The mouse surfeit locus contains a cluster of six genes associated with four CpG-rich islands in 32 kilobases of genomic DNA

Surf4, cargo trafficking, lipid metabolism, and therapeutic implications

Surfeit 4 is a polytopic transmembrane protein that primarily resides in the endoplasmic reticulum (ER) membrane. It is ubiquitously expressed and functions as a cargo receptor, mediating cargo transport from the ER to the Golgi apparatus via the canonical coat protein complex II (COPII)-coated vesicles or specific vesicles. It also participates in ER-Golgi protein trafficking through a tubular network. Meanwhile, it facilitates retrograde transportation of cargos from the Golgi apparatus to the ER through COPI-coated vesicles. Surf4 can selectively mediate export of diverse cargos, such as PCSK9 very low-density lipoprotein (VLDL), progranulin, α1-antitrypsin, STING, proinsulin, and erythropoietin. It has been implicated in facilitating VLDL secretion, promoting cell proliferation and migration, and increasing replication of positive-strand RNA viruses. Therefore, Surf4 plays a crucial role in various physiological and pathophysiological processes and emerges as a promising therapeutic target. However, the molecular mechanisms by which Surf4 selectively sorts diverse cargos for ER-Golgi protein trafficking remain elusive. Here, we summarize the most recent advances in Surf4, focusing on its role in lipid metabolism.

Arabidopsis thaliana SURFEIT1-like genes link mitochondrial function to early plant development and hormonal growth responses

Mutations in SURFEIT1 (SURF1) genes affect cytochrome c oxidase (COX) levels in different prokaryotic and eukaryotic organisms. In this work, we report that Arabidopsis thaliana has two genes that potentially encode SURF1 proteins, as a result of a duplication that took place in Brassicaceae. Both genes encode mitochondrial proteins and mutation in AtSURF1a causes embryonic lethality. Mutation in AtSURF1b, instead, causes defects in hypocotyl elongation under growth-stimulating conditions, such as low light intensity, increased ambient temperature and incubation with glucose. Mutants in AtSURF1b show reduced expression of the auxin reporter DR5:GUS and increased levels of the gibberellin reporter GFP-RGA, suggesting that auxin and gibberellin homeostasis are affected. In agreement, growth defects caused by AtSURF1b mutation can be overcome by treatment with indole-3-acetic acid and gibberellin A₃ , and also by increasing expression of the auxin biosynthesis gene YUC8 or the transcription factor PIF4, which shows lower abundance in AtSURF1b-deficient plants. Mutants in AtSURF1b display lower COX levels, higher alternative oxidase and superoxide levels, and increased expression of genes that respond to mitochondrial dysfunction. Decreased hypocotyl growth and DR5:GUS expression can be reversed by treatment with reduced glutathione, suggesting that redox changes, probably related to mitochondrial dysfunction, are responsible for the effect of AtSURF1b deficiency on hormone responses. The results indicate that changes in AtSURF1b affect mitochondrial function and the production of reactive oxygen species, which, in turn, impinges on a growth regulatory circuit that involves auxin, gibberellins and the transcription factor PIF4.

Murine Surf4 is essential for early embryonic development

Newly synthesized proteins co-translationally inserted into the endoplasmic reticulum (ER) lumen may be recruited into anterograde transport vesicles by their association with specific cargo receptors. We recently identified a role for the cargo receptor SURF4 in facilitating the secretion of PCSK9 in cultured cells. To examine the function of SURF4 in vivo, we used CRISPR/Cas9-mediated gene editing to generate mice with germline loss-of-function mutations in Surf4. Heterozygous Surf4^+/- mice exhibit grossly normal appearance, behavior, body weight, fecundity, and organ development, with no significant alterations in circulating plasma levels of PCSK9, apolipoprotein B, or total cholesterol, and a detectable accumulation of intrahepatic apoliprotein B. Homozygous Surf4^-/- mice exhibit embryonic lethality, with complete loss of all Surf4^-/- offspring between embryonic days 3.5 and 9.5. In contrast to the milder murine phenotypes associated with deficiency of known SURF4 cargoes, the embryonic lethality of Surf4^-/- mice implies the existence of additional SURF4 cargoes or functions that are essential for murine early embryonic development.

Tissue-specific processing of the Surf-5 and Surf-4 mRNAs

The mouse surfeit locus is an unusually tight cluster of at least six "housekeeping" genes that do not share any sequence homology and whose gene organization may play a role in gene expression. The transcription of each of the five well-characterized genes (Surf-1 to -5) alternates with respect to its neighbor(s) and no more than 159 bp separates any two adjacent genes with the Surf-4 and Surf-2 genes overlapping at their 3' ends by 133 bp. In this work, the expression of the Surf-5 and Surf-4 genes has been examined in various mouse tissues. In addition to the ubiquitously expressed 3.5-kb Surf-5 mRNA, a second alternatively spliced Surf-5 mRNA, Surf-5b, was discovered that was highly expressed in the brain, heart, testis, and skeletal muscle. The alternative splice donor site of the Surf-5b mRNA is similar to splice donor sites found in neuron-specific mRNAs. Surf-5b encodes a unique protein, which, like the ubiquitous Surf-5 protein, has been found to be primarily located in the soluble fraction of the cytoplasm. The expression of the Surf-5b protein was also found to increase in embryonal carcinoma cells differentiated into neuronal cultures. Although the Surf-5 gene is highly conserved through evolution, the presence of the Surf-5b alternative splice may be restricted to higher vertebrates. The Surf-4 gene was ubiquitously expressed in eight different mouse tissues; however, the ratios of the three previously reported Surf-4 mRNAs (two of which are known to derive from different sites of polyadenylation) altered dramatically between tissues. The use of different forms of mRNA processing for regulation of tissue-specific expression of ubiquitously expressed genes is discussed.

