Origin of gene overlap: the case of TCP1 and ACAT2

ACAT2 suppresses the ubiquitination of YAP1 to enhance the proliferation and metastasis ability of gastric cancer via the upregulation of SETD7

The contributions of aberrantly expressed metabolic enzymes to gastric cancer (GC) initiation and progression have been widely appreciated in recent years. Acetyl-CoA acetyltransferase 2 (ACAT2) is one member of the acetyl- CoA thiolase family. Previous studies demonstrated that ACAT2 either promotes or suppresses tumor progression in different conditions. However, the function and mechanisms of ACAT2 in GC remain unknown. We found that the expression of this enzyme was significantly increased in GC tissues compared with normal counterparts, which prompted us to further investigate the roles of this protein in GC biology. In vitro functional studies showed that ACAT2 knockdown markedly halted the proliferation and the motility of GC cells; these functions favoring malignant phenotypes of GC cells were further validated in animal experiments. Mechanistically, ACAT2 depletion significantly reduced the transcription of SETD7, which is a histone methyltransferase and plays critical roles in GC cells. We found that the pro-tumoral functions of ACAT2 were largely dependent on SETD7. Moreover, SETD7 decreased the ubiquitination level of Yes-associated protein 1 (YAP1), thereby protecting YAP1 from proteasome degradation. Increased YAP1 protein expression remarkably activated the YAP1/TAZ-TEAD1 signaling pathway, which further boosted the malignant phenotypes in GC cells. In conclusion, these findings highlight the pro-tumoral functions and molecular underpinnings of ACAT2 in GC cells, and suggest that ACAT2 could be a promising target in GC treatment.

Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair

For several decades, it has been known that a substantial number of genes within human DNA exhibit overlap; however, the biological and evolutionary significance of these overlaps remain poorly understood. This study focused on investigating specific instances of overlap where the overlapping DNA region encompasses the coding DNA sequences (CDSs) of protein-coding genes. The results revealed that proteins encoded by overlapping CDSs exhibit greater disorder than those from nonoverlapping CDSs. Additionally, these DNA regions were identified as GC-rich. This could be partially attributed to the absence of stop codons from two distinct reading frames rather than one. Furthermore, these regions were found to harbour fewer single-nucleotide polymorphism (SNP) sites, possibly due to constraints arising from the overlapping state where mutations could affect two genes simultaneously.While elucidating these properties, the NR1D1-THRA gene pair emerged as an exceptional case with highly structured proteins and a distinctly conserved sequence across eutherian mammals. Both NR1D1 and THRA are nuclear receptors lacking a ligand-binding domain at their C-terminus, which is the region where these gene pairs overlap. The NR1D1 gene is involved in the regulation of circadian rhythm, while the THRA gene encodes a thyroid hormone receptor, and both play crucial roles in various physiological processes. This study suggests that, in addition to their well-established functions, the specifically overlapping CDS regions of these genes may encode protein segments with additional, yet undiscovered, biological roles.

Circ_RPL23A acts as a miR-1233 sponge to suppress the progression of clear cell renal cell carcinoma by promoting ACAT2

Clear cell renal cell carcinoma (ccRCC) is a prevalent urological carcinoma with high metastatic risk. Circular RNAs (circRNAs) have been identified as effective diagnostic and therapeutic biomarkers for ccRCC. This research aims to disclose the effect and regulatory mechanism of circRNA ribosomal protein L23a (circ_RPL23A) in ccRCC. We performed quantitative real-time polymerase chain reaction (qRT-PCR) to examine circ_RPL23A, microRNA-1233 (miR-1233) and acetyl-coenzyme A acetyltransferase 2 (ACAT2). Cell cycle progression, apoptosis, cell viability, invasion and migration, which were respectively conducted by using flow cytometry, 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT), transwell assays. The levels of ACAT2 protein and cell cycle proteins, proliferation-associated protein, and epithelial-mesenchymal transition (EMT) associated proteins were measured by western blot. Target relationship was analyzed via dual-luciferase reporter assay and RNA pull down assay. The animal model was used to study how circ_RPL23A affects in vivo. Circ_RPL23A was lower expressed in ccRCC tissues and cells. The elevated circ_RPL23A suppressed cell cycle progression, proliferation, migration and invasion but promoted apoptosis in ccRCC cells. MiR-1233 was a target of circ_RPL23A and direct targeted to ACAT2. Besides, circ_RPL23A exerted its anti-tumor effect by sponging miR-1233, and then relieved the inhibition effect of miR-1233 on ACAT2. Overexpression of circ_RPL23A also curbed ccRCC tumor growth in vivo. Circ_RPL23A inhibited ccRCC progression by upregulating ACAT2 expression by competitively binding miR-1233, which might provide an in-depth cognition for ccRCC pathogenesis and circ_RPL23A might be a promising biomarker in ccRCC diagnosis and treatment.

