Human and mouse alpha-synuclein genes: comparative genomic sequence analysis and identification of a novel gene regulatory element

The human alpha-synuclein gene (SNCA) encodes a presynaptic nerve terminal protein that was originally identified as a precursor of the non-beta-amyloid component of Alzheimer's disease plaques. More recently, mutations in SNCA have been identified in some cases of familial Parkinson's disease, presenting numerous new areas of investigation for this important disease. Molecular studies would benefit from detailed information about the long-range sequence context of SNCA. To that end, we have established the complete genomic sequence of the chromosomal regions containing the human and mouse alpha-synuclein genes, with the objective of using the resulting sequence information to identify conserved regions of biological importance through comparative sequence analysis. These efforts have yielded approximately 146 and approximately 119 kb of high-accuracy human and mouse genomic sequence, respectively, revealing the precise genetic architecture of the alpha-synuclein gene in both species. A simple repeat element upstream of SNCA/Snca has been identified and shown to be necessary for normal expression in transient transfection assays using a luciferase reporter construct. Together, these studies provide valuable data that should facilitate more detailed analysis of this medically important gene.

Mutations are not uniformly distributed throughout the OCRL1 gene in Lowe syndrome patients

Lowe syndrome (OCRL) is an X-linked disorder involving the eyes, kidney, and nervous system that is caused by loss of function in the OCRL1 gene. OCRL1 contains 24 exons (23 of which are coding) and encodes a 105-kDa enzyme with phosphatidylinositol 4,5 bisphosphate (PtdIns[4,5]P2) 5-phosphatase activity. We published previously (1,2) 13 different mutations in 10 families. Four are missense other 8 mutations in 10 families. Four are missense mutations in highly conserved PtdIns (4,5)P2 5-phosphatase caused by nonsense mutations, and three others are premature terminations caused by frameshift mutations. One frameshift, a GT deletion in exon 21, has been observed previously in two unrelated Lowe syndrome patients, suggesting that it may be a relative "hotspot" for mutation in a disorder marked otherwise by allelic heterogeneity. We have also seen two other recurrent mutations. One is a nonsense mutation CGA > TGA in exon 2 observed in two patients and the second is a missense mutation CGA > CAA in exon 15 present in two unrelated patients. These 21 distinct mutations we have found in 25 Lowe syndrome patients occur in only 9 of the 24 exons: 10, 12, 13, 14, 15, 18, 19, 21, and 22. Interestingly, missense mutations have occurred only in exons 12 through 15 in highly conserved residues among the phosphatidylinositol 5-phosphatases. These observations suggest useful strategies for mutation screening in OCRL.

Spectrum of mutations in the OCRL1 gene in the Lowe oculocerebrorenal syndrome

The oculocerebrorenal syndrome of Lowe (OCRL) is a multisystem disorder characterized by congenital cataracts, mental retardation, and renal Fanconi syndrome. The OCRL1 gene, which, when mutated, is responsible for OCRL, encodes a 105-kD Golgi protein with phosphatidylinositol (4,5)bisphosphate (PtdIn[4,5]P2) 5-phosphatase activity. We have examined the OCRL1 gene in 12 independent patients with OCRL and have found 11 different mutations. Six were nonsense mutations, and one a deletion of one or two nucleotides that leads to frameshift and premature termination. In one, a 1.2-kb genomic deletion of exon 14 was identified. In four others, missense mutations or the deletion of a single codon were found to involve amino acid residues known to be highly conserved among proteins with PtdIns(4,5)P2 5-phosphatase activity. All patients had markedly reduced PtdIns(4,5)P2 5-phosphatase activity in their fibroblasts, whereas the ocrl1 protein was detectable by immunoblotting in some patients with either missense mutations or a codon deletion but was not detectable in those with premature termination mutations. These results confirm and extend our previous observation that the OCRL phenotype results from loss of function of the ocrl1 protein and that mutations are generally heterogeneous. Missense mutations that abolish enzyme activity but not expression of the protein will be useful for studying structure-function relationships in PtdIns(4,5)P2 5-phosphatases.