SURF4 has oncogenic potential in NIH3T3 cells

SURF4, which is located in the Surfeit gene cluster, encodes for a conserved integral membrane protein containing multiple putative transmembrane regions. However, the physiological role of SURF4 has not been determined. We found that SURF4 demonstrated aberrant amplification and increased expression in the tumor tissues of several human cancer patients. Overexpression of SURF4 led to increased cell proliferation, migration, and maintenance of anchorage-independent growth. In addition, NIH3T3 cells overexpressing SURF4 induced tumor growth in the mice. Collectively, our findings demonstrate that SURF4 has the potential for inducing cellular transformation and cell migration in vitro and has oncogenic transformation ability in vivo.

Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips

BACKGROUND

Affymetrix GeneChip technology enables the parallel observations of tens of thousands of genes. It is important that the probe set annotations are reliable so that biological inferences can be made about genes which undergo differential expression. Probe sets representing the same gene might be expected to show similar fold changes/z-scores, however this is in fact not the case.

RESULTS

We have made a case study of the mouse Surf4, chosen because it is a gene that was reported to be represented by the same eight probe sets on the MOE430A array by both Affymetrix and Bioconductor in early 2004. Only five of the probe sets actually detect Surf4 transcripts. Two of the probe sets detect splice variants of Surf2. We have also studied the expression changes of the eight probe sets in a public-domain microarray experiment. The transcripts for Surf4 are correlated in time, and similarly the transcripts for Surf2 are also correlated in time. However, the transcripts for Surf4 and Surf2 are not correlated. This proof of principle shows that observations of expression can be used to confirm, or otherwise, annotation discrepancies. We have also investigated groups of probe sets on the RAE230A array that are assigned to the same LocusID, but which show large variances in differential expression in any one of three different experiments on rat. The probe set groups with high variances are found to represent cases of alternative splicing, use of alternative poly(A) signals, or incorrect annotations.

CONCLUSION

Our results indicate that some probe sets should not be considered as unique measures of transcription, because the individual probes map to more than one transcript dependent upon the biological condition. Our results highlight the need for care when assessing whether groups of probe sets all measure the same transcript.

Increased longevity and refractoriness to Ca(2+)-dependent neurodegeneration in Surf1 knockout mice

Leigh syndrome associated with cytochrome c oxidase (COX) deficiency is a mitochondrial disorder usually caused by mutations of SURF1, a gene encoding a putative COX assembly factor. We present here a Surf1-/- recombinant mouse obtained by inserting a loxP sequence in the open reading frame of the gene. The frequency of -/-, +/+ and +/- genotypes in newborn mice followed a mendelian distribution, indicating that the ablation of Surf1 is compatible with postnatal survival. The biochemical and assembly COX defect was present in Surf1(loxP)-/- mice, but milder than in humans. Surprisingly, not only these animals failed to show spontaneous neurodegeneration at any age, but they also displayed markedly prolonged lifespan, and complete protection from Ca(2+)-dependent neurotoxicity induced by kainic acid. Experiments on primary neuronal cultures showed markedly reduced rise of cytosolic and mitochondrial Ca(2+) in Surf1(loxP)-/- neurons, and reduced mortality, compared to controls. The mitochondrial membrane potential was unchanged in KO versus wild-type neurons, suggesting that the effects of the ablation of Surf1 on Ca(2+) homeostasis, and possibly on longevity, may be independent, at least in part, from those on COX assembly and mitochondrial bioenergetics.

[Identification of muscle-type carnitine palmitoyltransferase I and characterization of its gene structure]

To characterize energy metabolism in brown adipose tissue (BAT), differential screening of a cDNA library of rat BAT with a cDNA probe of rat white adipose tissue was carried out. We isolated one novel cDNA clone encoding a protein of 88.2 kDa consisting of 772 amino acids. The deduced amino acid sequence showed the highest homology (62.6%) with that of rat liver carnitine palmitoyltransferase I (CPTI). The transcript corresponding to this cDNA was abundantly expressed not only in BAT but also in the heart and skeletal muscle. CPTI is a protein necessary for the beta-oxidation of long-chain fatty acids in mammalian mitochondria, and it has been suggested that at least two isoforms, the liver type and muscle (M-CPTI) type, exist. Based on these observations, we concluded that the novel cDNA clone isolated from rat BAT encodes M-CPTI. Isolation and characterization of a genomic DNA clone revealed that the gene for human M-CPTI consists of two 5'-noncoding exons, 18 coding exons, and one 3'-noncoding exon spanning approximately 10 kbp, and a gene encoding choline/ethanolamine kinase-beta (CK/EK-beta) was located about 300 bp upstream from the M-CPTI gene with the same strand direction. Furthermore, we found atypical transcripts containing exons of both CK/EK-beta and M-CPTI genes in humans and rodents. The physiologic role(s) of these transcripts is still unknown. However, it is interesting that such transcripts are produced from two tightly arranged and functionally unrelated genes in mammalian tissues.