Transcriptome Analysis Illuminates a Hub Role of SREBP2 in Cholesterol Metabolism by α-Mangostin

Whole-transcriptome analysis of α-mangostin-treated HepG2 cells revealed that genes relevant to lipid and cholesterol metabolic processes responded to α-mangostin treatment. α-Mangostin downregulated a series of cholesterol biosynthetic genes, including SQLE, HMGCR, and LSS, and controlled specific cholesterol trafficking-associated genes such as ABCA1, SOAT1, and PCSK9. In particular, the downregulation of SREBP2 expression highlighted SREBP2 as a key transcriptional factor controlling lipid or cholesterol metabolic processes. Gene network analysis of SREBP2 and responses of its target proteins demonstrated that the effect of α-mangostin on HepG2 cells was mediated by the downregulation of SREBP2 expression, which was further supported by the reduction of the amount of SREBP2-SCAP complex. In the presence of exogenous cholesterols, α-mangostin downregulated SREBP2 expression and suppressed PCSK9 synthesis, which might contribute to the increased cholesterol uptake in cells, in part explaining the cholesterol-lowering effect of α-mangostin.

Overlapping protein-coding genes in human genome and their coincidental expression in tissues

The completion of human genome sequences and the advancement of next-generation sequencing technologies have engendered a clear understanding of all human genes. Overlapping genes are usually observed in compact genomes, such as those of bacteria and viruses. Notably, overlapping protein-coding genes do exist in human genome sequences. Accordingly, we used the current Ensembl gene annotations to identify overlapping human protein-coding genes. We analysed 19,200 well-annotated protein-coding genes and determined that 4,951 protein-coding genes overlapped with their adjacent genes. Approximately a quarter of all human protein-coding genes were overlapping genes. We observed different clusters of overlapping protein-coding genes, ranging from two genes (paired overlapping genes) to 22 genes. We also divided the paired overlapping protein-coding gene groups into four subtypes. We found that the divergent overlapping gene subtype had a stronger expression association than did the subtypes of 5'-tandem overlapping and 3'-tandem overlapping genes. The majority of paired overlapping genes exhibited comparable coincidental tissue expression profiles; however, a few overlapping gene pairs displayed distinctive tissue expression association patterns. In summary, we have carefully examined the genomic features and distributions about human overlapping protein-coding genes and found coincidental expression in tissues for most overlapping protein-coding genes.

The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs

Long non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs. Further investigations showed that lncRNAs promoting the splicing of their embedded protein-coding partners was a unilateral interaction, but the existence of overlapping partners improving the gene expression was bidirectional and the effect was decreased with the increased evolutionary age of genes. Additionally, the expression of lncRNA-coding pairs showed an overall positive correlation and the expression correlation was associated with their overlapping configurations, local genomic environment and evolutionary age of genes. Comparison of the expression correlation of lncRNA-coding pairs between normal and cancer samples found that the lineage-specific pairs including old protein-coding genes may play an important role in tumorigenesis. This work presents a systematically comprehensive understanding of the evolution and the expression pattern of human lncRNA-coding pairs.

A unified framework of overlapping genes: towards the origination and endogenic regulation

Overlapping genes are pairs of adjacent genes whose genomic regions partially overlap. They are notable by their potential intricate regulation, such as cis-regulation of nested gene-promoter configurations, and post-transcriptional regulation of natural antisense transcripts. The originations and consequent detailed regulation remain obscure. Herein, we propose a unified framework comprising biological classification rules followed by extensive analyses, namely, exon-sharing analysis, a human-mouse conservation study, and transcriptome analysis of hundreds of microarrays and transcriptome sequencing data (mRNA-Seq). We demonstrate that the tail-to-tail architecture would result from sharing functional elements in 3'-untranslated regions (3'-UTRs) of pre-existing genes. Dissimilarly, we illustrate that the other gene overlaps would originate from a new gene arising in a pre-existing gene locus. Interestingly, these types of coupled overlapping genes may influence each other synergistically or competitively during transcription, depending on the promoter configurations. This framework discloses distinctive characteristics of overlapping genes to be a foundation for a further comprehensive understanding of them.

Is life unique?

Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity-heat agitation and the cause-and-effect determinism of nature's orderliness-cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.

Successful COG8 and PDF overlap is mediated by alterations in splicing and polyadenylation signals

Although gene-free areas compose the great majority of eukaryotic genomes, a significant fraction of genes overlaps, i.e., unique nucleotide sequences are part of more than one transcription unit. In this work, the evolutionary history and origin of a same-strand gene overlap is dissected through the analysis of COG8 (component of oligomeric Golgi complex 8) and PDF (peptide deformylase). Comparative genomic surveys reveal that the relative locations of these two genes have been changing over the last 445 million years from distinct chromosomal locations in fish to overlapping in rodents and primates, indicating that the overlap between these genes precedes their divergence. The overlap between the two genes was initiated by the gain of a novel splice donor site between the COG8 stop codon and PDF initiation codon. Splicing is accomplished by the use of the PDF acceptor, leading COG8 to share the 3'end with PDF. In primates, loss of the ancestral polyadenylation signal for COG8 makes the overlap between COG8 and PDF mandatory, while in mouse and rat concurrent overlapping and non-overlapping Cog8 transcripts exist. Altogether, we demonstrate that the origin, evolution and preservation of the COG8/PDF same-strand overlap follow similar mechanistic steps as those documented for antisense overlaps where gain and/or loss of splice sites and polyadenylation signals seems to drive the process.

Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture

Background

The biological dimensions of genes are manifold. These include genomic properties, (e.g., X/autosomal linkage, recombination) and functional properties (e.g., expression level, tissue specificity). Multiple properties, each generally of subtle influence individually, may affect the evolution of genes or merely be (auto-)correlates. Results of multidimensional analyses may reveal the relative importance of these properties on the evolution of genes, and therefore help evaluate whether these properties should be considered during analyses. While numerous properties are now considered during studies, most work still assumes the stereotypical solitary gene as commonly depicted in textbooks. Here, we investigate the Drosophila melanogaster genome to determine whether deviations from the stereotypical gene architecture correlate with other properties of genes.

Results

Deviations from the stereotypical gene architecture were classified as the following gene constellations: Overlapping genes were defined as those that overlap in the 5-prime, exonic, or intronic regions. Chromatin co-clustering genes were defined as genes that co-clustered within 20 kb of transcriptional territories. If this scheme is applied the stereotypical gene emerges as a rare occurrence (7.5%), slightly varied schemes yielded between ~1%-50%. Moreover, when following our scheme, paired-overlapping genes and chromatin co-clustering genes accounted for 50.1 and 42.4% of the genes analyzed, respectively. Gene constellation was a correlate of a number of functional and evolutionary properties of genes, but its statistical effect was ~1-2 orders of magnitude lower than the effects of recombination, chromosome linkage and protein function. Analysis of datasets on male reproductive proteins showed these were biased in their representation of gene constellations and evolutionary rate Ka/Ks estimates, but these biases did not overwhelm the biologically meaningful observation of high evolutionary rates of male reproductive genes.

Conclusion

Given the rarity of the solitary stereotypical gene, and the abundance of gene constellations that deviate from it, the presence of gene constellations, while once thought to be exceptional in large Eukaryote genomes, might have broader relevance to the understanding and study of the genome. However, according to our definition, while gene constellations can be significant correlates of functional properties of genes, they generally are weak correlates of the evolution of genes. Thus, the need for their consideration would depend on the context of studies.

A conserved gene structure and expression regulation of miR-433 and miR-127 in mammals

MicroRNAs play essential roles in many cellular processes. However, limited information is available regarding the gene structure and transcriptional regulation of miRNAs. We explored the gene cluster encoding miR-433/127 in mammalian species using bioinformatics and in vitro "gene" expression approaches. Multiple sequence alignments (MSA) showed that the precursors of miR-433 and of miR-127 exhibited 95% and 100% similarity, respectively, in human, chimpanzee, horse, dog, monkey, rat, cow, and mouse. MSA of the promoter sequences of miR-433 and of miR-127 revealed lower sequence similarity among these mammalian species. However, the distance between miR-433 and miR-127 was strikingly similar, which was between 986 and 1007 bp and the position of transcription factor (TF) binding motifs, including estrogen related receptor response element (ERRE), was well conserved. Transient transfection assays showed that promoters of miR-433 and of miR-127 from human, rat, and dog were activated by estrogen related receptor gamma (ERRgamma) and inhibited by small heterodimer partner (SHP). ChIP assays confirmed the physical association of ERRgamma with the endogenous promoters of miR-433 and miR-127. In vitro over-expression of the human, rat, or dog miR-433/127 loci in cells, using an expression vector containing miR-433/127 and their promoter regions, markedly induced a differential expression of both primary and mature miR-433 and miR-127, indicating that miR-433 and miR-127 were possessed from their independent promoters. Our studies for the first time demonstrate a conserved gene structure and transcriptional regulation of miR-433 and miR-127 in mammals. The data suggest that the miR-433/127 loci may have evolved from a common gene of origin.

Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation

Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs in human and nine other animals, using ESTs to increase coverage significantly over previous studies. The percentage of transcriptional units (TUs) involved in trans-SAs among all TUs was as high as 4.13%. Particularly 2896 human TUs (or 2.89% of all human TUs) were involved in 3327 trans-SAs. Sequence complementarities over multiple segments with predicted RNA hybridization indicated that some trans-SAs might have sophisticated RNA-RNA pairing patterns. One-fourth of human trans-SAs involved noncoding TUs, suggesting that many noncoding RNAs may function by a trans-acting antisense mechanism. TUs in trans-SAs were statistically significantly enriched in nucleic acid binding, ion/protein binding and transport and signal transduction functions and pathways; a significant number of human trans-SAs showed concordant or reciprocal expression pattern; a significant number of human trans-SAs were conserved in mouse. This evidence suggests important regulatory functions of trans-SAs. In 30 cases, trans-SAs were related to cis-SAs through paralogues, suggesting a possible mechanism for the origin of trans-SAs. All trans-SAs are available at http://trans.cbi.pku.edu.cn/.

Overlapping genes in the human and mouse genomes

BACKGROUND

Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes.

RESULTS

About 10% of the genes under study are overlapping genes, the majority of which are different-strand overlaps. The majority of the same-strand overlaps are embedded forms, whereas most different-strand overlaps are not embedded and in the convergent transcription orientation. Most of the same-strand overlapping gene pairs show at least a tenfold difference in length, much larger than the length difference between non-overlapping neighboring gene pairs. The length difference between the two different-strand overlapping genes is less dramatic. Over 27% of the different-strand-overlap relationships are shared between human and mouse, compared to only approximately 8% conservation for same-strand-overlap relationships. More than 96% of the same-strand and different-strand overlaps that are not shared between human and mouse have both genes located on the same chromosomes in the species that does not show the overlap. We examined the causes of transition between the overlapping and non-overlapping states in the two species and found that 3' UTR change plays an important role in the transition.

