coli DeltahemH strain. The expressed and purified enzymes were characterized biochemically and both were found to contain [2Fe-2S] clusters. These clusters have spectral characteristics essentially identical to those of human ferrochelatase, although their EPR spectra are recognizably distinct from the human one. The [2Fe-2S] clusters of both chicken and amphibian ferrochelatases are readily destroyed by NO. Sequence analysis of the 3' UTR of both chicken and amphibian cDNAs show that while both have poly(A) tails neither have a consensus polyadenylation signal. The 5' UTR of Xenopus as isolated contained 135 bp and possesses no identifiable stem-loop structure.

Stimulation of RNA 3' processing by flanking DNA in Xenopus oocytes

We have previously shown that the second poly(A) signal of the Xenopus laevis alpha-tubulin gene X alpha T14, which contains the rare hexanucleotide CAUAAA, requires a surprisingly large amount of 3' flanking DNA to be used efficiently in Xenopus oocytes. To investigate the nature of the interaction between the X alpha T14 3' flank and upstream 3' processing sites, we have developed a modified oocyte assay based on the stimulation of processing at a single poly(A) signal. We mutated both the hexanucleotide and GU/U-rich components of a strong synthetic poly(A) signal (SPA) in order to weaken it severely. We found that efficient use of the mutant signal could be fully restored by the addition of 1.2 kb of X alpha T14 3' flank, but only in its natural orientation. Functional dissection of the X alpha T14 3' flank defined two separate regions that were each capable of partially restoring processing efficiency, presumably because they contain multiple, relatively weak processing enhancers. We discuss how the stimulation of 3' processing by flanking regions in oocytes could be explained by mechanisms that operate on the processing machinery directly or by indirect effects mediated by transcriptional pausing.

Organization and expression of bovine TSPY

We have isolated genomic sequences as well as transcripts from the bovine homolog of the human testis-specific protein, Y-encoded, TSPY which-in both species-is located on the Y Chromosome (Chr), organized as a gene family with a variable number of members, and expressed exclusively in the testis. 1266 bp of bovine TSPY specific sequence have been isolated from a testis cDNA library, by RT-PCR analyses and by Rapid Amplification of cDNA Ends (RACE). A bovine TSPY gene 4 is organized in seven exons, and transcripts are polyadenylated at various 3' ends. Consensus polyadenylation signals AAUUAAA are missing. Microheterogeneous sequence variation is found between TSPY family members. In addition, homologies to other Y-located repeated sequence families, BRY, have been discovered; these sequences are presumably derived from ancient members of the TSPY cluster, now forming a separate, probably nonfunctional subfamily. Bovine TSPY is subject to differential splicing. In the adult, it is expressed in early germ-cell stages, and expression could also be detected in fetal testis. Comparison with the human homolog shows the highest degree of similarity in the coding regions of exons 2, 3, and 4, which are also precisely conserved regarding their length.

Genes encoding isoforms of transcription elongation factor TFIIS in Xenopus and the use of multiple unusual RNA processing signals

We have identified cDNAs encoding three related forms of transcription elongation factor TFIIS (S-II) in Xenopus laevis ovary. Comparison of Xenopus and mammalian sequences identifies likely diagnostic amino acids that distinguish classes of vertebrate TFIIS. The diversity of TFIIS polypeptides in Xenopus is due partly to the presence of two diverged genes in this tetraploid genome. We isolated genomic clones containing one of the genes, xTFIIS.oA, and, unlike a previously described vertebrate TFIIS gene, found that it contains introns. Alternative splicing at a CAG/CAG motif containing the 3' splice site of intron 4 produces the third form of xTFIIS, which differs from one of the others simply in lacking Ser109. Intron 6 of xTFIIS.oA contains splice and branch site consensus sequences conforming to those of the minor class of AT-AC introns and this was confirmed for the homeologous xTFIIS.oB gene by genomic PCR. Other unusual but functional variants of RNA processing signals were found in xTFIIS genes at the 5' splice site of intron 8 and the polyadenylation hexanucleotides. Utilization of multiple unusual processing signals may make the generation of mature xTFIIS.o mRNAs inefficient and the possible regulatory consequences of this are discussed.