The human homologue of the mouse Surf5 gene encodes multiple alternatively spliced transcripts

Hu-Surf5 is included within the Surfeit locus, a cluster of six genes originally identified in mouse. In the present study, we have cloned and characterized the Hu-Surf5 gene and its mRNA multiple transcripts. Comparison of the most abundant cDNA and genomic sequence shows that the Hu-Surf5 is spread over a region of approximately 7.5 kb and consists of five exons separated by four introns. The nucleotide sequence of the genomic region flanking the 3'-end of the Hu-Surf5 gene revealed the presence of a processed pseudogene of human ribosomal protein L21 followed by Hu-Surf6 gene. Only 110 bp separate the transcription start site of Hu-Surf5 and Hu-Surf3/L7a gene and the transcription direction is divergent. Earlier studies defined the 110 bp region essential for promoter activity of Hu-Surf3/L7a. Here, we show that this region stimulates transcription with a slightly different efficiency in both directions. The bidirectional promoter lacks an identifiable TATA box and is characterized by a CpG island that extends through the first exon into the first intron of both genes. These features are characteristic of housekeeping genes and are consistent with the wide tissue distribution observed for Hu-Surf5 expression. Hu-Surf5 encodes three different transcripts, Surf-5a, Surf-5b, and Surf-5c, which result from alternative splicing. Two protein products, SURF-5A and SURF-5B have been characterized. Production of chimaeras between the full-length SURF-5A or SURF-5B and the green fluorescent protein (GFP) allowed to localize both proteins in the cytoplasm.

Mutations in the SURF1 gene associated with Leigh syndrome and cytochrome C oxidase deficiency

Cytochrome c oxidase (COX) deficiency is one of the major causes of Leigh Syndrome (LS), a fatal encephalopathy of infancy or childhood, characterized by symmetrical lesions in the basal ganglia and brainstem. Mutations in the nuclear genes encoding COX subunits have not been found in patients with LS and COX deficiency, but mutations have been identified in SURF1. SURF1 encodes a factor involved in COX biogenesis. To date, 30 different mutations have been reported in 40 unrelated patients. We aim to provide an overview of all known mutations in SURF1, and to propose a common nomenclature. Twelve of the mutations were insertion/deletion mutations in exons 1, 4, 6, 8, and 9; 10 were missense/nonsense mutations in exons 2, 4, 5, 7, and 8; and eight were detected at splicing sites in introns 3 to 7. The most frequent mutation was 312_321del 311_312insAT which was found in 12 patients out of 40. Twenty mutations have been described only once. We also list all polymorphisms discovered to date.

The highly compact structure of the mitochondrial DNA polymerase genomic region of Drosophila melanogaster: functional and evolutionary implications

The structure of a Drosophila melanogaster genomic region containing five tightly clustered genes has been determined and evaluated with regard to its functional and evolutionary relationships. In addition to the genes encoding the two subunits (alpha and beta) of the DNA polymerase gamma holoenzyme, the key enzyme for mitochondrial DNA replication, other genes contained in the cluster may be also involved in the cellular distribution of mitochondria and in the coordination of mitochondrial and nuclear DNA replication. The gene cluster is extremely compact, with very little intergenic space. It contains two bidirectional promoter regions, and particularly notable is the 5' end overlap detected in two of its genes, an exceptional situation in both prokaryotic and eukaryotic genome organization.

Isolation and genomic analysis of the human surf-6 gene: a member of the Surfeit locus

The human Surfeit locus contains at least six tightly clustered genes (Surf-1 to Surf-6) of which five (Surf-1 to Surf-5) have been characterised and found not to share any sequence homology. The organisation and juxtaposition of the Surfeit genes are conserved between human and mouse. The Surf-6 gene that encodes a novel nucleolar-matrix protein with nucleic-acid binding properties has been characterised in mouse. In this work, we have isolated and analysed the human Surf-6 homologue and determined its genomic organisation in the Surfeit locus. The human Surf-6 gene has five exons spread over a distance of 4.3kb and has features of a housekeeping gene being ubiquitously expressed, having its 5' end located within a CpG rich island and lacking a canonical TATA box. The intragenic region between the 3' end of the Surf-5 gene and the 5' end of the Surf-6 gene is 3.2kb and contains a pseudogene of the ribosomal protein gene rpL21. The putative human Surf-6 protein is 361 amino acids long and includes motifs found in both the mouse and fish Surf-6 homologues, which may underlie the functions of Surf-6. Three amino acid polymorphisms have been detected at codons 163, 175 and 311 by SSCP analysis.

Expression and functional analysis of SURF1 in Leigh syndrome patients with cytochrome c oxidase deficiency

Leigh syndrome (LS) associated with cytochrome c oxidase (COX) deficiency is an autosomal recessive neurodegenerative disorder caused by mutations in SURF1. Although SURF1 is ubiquitously expressed, its expression is lower in brain than in other highly aerobic tissues. All reported SURF1 mutations are loss of function, predicting a truncated protein (hSurf1) product. Western blot analysis with anti-hSurf1 antibodies demonstrated a specific 30 kDa protein in control fibroblasts, but no protein in LS patient cells. Steady-state levels of both nuclear- and mitochondrial-encoded COX subunits were also markedly reduced in patient cells, consistent with a failure to assemble or maintain a normal amount of the enzyme complex. An epitope (FLAG)-tagged hSurf1 was targeted to mitochondria in COS7 cells and a mitochondrial import assay showed that the hSurf1 precursor protein (35 kDa) was imported and processed to its mature form (30 kDa) in a membrane potential-dependent fashion. The protein was resistant to alkaline carbonate extraction and susceptible to proteinase K digestion in mitoplasts. Mutant proteins in which the N-terminal transmembrane domain or central loop were deleted, or the C-terminal transmembrane domain disrupted, did not accumulate and could not rescue COX activity in patient cells. Co-expression of the N- and C-terminal transmembrane domains as independent entities also failed to rescue the enzyme deficiency. These data demonstrate that hSurf1 is an integral inner membrane protein with an essential role in the assembly or maintenance of the COX complex and that insertion of both transmembrane domains in the intact protein is necessary for function.