CONCLUSION

Our study contributes to the understanding of the evolutionary transition between overlapping genes and non-overlapping genes and demonstrates the high rates of evolutionary changes in the un-translated regions.

Birth and death of gene overlaps in vertebrates

Background

Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several mechanisms have been proposed to explain gene overlap origination the evolutionary basis of these phenomenon are still not well understood. Here, we present results of the comparative analysis of several vertebrate genomes. The purpose of this study was to examine overlapping genes in the context of their evolution and mechanisms leading to their origin.

Results

Based on the presence and arrangement of human overlapping genes orthologs in rodent and fish genomes we developed 15 theoretical scenarios of overlapping genes evolution. Analysis of these theoretical scenarios and close examination of genomic sequences revealed new mechanisms leading to the overlaps evolution and confirmed that many of the vertebrate gene overlaps are not conserved. This study also demonstrates that repetitive elements contribute to the overlapping genes origination and, for the first time, that evolutionary events could lead to the loss of an ancient overlap.

Conclusion

Birth as well as most probably death of gene overlaps occurred over the entire time of vertebrate evolution and there wasn't any rapid origin or 'big bang' in the course of overlapping genes evolution. The major forces in the gene overlaps origination are transposition and exaptation. Our results also imply that origin of overlapping genes is not an issue of saving space and contracting genomes size.

Conservation and functional significance of gene topology in the genome of Caenorhabditis elegans

We have systematically examined the correlation between transcriptional expression pattern and the physical layout of gene pairs in the genome of Caenorhabditis elegans using a public tissue-specific SAGE library data set. We find a strong positive correlation in the expression patterns of neighboring gene pairs that are close together and transcribed in the same direction as well as for neighboring pairs that are located on opposing strands and transcribed in divergent directions. Coupling between members of nonoverlapping neighboring gene pairs is independent of operons and decreases to background levels as the distance increases beyond 10 kb. These findings suggest the existence of regional transcriptional domains in the C. elegans genome. In contrast, genes that are on opposing strands and transcribed in convergent directions are less transcriptionally coupled than the genome-wide background, suggesting a mutual inhibition mechanism. We have also examined the conservation and functional consequences of extreme cases of topological entanglement in the C. elegans genome, in which two or more genes physically overlap in their UTRs or coding regions. We have found that overlapping gene pairs are more conserved and are enriched in essential genes and genes that cause various defined phenotypes revealed by RNAi trials. SAGE analysis indicates that genes that are on the same strand, physically overlap, and transcript at the same directions are very highly correlated in gene expression, while overlapping gene pairs in which one member of the pair resides within an intron of the other are weakly, if at all, coupled, similar to convergent overlapping genes.

Status and applications of genomic resources for the gray, short-tailed opossum, Monodelphis domestica, an American marsupial model for comparative biology

Owing to its small size, favourable reproductive characteristics, and simple husbandry, the gray, short-tailed opossum, Monodelphis domestica, has become the most widely distributed and intensively utilised laboratory-bred research marsupial in the world today. This article provides an overview of the current state and future projections of genomic resources for this species and discusses the potential impact of this growing resource base on active research areas that use M. domestica as a model system. The resources discussed include: fully arrayed, bacterial artificial chromosome (BAC) libraries; an expanding linkage map; developing full-genome BAC-contig and chromosomal fluorescence in situ hybridisation maps; public websites providing access to the M. domestica whole-genome-shotgun sequence trace database and the whole-genome sequence assembly; and a new project underway to create an expressed-sequence database and microchip expression arrays for functional genomics applications. Major research areas discussed span a variety of genetic, evolutionary, physiologic, reproductive, developmental, and behavioural topics, including: comparative immunogenetics; genomic imprinting; reproductive biology; neurobiology; photobiology and carcinogenesis; genetics of lipoprotein metabolism; developmental and behavioural endocrinology; sexual differentiation and development; embryonic and fetal development; meiotic recombination; genome evolution; molecular evolution and phylogenetics; and more.

Overlapping genes in vertebrate genomes

Overlapping genes in mammalian genomes are unexpected phenomena even though hundreds of pairs of protein coding overlapping genes have been reported so far. Overlapping genes can be divided into different categories based on direction of transcription as well as on sequence segments being shared between overlapping coding regions. The biologic functions of natural antisense transcripts, their involvement in physiological processes and gene regulation in living organisms are not fully understood. Number of documented examples indicates that they may exert control at various levels of gene expression, such as transcription, mRNA processing, splicing, stability, transport, and translation. Similarly, evolutionary origin of such genes is not known, existing hypotheses can explain only selected cases of mammalian gene overlaps which could originate as result of rearrangements, overprinting and/or adoption of signals in the neighboring gene locus.

Overlapping messages and survivability

The phenomenon of overlapping of various sequence messages in genomes is a puzzle for evolutionary theoreticians, geneticists, and sequence researchers. The overlapping is possible due to degeneracy of the messages, in particular, degeneracy of codons. It is often observed in organisms with a limited size of genome, possessing polymerases of low fidelity. The most accepted view considers the overlapping as a mechanism to increase the amount of information per unit length. Here we present a model that suggests direct evolutionary advantage of the message overlapping. Two opposing drives are considered: (a) reduction in the amount of vulnerable points when the overlapping of two messages involves common critical points and (b) cumulative compromising cost of coexistence of messages at the same site. Over a broad range of conditions the reduction of the target size prevails, thus making the overlapping of messages advantageous.