Transcription of c-mos protooncogene in the pig involves both tissue-specific promoters and alternative polyadenylation sites

The function of the c-mos gene has been intensively studied, but its role in the mammal is still a subject for debate. For this reason, and because the gene is regulated posttranscriptionally, further study of the gene from other mammalian species is timely. The pig c-mos gene has been cloned, and the genomic sequence is presented here. The gene has no introns and shows close similarity to human and monkey genes, with striking sequence similarities in both the 5' and 3' flanking regions. The significance of this similarity in the context of gene regulation is discussed. c-mos expression was found to be restricted to gonadal tissues in the pig. The major start sites for transcription initiation in ovary and testis were identified by primer extension and found to be distinct, as in the mouse. Within the ovary, expression is confined to oocytes. Messenger RNA is synthesized in growing oocytes, and remains stable during oocyte maturation, but begins to be degraded in electrically stimulated eggs. Unexpectedly, RNase protection assays revealed that the 3' ends of transcripts in the pig ovary are heterogeneous, and this, together with the identification of three distinct cDNA clones, shows that multiple polyadenylation sites are used. The significance of these transcripts in terms of translational control is discussed.

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.

Human CuZn superoxide dismutase enzymatic activity in cells is regulated by the length of the mRNA

Single functional human CuZnSOD gene encodes two species of mRNA differing in size by 200 nucleotides in the 3'-untranslated region (UTR). We studied the expression of the CuZnSOD cDNA with different 3'- and 5'-UTR. Deletion in the 5'-end does not affect the expression of the enzyme, however, deletion in the 3'-UTR decreases the level of expression of CuZnSOD. The plasmids containing the long CuZnSOD cDNA with all polyadenylation signal sequences utilize primarily the last polyadenylation site and give a long mRNA, which produces three times more enzyme than the short mRNA lacking the last polyadenylation site and the AU-rich region.

Tissue specific expression and cDNA structure of a human transcript encoding a nucleic acid binding [oligo(dC)] protein related to the pre-mRNA binding protein K

In human cells at least 20 different proteins or groups of proteins have been identified that are associated with hnRNAs. These proteins (designated A1-U) are highly abundant in the nucleus. In this study, we present the sequence of a novel cDNA clone, sub2.3, isolated from a human lymphocyte cDNA library. The predicted amino acid sequence shows homology to repeated domains in the human hnRNA binding protein K (hnRNP K), which are believed to be of functional importance. hnRNP K is among the major oligo(rC/dC) binding proteins in vertebrate cells and we show here that the protein product of sub2.3 also binds to oligo(dC). This is shown by a novel approach where we demonstrated specific binding of in vitro translated sub2.3 protein to biotinylated oligo(dC) which was immobilized on magnetic streptavidin-coated Dynabeads. Moreover we found that the sub2.3 transcript is expressed in a tissue dependent manner with the highest expression observed in several lymphoid tissues and skeletal muscle. The gene was also abundantly expressed in several lymphoid cell lines and the hepatoma cell line HepG2 while a low expression was observed in the HL60 myeloid cell line and in the HeLa cervical carcinoma cell line. In conclusion, this study presents the cDNA sequence of a novel transcript which shows tissue specific expression and encodes a protein with oligo(dC) binding specificity in vitro.

Xl-fli, the Xenopus homologue of the fli-1 gene, is expressed during embryogenesis in a restricted pattern evocative of neural crest cell distribution

The Xenopus laevis fli cDNA, belonging to the ets family of transcription factors, was isolated from a library prepared from unfertilized eggs. It encodes a polypeptide with extensive homology to murine and human Fli proteins. The long 3'-untranslated region contains five nuclear polyadenylation signals and three cytoplasmic polyadenylation elements, as well as many A/T rich elements. Two polyadenylated transcripts appear at the early neurula and accumulate up to the tadpole stage. In situ hybridization reveals an expression in territories invaded by neural crest cells. In the head region, fli is expressed in the peri-ocular zone, in the branchial buds and at the level of the brain floor. In the trunk, a metamerized expression is detected in the dorsum. At a lower level, the tailbud and the peri-cardiac region also appear positive.

The c-ets-1 proto-oncogenes in Xenopus laevis: expression during oogenesis and embryogenesis

We previously reported the cloning and sequencing of two cDNAs derived from the Xenopus laevis ets-1 gene (Stiegler et al., 1990). The Xl-ets-1a cDNA encodes a polypeptide highly homologous to known ets-1 proteins. The 3'-UTR contains two AATAAA polyadenylation signals together with three copies of the TTTTTAT sequence thought to confer a maturation-specific polyadenylation and implicated in the deadenylation of dormant mRNAs. Several transcripts with maternal characteristics were detected in oogenesis and early embryogenesis. A marked augmentation of the major transcript in the poly(A)+ fraction was detected at fertilization. Ets-1 transcripts were observed at constant levels during the cleavage stages but decreased abruptly at gastrulation, to reappear from neurulation to late embryogenesis. The possible contribution of 3'-UTR sequence elements to this behavior is discussed.