SURFEIT-1 gene analysis and two-dimensional blue native gel electrophoresis in cytochrome c oxidase deficiency

Leigh syndrome, a progressive, often fatal, neurodegenerative disorder, is frequently associated with a deficiency in the activity of cytochrome c oxidase (COX), the last enzyme of the mitochondrial respiratory chain. In contrast to NADH:ubiquinone oxidoreductase and succinate dehydrogenase deficiencies, no mutations in nuclear genes encoding COX subunits have been identified thus far. Very recently, however, a Leigh syndrome complementation group has been identified which showed mutations in the SURFEIT-1 (SURF-1) gene. The results of a mutational detection study in 16 new randomly selected COX-deficient patients revealed a new mutation (C688T) in 2 patients and the earlier reported 845delCT mutation in 2 additional patients. In addition, we evaluated the diagnostic value of two-dimensional blue native gel electrophoresis. We show that this technique reveals distinct patterns of both fully and partially assembled COX complexes and is thereby capable of discrimination between COX-deficient SURF-1 and non-SURF-1-mutated patients.

SURF1, encoding a factor involved in the biogenesis of cytochrome c oxidase, is mutated in Leigh syndrome

Leigh Syndrome (LS) is a severe neurological disorder characterized by bilaterally symmetrical necrotic lesions in subcortical brain regions that is commonly associated with systemic cytochrome c oxidase (COX) deficiency. COX deficiency is an autosomal recessive trait and most patients belong to a single genetic complementation group. DNA sequence analysis of the genes encoding the structural subunits of the COX complex has failed to identify a pathogenic mutation. Using microcell-mediated chromosome transfer, we mapped the gene defect in this disorder to chromosome 9q34 by complementation of the respiratory chain deficiency in patient fibroblasts. Analysis of a candidate gene (SURF1) of unknown function revealed several mutations, all of which predict a truncated protein. These data suggest a role for SURF1 in the biogenesis of the COX complex and define a new class of gene defects causing human neurodegenerative disease.

Preliminary characterization of the protein encoded by human testis-enhanced gene transcript (TEGT)

TEGT is a conserved, widely expressed gene transcript of unknown function that has been studied previously only at the nucleic acid level. The deduced amino acid sequence predicts a highly hydrophobic, 26.5 kDa integral membrane protein with seven potential transmembrane domains. Little else is known about TEGT protein because of the lack of definitive homology to other known sequences and the absence of informative consensus motifs. The present report details a preliminary study of human TEGT (hTEGT) protein. (i) In vitro translation of hTEGT in reticulocyte lysates required the presence of microsomes for efficient synthesis, suggesting that hTEGT must target to the endoplasmic reticulum to be translated. Immunofluorescence of cells transiently expressing haemagglutinin-tagged hTEGT localized the protein mainly to the endoplasmic reticulum. The protein demonstrated no obvious post-translational modifications such as signal-peptide cleavage, N-linked glycosylation or O-linked glycosylation. (ii) Both hTEGT and haemagglutinin-tagged hTEGT appeared to retain partial secondary and tertiary structure in the presence of SDS. Both electrophoresed as a broad band or doublet with apparent molecular weights of 22-24.5 kDa on SDS-PAGE, aggregated either homotypically or heterotypically when boiled in SDS, and were toxic after 24 h when highly overexpressed in 293 T cells. These properties are believed to be caused by the protein's hydrophobicity. (iii) The protein appeared to associate strongly with other intracellular molecules since haemagglutinin-tagged hTEGT was extracted poorly from transiently transfected HeLa cells. Further study will be required to determine the cellular function of TEGT.

The human Surfeit locus

The organization of the human Surfeit locus containing the six sequence-unrelated housekeeping genes Surf-1 to Surf-6 (HGMW-approved symbols SURF1-SURF6) has been determined. The human surfeit locus occupies about 60 kb of DNA, and the tightly clustered gene organization and the juxtaposition of the human genes are similar to the mouse and chicken surfeit loci with the 5' end of each gene associated with a CpG-rich island. Whereas in the mouse the Surf-2 and Surf-4 genes overlap at their 3' ends, the human Surf-2 and Surf-4 genes have been found to be separated by 302 bp due to a much shorter 3' untranslated region in the human Surf-2 gene. The distance between the 3' ends of the human Surf-1 and Surf-3 genes is 374 bp, and the distance between the 5' ends of the human Surf-3 and Surf-5 genes is only 112 bp. Unusually the human Surf-5 gene contains an intron in its 5' untranslated region not found in the mouse or rat Surf-5 genes. This additional intron is also found in the Surf-5 gene of both Old and New World monkeys, being generated before the divergence of human and prosimians but after the divergence of primates and rodents. A contig of 200 kb containing the human Surfeit locus has been constructed from overlapping cosmid, P1, and PAC clones. Approximately 40 kb proximal to the 3' end of the Surf-6 gene, the 5' region of the ABO glycosyltransferase gene has been detected. This allows us to determine the orientation of the Surfeit and ABO loci with respect to each other and to the telomere and centromere of human chromosome 9.

Gene clusters and polycistronic transcription in eukaryotes

Sometimes genes are arranged nonrandomly on the chromosomes of eukaryotes. This review considers instances of gene clusters in which two genes or more are expressed from a single promoter. This includes cases in which a polycistronic pre-mRNA is processed to make monocistronic mRNAs in nematodes, as well as isolated examples of polycistronic mRNAs found in mammals, flies, and perhaps plants.