Physical mapping and genomic structure of the Lowe syndrome gene OCRL1

The oculocerebrorenal syndrome of Lowe (OCRL; McKusick 309,000) is a rare X-linked disorder characterized by mental retardation, congenital cataracts, and Fanconi syndrome of the proximal renal tubules. We have carried out physical mapping of the OCRL1 gene and determined that it contains 24 exons occupying 58 kb. The gene, located in Xq25-26, is transcribed in a centromeric to telomeric direction. Primers have been developed that allow all coding exons and their intron/exon boundaries to be amplified from genomic DNA for mutation detection. Two tetranucleotide tandem repeat polymorphisms were characterized that immediately flank the OCRL1 gene and, together, are informative in over 90% of females. Variable splicing was seen in the OCRL1 transcript, involving a small 24-bp exon. These results should prove useful to medical and molecular geneticists studying mutations and providing DNA diagnostic services to families dealing with Lowe syndrome as well as to cell biologists interested in structure-function relationships for the OCRL1 protein.

Two additional cases of osteogenesis imperfecta with substitutions for glycine in the alpha 2(I) collagen chain. A regional model relating mutation location with phenotype

The relationship between the clinical severity of osteogenesis imperfecta (OI) and the location and type of amino acid substitution in type I collagen is not identical for mutations in the alpha 1(I) and alpha 2(I) chains. Furthermore, the alpha 2(I) chain, once thought to be associated with moderate forms of OI, has now been associated with approximately as many lethal as non-lethal cases. We describe two novel substitutions for glycine in the alpha 2(I) chain, one associated with a lethal phenotype in twins and the other with a moderate non-lethal phenotype. The type I collagen of all probands was characterized electrophoretically by two populations of alpha chains, one normal and one with delayed migration. Cyanogen bromide peptides of the overmodified alpha 1(I) chains revealed delayed migration of all peptides except CB6. The indicated target region of alpha 1(I) and alpha 2(I) cDNA of the probands was analyzed by RNA-DNA hybrid analysis with RNase A digestion. All probands had mismatches in the region of alpha 2(I) coding for amino acids 642-912. The lethal phenotype was associated with a G-->A mutation, resulting in Gly706-->serine; the non-lethal mutation was a G-->T change resulting in Gly676-->valine. Both mutations occurred de novo in the probands; parental leukocyte DNA was normal. In conjunction with the previously described exon deletions and point mutations in alpha 2(I), these mutations define five alternating non-lethal/lethal regions along the chain and support a regional, as opposed to a gradient, model of OI pathophysiology. These mutations in particular help to define a lethal/non-lethal junction at about alpha 2(I) amino acid 700.

Serine for glycine substitutions in type I collagen in two cases of type IV osteogenesis imperfecta (OI). Additional evidence for a regional model of OI pathophysiology

Serine for glycine substitutions in type I collagen have been described in seven cases of lethal type II osteogenesis imperfecta (OI), and six cases of nonlethal OI. We describe here two cases of moderately severe type IV OI with serine substitutions at alpha 1(I) Gly352 and alpha 2(I) Gly922, respectively. In both cases, G-->A point mutations were detected by RNase A cleavage of RNA/RNA and RNA/DNA hybrids. These cases extend the location for serine substitutions producing the moderately severe OI phenotype to the alpha 2(I) chain and the amino-terminal end of the alpha 1(I) chain. Their location supports a regional model of OI pathophysiology for serine substitutions. The proband with alpha 2(I) Gly922-->Ser has both normal and overmodified forms of both type I collagen chains. The overmodified form has delayed migration of all CNBr peptides. Helix thermal stability is decreased 4 degrees C. The fibroblast collagen protein and RNA of her unaffected parents are normal. However, the father was demonstrated to be a mosaic carrier using leukocyte DNA. The fibroblasts of the proband whose serine substitution is at alpha 1(I) Gly352 synthesize type I procollagen chains with delayed electrophoretic migration; normally migrating forms are difficult to detect. Only alpha 1(I) CB 8 displayed delayed migration. Helix thermal stability is reduced 2 degrees C. Parental genomic DNA was normal.

A de novo G+1-->A mutation at the alpha 2(I) exon 16 splice donor site causes skipping of exon 16 in the cDNA of one allele of an OI type IV proband