Comparative analysis of the PDCD2–TBP–PSMB1 region in vertebrates

Three orthologous genes encoding programmed cell death 2 (PDCD2), TATA-binding protein (TBP), and proteasomal subunit C5 (PSMB1) proteins have been shown previously to be nonrandomly distributed in both mammalian and invertebrate genomes. Here we analyze a conserved synteny of the PDCD2, TBP, and PSMB1 orthologs in four nonmammalian vertebrates. Homologous genes of the chicken, zebrafish, fugu, and Tetraodon nigroviridis were identified. A chicken cosmid harboring the orthologs of these three genes was completely sequenced. The fish genes were analyzed in silico. In all seven vertebrates thus far investigated, the PDCD2 and TBP genes are located tail-to-tail. In six tested species but the zebrafish, the PSMB1 gene mapped head-to-head or in the close vicinity to the TBP, but even in the zebrafish, all three genes were syntenic. In contrast, a three times reused synteny breakpoint in the 5'-region from PDCD2 was detected. A comparative analysis revealed the distribution of putative matrix-attached regions (MARs), which may affect the synteny conservation.

Mammalian overlapping genes: the comparative perspective

It is believed that 3.2 billion bp of the human genome harbor approximately 35000 protein-coding genes. On average, one could expect one gene per 300000 nucleotides (nt). Although the distribution of the genes in the human genome is not random,it is rather surprising that a large number of genes overlap in the mammalian genomes. Thousands of overlapping genes were recently identified in the human and mouse genomes. However,the origin and evolution of overlapping genes are still unknown. We identified 1316 pairs of overlapping genes in humans and mice and studied their evolutionary patterns. It appears that these genes do not demonstrate greater than usual conservation. Studies of the gene structure and overlap pattern showed that only a small fraction of analyzed genes preserved exactly the same pattern in both organisms.

Identification and characterization of ameloblastin gene in an amphibian, Xenopus laevis

Ameloblastin (AMBN) is an enamel sheath protein that presumably has a role in determining the prismatic structure of growing enamel crystals. To investigate the relationship between the molecular evolution of the AMBN gene and development of enamel prismatic structures, it is considered to be of great significance in the identification of homologues of the AMBN genes in nonmammals whose teeth lack an enamel prismatic structure. Several clones containing AMBN cDNA were isolated from an African clawed toad tooth cDNA library by screening with a polymerase chain reaction (PCR) method. Sequence analysis of the clones revealed that they were derived from different genes (toad-A and toad-B), which were found to contain ORFs encoding 408- and 352-amino-acid proteins, respectively. The N-terminal part of the toad AMBN proteins and the phosphorylation motif for casein kinase II, as well as several features, were found to be highly conserved throughout the evolution of tetrapods. Exon-intron boundaries were shared by toad and caiman genes with the exception of exons 6, 7 and 10 while human and caiman genes shared them exclusive of exons 8 and 9 which have been found only in the human. As for exon 7, it was absent in both toad genes. Moreover, the AMBN genes were transcribed only in the upper jaw, presumably in teeth. These results may provide useful information for investigation of the evolution of enamel.

Overlapping gene structure of human VLCAD and DLG4

Very-long-chain acyl-CoA dehydrogenase (VLCAD) is a major enzyme catalysing the first step in mitochondrial beta-oxidation of long-chain fatty acids. During analysis of the VLCAD promoter, we discovered that another gene, discs-large-related 4 (DLG4), overlaps VLCAD and is transcribed in the opposite direction. DLG4 encodes postsynaptic density-95 (PSD95) protein, which plays critical roles in the formation and maintenance of synaptic junctions. The transcription start site of the VLCAD gene was determined by primer extension analysis and the overlapping structure of VLCAD and DLG4 was clarified. VLCAD and DLG4 are arranged in a head-to-head orientation on chromosome 17p13, and share a 245 bp overlapping region that contains part of DLG4 exon 1 and the entire exon 1 of VLCAD including 62 bp of protein coding sequence. Despite the overlap of their 5' ends, DLG4 and VLCAD exhibit peak mRNA expression in different tissues, suggesting that they are independently regulated at the transcriptional level. Interestingly, VLCAD and DLG4 genes do not overlap in the mouse or Drosophila genomes.

Male-enhanced antigen-1 gene flanked by two overlapping genes is expressed in late spermatogenesis

The male-enhanced antigen-1 gene (Mea1) was originally isolated from a murine testicular cDNA library using anti-H-Y antigen antisera and was assigned to chromosome 17. On analysis of its structure and expression, we found that the Mea1 genomic sequence is flanked by two other genes: Ppp2r5d present in its 3'-terminus in a tail-to-tail orientation and a novel gene called Peas in its 5'-terminus in a head-to-head orientation. The coding sequences of the two genes embedded in the Mea1 sequence are located on the opposite DNA strands of Mea1. Cap-site analysis of Mea1 revealed that it is transcribed from at least seven sites. Most splice variants of Mea1 were abundantly expressed in the testis; the d-type was weakly expressed in the other tissues. AP-2-binding motifs were detected in the transcription-initiation sites. In situ hybridization and immunohistochemical studies revealed Mea1 expression in pachytene spermatocytes. This expression was most prominent in spermatids and residual bodies. The Mea1 protein was also localized in the cytoplasm of elongated spermatids and residual bodies. Localization of the Mea1 suggests that it may function in the very late stages of spermiogenesis. The possibility that Mea1 is one of the serologically detectable male antigens is discussed.

