Human genes involved in chromatin remodeling in transcription initiation, and associated diseases: An overview using the GENATLAS database

Chromatin structure is inextricably linked to transcription regulation and differentiation. It consists of a multicomponent system, and impairments in such complex arrays may elicit dramatic biological effects and diseases. We present an overview of human genes involved in chromatin remodeling, which consist of the histone acetyltransferase/deacetylase system and the SWI/SNF-like complexes containing DNA-dependent ATPase activity. Special attention is given to the functional and physical interactions in which these components are involved, notably as transcriptional coactivators and/or corepressors of a large variety of genes. Linking seemingly distinct pathways allows integration of individual components into complex genetic and molecular processes and assessment of the underlying molecular bases of diseases. This was performed using GENATLAS (http://www.infobiogen.fr/), a gene database which compiles the information relevant to the mapping efforts from the published literature.

Report on the Fifth International Workshop on Chromosome 9 held at Eynsham, Oxfordshire, UK, September 4-6, 1996

The Fifth International workshop on chromosome 9 comprised a gathering of 36 scientists from seven countries and included a fairly even distribution of interests along chromosome 9 as well as a strong input from more global activities and from comparative mapping. At least eight groups had participated in the goal set at the previous workshop which was to improve the fine genetic mapping in different regions of chromosome 9 by meiotic breakpoint mapping in allocated regions and this has resulted in some greatly improved order information. Excellent computing facilities were available and all contributed maps were entered not only into SIGMA (and thence submitted to GDB) but also into a dedicated version of ACEDB which can be accessed on the Web in the form of one of 28 slices into which the chromosome has been arbitrarily divided. It was generally agreed that the amount of data is now overwhelming and that the integration and validation of all data is not only unrealistic in a short meeting but probably impossible until the whole chromosome has been sequenced and fully annotated. Sequence-ready contigs presented at the meeting totalled about 3 MB which is about one fiftieth of the estimated length. The single biggest barrier to integration of maps is the problem of non-standard nomenclature of loci. In the past 2 workshops efforts have been made to compare traditional 'consensus' maps made by human insight (still probably best for small specific regions) with those generated with some computer assistance (such as SIGMA) and those generated objectively by defined computer algorithms such as ldb. Since no single form of map or representation is entirely satisfactory for all purposes the maps reproduced in the published version of the report are confined to one of the genetic maps, in which Genethon and older markers have been incorporated, a Sigma map of the genes as symbols together with a listing of known 'disease' genes on chromosome 9, and a revised assessment of the mouse map together with a list of mouse loci predicted to be on human chromosome 9. One of the 28 ACEDB slices is also shown to illustrate strengths and weaknesses of this approach. Workshop files include not only all maps available at the time but also details of loci and details of the meiotic breakpoints in the CEPH families (http:/(/)www.gene.ucl.ac.uk/scw9db.shtml) .

A metric map of humans: 23,500 loci in 850 bands

High-resolution maps integrated with the enhanced location data base software (LDB+) give improved estimates of genetic parameters and reveal characteristics of cytogenetic bands. Chiasma interference is intermediate between Kosambi and Carter-Falconer levels, as in Drosophila and the mouse. The autosomal genetic map is 2832 and 4348 centimorgans in males and females, respectively. Telomeric T-bands are strikingly associated with male recombination and gene density. Position and centromeric heterochromatin have large effects, but nontelomeric R-bands are not significantly different from G-bands. Several possible reasons are discussed. These regularities validate the maps, despite their high resolution and inevitable local errors. No other approach has been demonstrated to integrate such a large number of loci, which are increasing at about 45% per year. The maps and the data and software from which they are constructed are available through the Internet (http:@cedar.genetics.soton.ac.uk/public_html). Successive versions of this location data base may also be accessed on CD-ROM.

Exclusion of the cone-specific alpha-subunit of the transducin gene in Stargardt's disease