We have investigated the procollagen, collagen, alpha 2(I) mRNA, and DNA of a proband with type IV OI. The proband synthesized two alpha 2(I) chains, one with normal electrophoretic migration and one more rapidly migrating. The fast alpha 2(I) chain was relatively retained within the cell and was present in collagens synthesized in the presence of alpha,alpha'-dipyridyl. The alpha 2(I) cyanogen bromide peptide CB 4-2 contained both normal and rapidly migrating components. Thermal stability of helices containing the rapidly migrating alpha 2(I) chain was reduced 6 degrees C. Parental fibroblast collagens were normal. RNA/RNA hybrids between proband total RNA and antisense riboprobe complementary to alpha 2(I) nt 236-1390 were digested with RNase A and T1. Digestion products seen exclusively in the proband suggested a structural change in the region coding for exons 16-19. The region which hybridized to the riboprobe was amplified using RNA-PCR and subcloned. Multiple restriction enzyme digestions of the two subcloned alleles suggested a structural change localized to the region coding for exons 16-17. Sequencing revealed a deletion of the 54 bp comprising exon 16 in the cDNA of one allele. The region of the proband's genomic DNA spanning exons 15-17 was amplified by PCR. The subcloned genomic fragments of each allele were distinguished by RNA/DNA hybrid analysis using a riboprobe complementary to normal genomic DNA from this region. Sequencing revealed a G+1-->A mutation at the exon 16 donor site in one allele. The mutation eliminates a StyI site.(ABSTRACT TRUNCATED AT 250 WORDS)

New autosomal recessive syndrome of sparse hair, osteopenia, and mental retardation in Mennonite sisters

We report on 2 Mennonite sisters with a syndrome of sparse hair, osteopenia, mental retardation, minor facial abnormalities, joint laxity, and hypotonia. Their asymptomatic consanguineous parents (inbreeding coefficient F = 1/64) have 6 other offspring, 3 of whom died in infancy of type II osteogenesis imperfecta (OI), and 3 of whom are normal. We analyzed collagens synthesized by cultured fibroblasts from these 2 sisters and their parents and detected no major abnormalities. Results of chromosomal and metabolic evaluations including amino acid analysis of plasma, urine, and hair were unremarkable. A literature search and survey of a computerized syndrome identification database did not disclose an identical phenotype. The sisters bear superficial resemblance to several known syndromes which we excluded on clinical and/or biochemical grounds. We conclude that they represent a new autosomal recessive syndrome, distinct from type II OI and perhaps unique to the Mennonite population or to this particular family.

Induction of major histocompatibility class I antigens by interferons in undifferentiated F9 cells

Mouse embryonal carcinoma F9 cells, upon treatment with interferons (IFNs), express major histocompatibility (MHC) Class I antigens, which are otherwise not expressed in these cells. Both IFN-gamma and IFN-alpha/beta increase the steady-state level of Class I mRNA within 60 min of the treatment which leads to the subsequent surface expression of the H-2Kb and H-2Db antigens, suggesting that undifferentiated F9 cells express IFN receptors. IFNs induce Class I antigen expression in F9 cells in a highly selective manner: unlike retinoic acid treatment which also stimulates the antigen expression, IFNs induce neither morphological differentiation, increased binding of epidermal growth factor, nor reduction of expression of stage specific embryonic antigen. The effect of IFNs is reversible; removal of IFNs, even after prolonged exposures, results in a rapid loss of the Class I gene expression. Further, Class I mRNA induction is not inhibited by cycloheximide, suggesting possible independence from de novo protein synthesis. This Class I antigen induction in F9 cells is reminiscent of that observed in somite stage mouse embryos by IFN treatment and may offer a model system to study activation of MHC genes during development.

Mouse major histocompatibility class I gene expression begins at midsomite stage and is inducible in earlier-stage embryos by interferon

To determine the timing of major histocompatibility complex class I gene expression during embryonic development, binding of anti-class I antibodies and appearance of class I gene transcripts were examined in mouse embryos from the egg-cylinder stage through day 16 of gestation. By using two series of monoclonal antibodies reactive with monomorphic and polymorphic determinants of class I antigens, it was found that cell-surface expression of the antigens becomes detectable at a low level only after midsomite stage on gestation day 10, at a time when embryos are developed beyond primordial organogenesis and have partial blood circulation. In agreement with the above finding, a low level of class I mRNA became detectable in day 9 and older embryos in blot hybridization. The level of class I transcripts in embryos at least to day 13 remained less than 1/50th that in adult spleen cells. Cells from head-fold stage embryos (gestation day 8), which otherwise do not have an appreciable amount of class I mRNA or surface antigens, begin to express a high level of antigens upon treatment with mouse alpha/beta or gamma interferon. This induction of class I antigen expression appears to be stage specific in that embryos in an earlier egg-cylinder stage (day 6) failed to express the antigens after interferon treatment. A possible role of interferons in activating class I genes during in vivo embryonic development is suggested.