Identification and characterization of ameloblastin gene in a reptile

Ameloblastin (AMBN) is one of the enamel sheath proteins which presumably has a role in determining the prismatic structure of growing enamel crystals. There may therefore be a relationship between the molecular evolution of the AMBN gene and the development of enamel prismatic structures. To investigate whether such a relationship exists, it was necessary to identify the homologues of the AMBN gene in a reptile whose teeth lack an enamel prismatic structure. To this end, several clones containing AMBN cDNA were isolated from caiman jaws using the reverse transcription-polymerase chain reaction (RT-PCR) method. Sequence analysis of the AMBN cDNA revealed an open reading frame of 1221 bp encoding a 407-amino-acid protein. Translation of the caiman cDNA starts at the methionine corresponding to the second of two putative start codons conserved in mammalian AMBN genes. The N-terminal part of the caiman AMBN shows high amino acid sequence similarities to human, pig, cattle, rat and mouse AMBN sequences, as well as several other features that have been conserved throughout the evolution of reptiles and mammals. Unexpectedly, the nucleotide sequences of the 3' untranslated region (UTR) are also conserved, not only within mammalian genes but also between reptilian and mammalian genes. The caiman AMBN gene is a single-copy gene, transcribed only in the jaws, presumably in teeth.

Physical and transcriptional map of the critical region for keratolytic winter erythema (KWE) on chromosome 8p22-p23 between D8S550 and D8S1759

Keratolytic winter erythema is an autosomal dominant skin disorder characterised by erythema, hyperkeratosis, and peeling of the skin of the palms and soles, especially during winter. The keratolytic winter erythema locus has been mapped to human chromosome 8p22-p23. This chromosomal region has also been associated with frequent loss of heterozygosity in different types of cancer. To identify positional candidate genes for keratolytic winter erythema, a BAC contig located between the markers at D8S550 and D8S1695 was constructed and sequenced. It could be extended to D8S1759 by a partially sequenced BAC clone identified by database searches. In the 634 404 bp contig 13 new polymorphic microsatellite loci and 46 single nucleotide and insertion/deletion polymorphisms were identified. Twelve transcripts were identified between D8S550 and D8S1759 by exon trapping, cDNA selection, and sequence analyses. They were localised on the genomic sequence, their exon/intron structure was determined, and their expression analysed by RT-PCR. Only one of the transcripts corresponds to a known gene, encoding B-lymphocyte specific tyrosine kinase, BLK. A putative novel myotubularin-related protein gene (MTMR8), a potential human homologue of the mouse acyl-malonyl condensing enzyme gene (Amac1), and two transcripts showing similarities to the mouse L-threonine 3-dehydrogenase gene and the human SEC oncogene, respectively, were identified. The remaining seven transcripts did not show similarities to known genes. There were no potentially pathogenic mutations identified in any of these transcripts in keratolytic winter erythema patients.

Overlapping genes in parasitic protist Giardia lamblia

The parasitic protist Giardia lamblia lacks mitochondria and peroxisomes, as well as many typical membrane-bound organella characteristics of higher eukaryotic cells, together with extremely economized usage of DNA sequence, as demonstrated by the lack of introns. We describe here the presence of overlapping genes in G. lamblia, in which a part of the protein coding sequence of one mRNA exists in a region corresponding to the 3'-noncoding region of another mRNA transcribed from a gene on the opposite strand. Recently we isolated 13 kinesin-related cDNAs from G. lamblia. Nine of these cDNAs contain long 3'-noncoding sequences in which long open reading frames (ORFs) exist (in the remaining four cDNAs, the lengths of the 3'-noncoding sequences are very short). The predicted amino acid sequences of these ORFs were subjected to a search for homologies with sequences in databases. The amino acid sequences of the six ORFs exhibited significant sequence similarities with known sequences. These lines of evidence suggest the frequent occurrence of gene overlap in Giardial genome.

Phylogenetic conservation of the makorin-2 gene, encoding a multiple zinc-finger protein, antisense to the RAF1 proto-oncogene

Natural endogenous antisense RNAs have been reported in multiple loci, with evidence in some cases supporting a regulatory role for the antisense transcript. Here, we describe a novel gene, makorin RING zinc finger-2 (MKRN2), that overlaps and is antisense to the gene RAF1 in mammals. Phylogenetic analysis of the 3' untranslated region of RAF1 orthologues suggests that this relationship may have existed for up to 450 million years. We have also identified MKRN2 orthologues in two species of fish. This places the gene duplication event that created this locus from an ancestral MKRN1 gene early in vertebrate evolution, over 450 million years ago. Northern blot analyses show that human MKRN2 and RAF1 are co-expressed in tissues and cell lines, raising the possibility of mRNA duplex formation. The encoded makorin-2 protein is likely a ribonucleoprotein of unknown function, but its conservation suggests an important cellular role. The data presented here describe a conserved vertebrate MKRN2 gene that is closely associated with the RAF1 locus.