Duplication and distribution of repetitive elements and non-unique regions in the human genome

Genome mapping efforts and the initial sequencing of large segments of human DNA permit ongoing assessment of the patterns and extent of sequence duplication and divergence in the human genome. Initial sequence data indicate that the most highly repetitive sequences show isochore-related enrichment and clustering produced by successive insertional recombination and local duplication of particular repetitive elements. Regional duplication is also observed for a number of otherwise unique genomic sequences and thereby makes these segments become repetitive. The consequences of these duplication events are: (1) clustering of related genes, along with a variety of coregulatory mechanisms; and (2) recombinations between the nearby homologous sequences, which can delete genes in individuals and account for a significant fraction of human genetic disease.

The comparative genomic structure and sequence of the surfeit gene homologs in the puffer fish Fugu rubripes and their association with CpG-rich islands

The puffer fish Fugu rubripes (Fugu) has a compact genome approximately one-seventh the size of man, mainly owing to small intron size and the presence of few dispersed repetitive DNA elements, which greatly facilitates the study of its genes at the genomic level. It has been shown previously that, whereas the Surfeit genes are tightly clustered at a single locus in mammals and birds, the genes are found at three separate loci in the Fugu genome. Here, Fugu gene homologs of all six Surfeit genes (Surf-1 to Surf-6) have been cloned and sequenced, and their gene structure has been compared with that of their mammalian and avian homologs. The predicted protein products of each gene are well conserved between vertebrate species, and in most cases their gene structures are identical to their mammalian and avian homologs except for the Fugu Surf-6 gene, which was found to lack an intron present in the mouse gene. In addition, we have identified conserved regulatory elements at the 5' and 3' ends of the Surf-3/rpL7a gene by comparison with the mammalian and chicken Surf-3/rpL7a gene homologs, including the presence of a polypyrimidine tract at the extreme 5' end of this ribosomal protein gene. The Fugu Surfeit gene homologs appear to be associated with CpG-rich islands, like the Surfeit genes in higher vertebrates, but these Fugu CpG islands are similar to the nonclassical islands characteristic of other fish species. Our observations support the use of the Fugu genome to study vertebrate gene structure, to predict the structure of mammalian genes, and to identify vertebrate regulatory elements. [The sequence data described in this paper have been submitted to the data library under accession nos. Y15170 (Surf-2, Surf-4), Y15171 (Surf-3, Surf-1, Surf-6), and Y15172 (Surf-5.)]

Gene within gene configuration and expression of the Drosophila melanogaster genes lethal(2) neighbour of tid [l(2)not] and lethal(2) relative of tid[l(2)rot]

In this paper, we describe the structure and temporal expression pattern of the Drosophila melanogaster genes l(2)not and l(2)rot located at locus 59F5 vis à vis the tumor suppressor gene l(2)tid described previously and exhibiting a gene within gene configuration. The l(2)not protein coding region, 1530 nt, is divided into two exons by an intron, 2645 nt, harboring the genes l(2)rot, co-transcribed from the same DNA strand, and l(2)tid, co-transcribed from the opposite DNA strand, located vis à vis. To determine proteins encoded by the genes described in this study polyclonal rabbit antibodies (Ab), anti-Not and anti-Rot, were generated. Immunostaining of developmental Western blots with the anti-Not Ab resulted in the identification of a 45-kDa protein, Not45, which is smaller than the Not56 protein predicted from the sequence. Its localization in endoplasmic reticulum (ER) was established by immunoelectron microscopy of Drosophila melanogaster Schneider 2 cells. Not45 shows significant homology to yeast ALG3 protein acting as a dolichol mannosyltransferase in the asparagine-linked glycosylation. It is synthesized ubiquitously throughout embryonic life. The protein predicted from the l(2)rot sequence, Rot57, shows a homology to the NS2B protein of the yellow fever virus1 (yefv1). The results of l(2)rot RNA analysis by developmental Northern blot and by in situ RNA localization, as well as the results of the protein analysis via Western blot and immunohistochemistry suggest that l(2)rot is transcribed but not translated. Since RNAs encoded by the genes l(2)tid and l(2)rot are complementary and l(2)rot is presumably not translated we performed preliminary experiments on the function of the l(2)rot RNA as a natural antisense RNA (asRNA) regulator of l(2)tid expression, expressed in the same temporal and spatial manner as the l(2)tid- and l(2)not RNA. l(2)tid knock-out by antisense RNA yielded late embryonic lethality resulting from multiple morphogenetic defects.

A functional YY1 binding site is necessary and sufficient to activate Surf-1 promoter activity in response to serum growth factors

The human Surf-1 and Surf-2 housekeeping genes are divergently transcribed and share a bi-directional, TATA-less promoter. Housekeeping promoters typically contain complex arrays of transcription factor binding sites and several studies have suggested that many of these sites might be functionally redundant. The Surf-1/Surf-2 promoter region contains four factor binding sites; members of the ETS family of transcription factors bind to two of these sites whilst YY1 binds to a third site immediately downstream of the major Surf-1 transcription start point. Here we show that Sp1 binds to the fourth transcription factor binding site. Although YY1 and Sp1 have previously been shown to interact both in vitro and in vivo, these proteins function independently at the Surf-1/Surf-2 promoter. The binding of Sp1 alone is sufficient to bring about full promoter activity in the Surf-2 direction. In contrast, both Sp1 and ETS proteins are required to bring about full promoter activity in the Surf-1 direction. The YY1 binding site is not required for basal transcription in either direction. The YY1 binding site is, however, both necessary and sufficient to confer growth factor inducibility on transcription in the Surf-1 direction. Our data suggest that functionally redundant transcription factor binding sites might not be a general feature of housekeeping promoters.