Human-mouse comparative sequence analysis of the NEMO gene reveals an alternative promoter within the neighboring G6PD gene

NEMO (NFkappaB essential modulator) is a non-catalytic subunit of the cytokine-dependent IkappaB kinase complex that is involved in activation of the transcription factor NFkappaB. The human NEMO gene maps to Xq28 and is arranged head to head with the proximal G6PD gene. Mutations in NEMO have recently been associated with Incontinentia Pigmenti (Smahi et al., Nature 405 (2000) 466), an X-linked dominant disorder. Three alternative transcripts with different non-coding 5' exons (1a, 1b and 1c) of NEMO have been described. In order to identify regulatory elements that control alternative transcription we have established the complete genomic sequence of the murine orthologs Nemo and G6pdx. Sequence comparison suggests the presence of two alternative promoters for NEMO/Nemo. First, a CpG island is shared by both genes driving expression of the NEMO/Nemo transcripts containing exons 1b and 1c in one direction and the housekeeping gene G6PD/G6pdx in the opposite direction. In contrast to human, an additional variant of exon 1c, named 1c+, was identified in several tissues of the mouse. This larger exon utilizes an alternative donor site located 1594 bp within intron 1c. The putative second promoter for NEMO/Nemo transcripts starting with exon 1a is unidirectional, and not associated with a CpG island. Surprisingly, this promoter is located in the second intron of G6PD/G6pdx. It shows very low basal activity and may be involved in stress/time- and/or tissue-dependent expression of NEMO. To our knowledge, an overlapping gene order similar to the G6PD/NEMO complex has not been described before.

Fliih, the murine homologue of the Drosophila melanogaster flightless I gene: nucleotide sequence, chromosomal mapping and overlap with Llglh

The Drosophila melanogaster flightless I gene is involved in cellularization processes in early embryogenesis and in the structural organization of indirect flight muscle. The encoded protein contains a gelsolin-like actin binding domain and an N-terminal leucine-rich repeat protein-protein interaction domain. We have cloned Fliih, the corresponding chromosomal gene from the mouse, and determined its nucleotide sequence (15.6 kb). The predicted Fliih protein of 1271 amino acids is 95% identical to the human FLII protein. Like the human gene, Fliih has 29 introns, compared with 13 in C. elegans and 3 in D. melanogaster. Fluorescence in situ hybridization was used to map Fliih to Chromosome 11B. Fliih lies adjacent to Llglh, the mouse homologue of the D. melanogaster tumor suppressor gene lethal(2) giant larvae. The sequence of the genomic DNA in this area, combined with cDNA sequences, establishes that the 3' ends of the Fliih and Llglh transcripts overlap. The overlap region contains polyA signals for both genes and is conserved between human and mouse.

Conservation of Mhc class III region synteny between zebrafish and human as determined by radiation hybrid mapping

In the HLA, H2, and other mammalian MHC:, the class I and II loci are separated by the so-called class III region comprised of approximately 60 genes that are functionally and evolutionarily unrelated to the class I/II genes. To explore the origin of this island of unrelated loci in the middle of the MHC: 19 homologues of HLA class III genes, we identified 19 homologues of HLA class III genes as well as 21 additional non-class I/II HLA homologues in the zebrafish and mapped them by testing a panel of 94 zebrafish-hamster radiation hybrid cell lines. Six of the HLA class III and eight of the flanking homologues were found to be linked to the zebrafish class I (but not class II) loci in linkage group 19. The remaining homologous loci were found to be scattered over 14 zebrafish linkage groups. The linkage group 19 contains at least 25 genes (not counting the class I loci) that are also syntenic on human chromosome 6. This gene assembly presumably represents the pre-MHC: that existed before the class I/II genes arose. The pre-MHC: may not have contained the complement and other class III genes involved in immune response.

Eleven densely clustered genes, six of them novel, in 176 kb of mouse t-complex DNA

Targeted sequencing of the mouse t-complex has started with a 176-kb, gene-rich BAC localized with six PCR-based markers in inversion 2/3 of the highly duplicated region. The sequence contains 11 genes recovered primarily as cDNAs from early embryonic collections, including Igfals (previously placed on chromosome 17), Nubp2 (a fully characterized gene), Jsap1 (a JNK-binding protein), Rsp29 (the mouse homologue of the rat gene), Ndk3 (a nucleoside diphosphate kinase), and six additional putative genes of unknown function. With 50% GC content, 75% of the DNA transcribed, and one gene/16.0 kb (on average), the region may qualify as one of the most gene-dense segments in the mouse genome and provides candidates for dosage-sensitive phenotypes and mouse embryonic lethals mapped to the vicinity.

A novel composite locus of Arabidopsis encoding two polypeptides with metabolically related but distinct functions in lysine catabolism

Both plants and animals catabolize lysine via saccharopine by two consecutive enzymes, lysine-ketoglutarate reductase (LKR) and saccharopine dehydrogenase (SDH), which are linked on a single polypeptide. We recently demonstrated that Arabidopsis plants possess not only a bifunctional LKR/SDH but in addition a monofunctional SDH enzyme. We also speculated that these two enzymes may be controlled by a single gene (G. Tang et al. Plant Cell, 1997, 9, 1305-1316). By expressing several epitope-tagged and GUS reporter constructs, we demonstrate in the present study that the Arabidopsis monofunctional SDH is encoded by a distinct gene, which is, however, nested entirely within the coding and 3' non-coding regions of the larger bifunctional LKR/SDH gene. The entire open reading frame of the monofunctional SDH gene, as well as some components of its promoter, are also parts of the translated coding sequence of the bifunctional LKR/SDH gene. These special structural characteristics, combined with the fact that the two genes encode simultaneously two metabolically related but distinct enzymes, render the LKR/SDH locus a novel type of a composite locus. Not all plant species possess an active monofunctional SDH gene and the production of this enzyme is correlated with an increased flux of lysine catabolism. Taken together, our results suggest that the composite LKR/SDH locus serves to control an efficient, highly regulated flux of lysine catabolism

Do lampreys have lymphocytes? The Spi evidence

It is generally accepted that living jawless vertebrates (lampreys and hagfishes) lack the capability of mounting an adaptive immune response. At the same time, however, there are reports describing histological evidence for the presence in agnathan tissues of lymphocytes, the key players in adaptive immunity. The question therefore arises whether the cells identified morphologically as lymphocytes are true lymphocytes in terms of their genetic developmental program. In this study, evidence is provided that the lampreys express a member of the purine box 1 (PU.1)/spleen focus-forming virus integration B (Spi-B) gene family known to be critically and specifically involved in the differentiation of lymphocytes in jawed vertebrates. The lamprey gene is expressed in the lymphocyte-like cells of the digestive tract and inexplicably also in the ovary.

Cloning and functional characterization of a putative sodium channel auxiliary subunit gene from the house fly (Musca domestica)

The functional expression of cloned Drosophila melanogaster and house fly (Musca domestica) voltage-sensitive sodium channels in Xenopus oocytes is enhanced, and the inactivation kinetics of the expressed channels are accelerated, by coexpression with the tipE protein, a putative sodium channel auxiliary subunit encoded by the tipE gene of D. melanogaster. These results predict the existence of a tipE ortholog in the house fly. Using a PCR-based homology probing approach, we isolated cDNA clones encoding an ortholog of tipE (designated Vssc beta) from adult house fly heads. Clones comprising 3444 bp of cDNA sequence contained a 1317 bp open-reading frame encoding a 438 amino acid protein. The predicted Vssc beta protein exhibited 72% amino acid sequence identity to the entire D. melanogaster tipE protein sequence and 97% identity within the two hydrophobic segments identified as probable transmembrane domains. Coexpression of Vssc beta with the house fly sodium channel alpha subunit (Vssc1) in oocytes enhanced the level of sodium current expression five-fold and accelerated the rate of sodium current inactivation 2.2-fold. Both of these effects were significantly larger in magnitude than the corresponding effects of the D. melanogaster tipE protein on the expression and kinetics of Vssc1 sodium channels. These results identify a second example of a putative sodium channel auxiliary subunit from an insect having functional but not structural homology to vertebrate sodium channel beta subunits.

Ancient allelism at the cytosolic chaperonin-alpha-encoding gene of the zebrafish

The T-complex protein 1, TCP1, gene codes for the CCT-alpha subunit of the group II chaperonins. The gene was first described in the house mouse, in which it is closely linked to the T locus at a distance of approximately 11 cM from the Mhc. In the zebrafish, Danio rerio, in which the T homolog is linked to the class I Mhc loci, the TCP1 locus segregates independently of both the T and the Mhc loci. Despite its conservation between species, the zebrafish TCP1 locus is highly polymorphic. In a sample of 15 individuals and the screening of a cDNA library, 12 different alleles were found, and some of the allelic pairs were found to differ by up to nine nucleotides in a 275-bp-long stretch of sequence. The substitutions occur in both translated and untranslated regions, but in the former they occur predominantly at synonymous codon sites. Phylogenetically, the alleles fall into two groups distinguished also by the presence or absence of a 10-bp insertion/deletion in the 3' untranslated region. The two groups may have diverged as long as 3.5 mya, and the polymorphic differences may have accumulated by genetic drift in geographically isolated populations.

OTC and AUL1, two convergent and overlapping genes in the nuclear genome of Arabidopsis thaliana

In contrast to bacterial, fungal and vertebrate ornithine transcarbamylases (OTCs; EC 2.1.3.3), very little is known about the enzyme in plants. We report here the isolation of a T-DNA-tagged mutant displaying sensitivity to ornithine, whose characterization has allowed for the identification of several complementary and genomic DNA clones encoding the OTC and auxilin-like 1 (AUL1) proteins of the crucifer Arabidopsis thaliana. Transcript mapping revealed that at least 22 bp within the OTC-AUL1 intercoding region are transcribed from both strands, which makes this one of the rarely described cases of convergent and overlapping transcription units in the nuclear genome of a multicellular eukaryote. Transcription of the OTC gene was shown to be ubiquitous in aerial organs of adult plants, whereas that of AUL1 was obscured by the existence of a putative second copy of the gene. The OTC-AUL1 locus maps at the bottom of chromosome 1.