Sequence analysis of a near-subtelomeric 35.4 kb DNA segment on the right arm of chromosome VII from Saccharomyces cerevisiae carrying the MAL1 locus reveals 15 complete open reading frames, including ZUO1, BGL2 and BIO2 genes and an ABC transporter gene

The nucleotide sequence of 35,400 bp at approximately 10 kb from the right telomere of chromosome VII was determined. The segment contains the MAL1 locus, one of the five unlinked loci sufficient for maltose utilization. Until now, each of these loci was considered to contain three genes (for regulator, permease and alpha-glucosidase), but a fourth gene, presumably an extra alpha-glucosidase gene, was found at MAL1 adjacent to the usual cluster of three genes. The two glucosidase genes are present in opposite orientation, forming an inverted repeat structure. In addition to the four genes at MAL1, there are 11 complete, non-overlapping open reading frames (ORFs) longer than 300 bp in the sequence presented here. A new ABC transporter gene (YGR281w), required for oligomycin resistance was found (YOR1; Katzman et al., 1995), and the previously sequenced BGL2 (YGR282c), ZUO1 (YGR285c) and BIO2 (YGR286c) genes were located. The sequence of BIO2, a biotin synthetase gene, required substantial correction and the size of Bio2p is 375, rather than 356, amino acids. Two ORFs show rather weak similarities to animal genes: YGR278w to an unknown ORF of Caenorhabditis elegans and YGR284c to the murine Surf-4, a member of a cluster of at least four housekeeping genes. The remaining five ORFs do not encode known functions, but three of these show weak to high similarities to other ORFs in the Saccharomyces cerevisiae genome and one (YGR280c) codes for a particularly lysine-rich protein.

Identification of a novel Drosophila melanogaster gene, angel, a member of a nested gene cluster at locus 59F4,5

The identification of a novel Drosophila melanogaster gene, angel, is presented in this study. angel is located on the right arm of the second chromosome at locus 59F5, close to the nested genes l(2)tid, l(2)not, l(2)rot and l(2)dtl. We describe the genetic and molecular localization of angel and present its temporal expression in the wild-type. The deduced amino acid sequence of the ANG39 protein is characterized by a nuclear localization signal. Furthermore, the central part of the predicted ANG39 protein shows significant homology to the C-terminal portion of the yeast transcriptional effector CCR4.

The Surf-6 gene of the mouse surfeit locus encodes a novel nucleolar protein

The Surfeit locus contains the tightest cluster of mammalian genes so far described. The five Surfeit genes (Surf-1 to -5) that have been previously isolated and characterized do not share any DNA or amino acid sequence homology. These Surfeit genes appear to be housekeeping genes, with the Surf-3 gene encoding the 1.7a ribosomal protein and the Surf-4 gene encoding an integral membrane protein most likely associated with the endoplasmic reticulum. In this work, we have isolated the Surf-6 gene, a sixth member of the Surfeit locus. The Surf-6 gene contains four exons spanning a genomic region of 14 kb and specifies a mRNA of 2,571 bases. Surf-6 has features common to housekeeping genes because its transcript is present in every tissue tested, its 5' end is associated with a CpG-rich island, and its promoter does not contain a canonical TATA box. The Surf-6 long open reading frame encodes a novel highly basic polypeptide of 355 amino acids (28% Arg and Lys). By immunofluorescence and immunoblot analyses, the Surf-6 protein has been found to be located in the nucleolus and by immunocytochemical microscopy to be localized predominantly in the nucleolar granular component, a structure that is involved in ribosome maturation. These results indicate that the novel Surf-6 gene is involved in a nucleolar function.

CpG methylation and the binding of YY1 and ETS proteins to the Surf-1/Surf-2 bidirectional promoter

The divergently transcribed Surf-1 and Surf-2 genes are separated by a bi-directional, TATA-less promoter which contains three important factor-binding sites, Su1, Su2 and Su3. The transcription initiation factor YY1 binds to the Su1 site and stimulates transcription in the direction of Surf-1 and, to a lesser extent, Surf-2. Members of the ETS family of transcription factors bind to the Su2 and Su3 sites. Here we show that in transient transfection assays, transcription in both the Surf-1 and the Surf-2 direction is severely reduced by CpG methylation. Although the Su1 site contains three CpG dinucleotides, the binding of YY1 is not affected by CpG methylation. In contrast, the binding of two ETS factors (ETS-2 and PEA-3) to the Su2 site (which also contains three CpG dinucleotides) is totally abolished by CpG methylation. Finally, we show that methylation of a single C within the Su2 site is sufficient to prevent ETS factor binding.

UVB radiation-activated genes induced by transcriptional and posttranscriptional mechanisms in rat keratinocytes

The mechanisms utilized by ultraviolet B (UVB) radiation in the regulation of gene expression, as well as the genetic targets for transmission of the UVB signal, remain incompletely understood. To elucidate the mechanisms and targets for UVB activation in mammalian cells, we screened a keratinocyte cDNA library with differentially subtracted UVB-enriched cDNA probes. Twenty-three UVB-induced cDNA clones were isolated, including cDNAs for keratin, elongation factor-1 alpha, ferritin heavy chain, thioltransferase, cyclin G, cornifin, cellubrevin, poly(A) binding protein, and the surfeit locus. The temporal kinetics of maximal RNA induction following UVB exposure were heterogeneous, varying from 1 to 24 h post-UVB radiation. Analysis of the regulation of gene expression demonstrated that the levels of most UVB-induced mRNAs were also independently induced by serum and cycloheximide, features previously described for genes induced by DNA damage and members of the immediate early gene family. In contrast to results from studies of immediate early genes, treatment of keratinocytes with both serum and cycloheximide resulted in superinduction of only one mRNA transcript. Nuclear run-on assays demonstrated that UVB radiation increased the transcription rate in 8 of 23 genes, suggesting that UVB radiation utilizes both transcriptional and posttranscriptional mechanisms for the modulation of keratinocyte gene expression. The identification of a group of UVB-inducible keratinocyte genes should prove useful for the characterization of the genomic response to UVB radiation and the analysis of the molecular mechanisms underlying the UVB regulation of gene expression.

The surf-4 gene encodes a novel 30 kDa integral membrane protein

The mouse surfeit locus is a tight cluster of at least six genes (surf-1 to -6), unrelated by sequence homology, whose unique organization is conserved in vertebrates. We show that the surf-4 coding sequence is conserved between mouse and human. Primary sequence analysis predicts that the mouse surf-4 protein contains seven transmembrane domains and a double lysine endoplasmic reticulum (ER) retrieval motif on the carboxyl terminus. Translation of the mouse surf-4 cDNA in vitro resulted in the production of a 30 kDa membrane protein. Salt and detergent extraction procedures showed that the surf-4 protein associated tightly with the microsomal membranes. Proteolysis protection of 14 and 3 kDa fragments indicates that the surf-4 protein contains at least two membrane spanning domains: this is consistent with the proposed topology. Addition of the c-Myc epitope into three different regions of the surf-4 protein resulted in transfectants that expressed a myc-tagged protein. Immunofluorescence analysis of the three surf-4 myc chimeras yielded a cytoplasmic staining pattern. Consistent with the presence of the ER retrieval motif, the surf-4 myc protein was not detected at the plasma membrane. A model for the proposed structure of the surf-4 protein is presented.

The L19 ribosomal protein gene (RPL19): gene organization, chromosomal mapping, and novel promoter region

The intron-containing genes encoding rat and human ribosomal protein L19 (RPL19) have been cloned. The DNA sequences of the entire rat RPL19 gene and the 5' end of the human RPL19 gene have been determined. Sequence comparison of corresponding regions of the two genes reveals a striking interspecies homology in the 5' upstream region, outside the transcribed and coding regions. The transcriptional start sites of the two genes have been determined and are identical. Both rat and human RPL19 genes have 5' ends associated with CpG islands. A promoter deletion analysis of the rat RPL19 gene suggests that this promoter may differ from those of all previously characterized ribosomal protein genes in requiring far upstream sequences for efficient gene expression. By fluorescence in situ hybridization analysis, the position of the human RPL19 gene has been sublocalized to 17q11 and may be coamplified with the erbB-2 gene in human breast cancer cells. The similarities and differences between RPL19 and other previously characterized ribosomal protein genes are discussed.

The Surf-1 and Surf-2 genes and their essential bidirectional promoter elements are conserved between mouse and human

The organization of the Surfeit locus and the juxtaposition of at least five of the Surfeit genes (Surf-1 to -5) are conserved between mouse and human (Williams et al., 1988; Yon et al., 1993). In the mouse, the heterogeneous transcription start sites of the divergent Surf-1 and Surf-2 genes are separated by a maximum of only 73 bp (Williams and Fried, 1986). This region contains a bidirectional promoter composed of three major factor binding sites required for the efficient expression of both the Surf-1 and Surf-2 genes (Lennard and Fried, 1991). Here we report the isolation and characterization of the human Surf-1 and Surf-2 genes and their intergenic region. Although the major Surf-1 and Surf-2 transcription start sites are separated by 97 bp in the human and there are multiple differences in the mouse and human sequence between and around the transcriptional start sites, there is high conservation of the sequence specifying the three major factor binding sites of the bidirectional promoter. The three factor binding sites (HSu1, 2, and 3) present within the human promoter bind nuclear factors, of which the binding of HSu1 and HSu2 are competed by oligonucleotides carrying the corresponding mouse factor binding sites. The HSu3 site binds factors that are similar but apparently not direct homologs of those that bind to the equivalent mouse sequences. Human Surf-1 and Surf-2 cDNAs have been cloned and sequenced. The putative human Surf-1 and Surf-2 proteins are 77% and 69% identical to the corresponding mouse proteins.

YY1 is involved in the regulation of the bi-directional promoter of the Surf-1 and Surf-2 genes

The Surfeit locus is an unusual cluster of at least 6 housekeeping genes whose organisation is conserved between birds and mammals. We have previously shown that the divergently transcribed Surf-1 and Surf-2 genes are separated by a bi-directional, TATA-less promoter. In mouse, the Surf-1/Surf-2 promoter contains three important factor binding sites: Su1, Su2, and Su3. These sites are conserved between the mouse and human Surf-1/Surf-2 promoters, bind nuclear factors in vitro, and are required for accurate and efficient expression of Surf-1 and Surf-2 in vivo. Using gel retardation assays, methylation interference experiments, and specific antibodies we demonstrate that the Su1 binding factor is the initiator protein YY1. Over-expression of YY1 results in a major stimulation of transcription in the Surf-1 direction and a minor stimulation of transcription in the Surf-2 direction.

The pseudoautosomal regions of the human sex chromosomes

In human females, both X chromosomes are equivalent in size and genetic content, and pairing and recombination can theoretically occur anywhere along their entire length. In human males, however, only small regions of sequence identity exist between the sex chromosomes. Recombination and genetic exchange is restricted to these regions of identity, which cover 2.6 and 0.4 Mbp, respectively, and are located at the tips of the short and the long arm of the X and Y chromosome. The unique biology of these regions has attracted considerable interest, and complete long-range restriction maps as well as comprehensive physical maps of overlapping YAC clones are already available. A dense genetic linkage map has disclosed a high rate of recombination at the short arm telomere. A consequence of the obligatory recombination within the pseudoautosomal region is that genes show only partial sex linkage. Pseudoautosomal genes are also predicted to escape X-inactivation, thus guaranteeing an equal dosage of expressed sequences between the X and Y chromosomes. Gene pairs that are active on the X and Y chromosomes are suggested as candidates for the phenotypes seen in numerical X chromosome disorders, such as Klinefelter's (47,XXY) and Turner's syndrome (45,X). Several new genes have been assigned to the Xp/Yp pseudoautosomal region. Potential associations with clinical disorders such as short stature, one of the Turner features, and psychiatric diseases are discussed. Genes in the Xq/Yq pseudoautosomal region have not been identified to date.

Human L7a ribosomal protein: sequence, structural organization, and expression of a functional gene

A cDNA coding for the human L7a ribosomal protein (r-protein) was used to isolate the corresponding gene by screening two human genomic libraries constructed in bacteriophage lambda and in a cosmid vector. One of the cosmid clones isolated, cos1.1, contains the whole L7 alpha gene, composed of eight exons and seven introns spanning 3226 bp. As in other mammalian housekeeping genes, the promoter and the first exon of the L7 alpha reside within a CpG-rich island. Furthermore, similar to the other higher eukaryote r-protein-encoding genes characterized so far, the human L7 alpha gene has a C as the major transcriptional start point localized in a pyrimidine-rich region and lacks a canonical TATA sequence. We show that 130 bp of the human L7 alpha gene 5'-flanking region represent the minimal element required to promote its transcription. This element is strikingly conserved between the mouse and human L7 alpha genes. Finally, a comparison of the human L7 alpha gene coding sequence and the predicted amino acid (aa) sequence with the sequences of mouse L7a, rat L7a, and the homologous yeast L4 shows that the aa sequence has been highly conserved during evolution.

Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin

Current models suggest that tissue-specific genes are arranged in discrete, independently controlled segments of chromatin referred to as regulatory domains. Transition from a closed to open chromatin structure may be an important step in the regulation of gene expression. To determine whether the human alpha-globin cluster, like the beta-globin cluster, lies within a discrete, erythroid-specific domain, we have examined the long-range genomic organization and chromatin structure around this region. The alpha genes lie adjacent to at least four widely expressed genes. The major alpha-globin regulatory element lies 40 kb away from the cluster within an intron of one of these genes. Therefore, unlike the beta cluster, cis-acting sequences controlling alpha gene expression are dispersed within a region of chromatin that is open in both erythroid and nonerythroid cells. This implies a difference in the hierarchical control of alpha- and beta-globin expression.

Molecular cloning of mouse alcohol dehydrogenase-B2 cDNA: nucleotide sequences of the class III ADH genes evolve slowly even for silent substitutions

We have cloned and sequenced a cDNA encoding the mouse class III alcohol dehydrogenase, Adh-B2. Adh-B2 mRNA is detectable in all the mouse tissues tested. Class III ADHs are highly conserved: the deduced amino acid sequence of the mouse Adh-B2 is 91 to 97% identical to the human, horse and rat liver enzymes. The mouse Adh-B2 cDNA is 87% identical in nucleotide sequence to the human chi-ADH cDNA. Previously, a slower rate of evolutionary divergence of the amino acid sequences of class III ADH proteins was detected and ascribed to functional constraints upon the protein. Our analysis of the nucleotide sequences demonstrates that this cannot be the entire explanation, since the rate of silent (synonymous) nucleotide substitutions is also lower in the class III ADHs than in the class I ADHs.

Characterization of the opposite-strand genes from the mouse bidirectionally transcribed HTF9 locus

The mouse HTF9 locus contains two genes that are bidirectionally transcribed with opposite polarity from a shared CpG-rich island. Both genes were previously shown to be expressed in a housekeeping fashion in mouse. We have now determined the molecular organization of the genes over 12 kb surrounding the island. In addition, we show that the HTF9 locus resides in the proximal region of mouse chromosome 16. We have sequenced the cDNAs corresponding to both divergent transcripts. Both genes appear to code for novel proteins that are structurally unrelated to each other. Finally, we show that both genes are highly conserved and efficiently expressed in human cells.

Human VNTR sequences in porcine HTF-islands

Mapping of complex genomes has been influenced substantially by the isolation of locus-specific, but repetitive DNA elements known as VNTRs. Since a high GC-content is characteristic of most of these elements one might expect them to be clustered at least partially in CpG-islands. To address this question we have constructed a porcine liver DNA NotI-linkage library in pUC18 using isolated HTF-islands. HpaII tiny fragments ranging from less than 100 bp to 1 kb in length were randomly selected and analysed by sequencing. As expected from the source of DNA the clones were rich in CpG-, C- and G-content. Several clones exhibiting a repetitive (GGC)n-motif and sequences originally present in human VNTR-markers were shown to detect DNA fingerprints in different species (Homo sapiens, Sus scrofa domestica, Gallus domesticus, Glycine max, Saccharomyces cerevisiae). A subset of clones was used for hybridization experiments with porcine DNA and were shown to detect single-copy linkage fragments.