Stargardt's disease is an autosomal recessive infantile macular degeneration of unknown origin whose gene has been recently mapped to chromosome 1p21-p13 by linkage analysis in eight multiplex families. Since the cone-specific alpha-subunit of the transducin gene (GNAT2) has been mapped to chromosome 1p13, we tested GNAT2 as the disease-causing gene in our series. Using a novel intragenic polymorphism, we show here that GNAT2 is most probably located centromeric to the genetic interval encompassing the disease gene (D1S424-D1S236, location score = 3.54). In addition, single-strand conformation polymorphism and sequence analyses of the eight exons of the GNAT2 gene was performed in our probands. No evidence of a deleterious base substitution was observed in any affected individual. Taken together, these results support the exclusion of GNAT2 as the causal disease gene of Stargardt's disease. come. The pathogenesis is unknown and the treatment is limited to ultraviolet ray protection with dark glasses. Stargardt's disease has been recently mapped to chromosome 1p21-p13 in the genetic interval defined by loci D1S424 and D1S236. In addition, our previous study has suggested that Stargardt's disease is genetically homogeneous (Kaplan et al. 1993). With respect to the physical mapping of the proteins specific to the retinal pigmentary epithelium or to cones we noted that the cone-specific alpha-subunit of the transducin gene (GNAT2) has been mapped to chromosome 1p13 (Wilkie et al. 1992). The human GNAT2 is 9967 bp in length and consists of eight exons with seven introns (Morris and Fong 1993). In the present study, we examined this gene as the candidate gene in eighteen unrelated patients affected with Stargardt's disease.

Stargardt's disease is not allelic to the genes for neuronal ceroid lipofuscinoses

Stargardt's disease is an autosomal recessive condition characterised by a rapid and bilateral loss of central vision at around 7 to 12 years, with typical changes in the macular and perimacular region. It is one of the most frequent causes of macular degeneration in childhood and accounts for 7% of all retinal dystrophies. Considering that inclusions of lipofuscin-like substances are observed in retinal pigmentary cells of patients with Stargardt's disease on the one hand, and that the early symptoms of neuronal ceroid lipofuscinosis (CLN3) are suggestive of Stargardt's disease on the other hand (age of loss of visual acuity, appearance of the fundus), we decided to test allelism of Stargardt's disease with the infantile (CLN1) and juvenile forms of neuronal ceroid lipofuscinosis (CLN3), which map to chromosomes 1p32 and 16p12-p11 respectively. Using highly informative microsatellite DNA markers in eight multiplex families, we were able to exclude Stargardt's disease from the vicinity of the CLN1 and CLN3 loci. These results strongly reject the hypothesis of allelism of Stargardt's disease with the neuronal forms of ceroid lipofuscinosis.

Mapping of acute (type I) spinal muscular atrophy to chromosome 5q12-q14. The French Spinal Muscular Atrophy Investigators

Linkage analysis in twenty-five families with acute (type I) spinal muscular atrophy (SMA) showed that the mutant gene responsible for the disorder is tightly linked to the D5S39 locus. The mutation(s) causing the intermediate (type II) and juvenile chronic (type III) forms of SMA were also mapped to DNA marker D5S39 on chromosome 5 (5q12-q14). Thus, the three forms, which have been differentiated clinically on the basis of age of onset and clinical course, are most probably due to different mutations at a single locus on chromosome 5. Prenatal diagnosis of SMA type I will now be possible.

[Prenatal diagnosis of various hereditary blinding diseases]

The availability of more and more reliable obstetrical echographies makes now possible to screen fetuses for microphtalmies and anophtalmies. More over, by mean of linkage studies with DNA markers within a family, we can identify the women who will transmit X-linked diseases, and realize a prenatal diagnosis. This technology can be applied to the following ophthalmological diseases: the X-linked retinoschisis, the choroideremia, the ocular albinism, the Noorie disease, and recently the retinoblastoma. From now on, the use of such a technology which makes it possible to detect ophthalmological diseases in the fetuses, is posing ethical problems especially in case of diseases without any survival prognosis involvement.

[Associated forms of hereditary chorioretinal degeneration]

A retrospective study of 324 cases of chorioretinal heredodegeneration of all kinds shows an associated pathology in 44% of cases. These associated anomalies point out the need of a complete physical examination, a familial inquest keeping in mind genetic counseling. They are a good model for a high resolution cytogenetic study to find microdeletions which can allow to precise the genome's map.

[Heterogeneity of carnitine palmitoyltransferase deficiencies. Deficiency of CPT I in the hepatic form and CPT II in the muscular form]

Carnitine Palmitoyl Transferase (CPT) deficiencies are found in 2 different clinical forms: muscular and hepatic. The study of fibroblasts of 2 patients corresponding to each of these situations showed that these phenotypes are associated with different abnormalities of CPT, CPT I in the hepatic type and CPT II in the muscular type. The functional consequences of both abnormalities are different. In the hepatic type, CPT I deficiency induces a lack of long chain fatty acid (LCFA) oxidation in fibroblasts as well as, probably, in the patient's liver. In the muscular type, CPT II deficiency has no functional consequences in the fibroblast, contrary to what is observed in the patient's muscle. It is postulated that control of the mitochondrial LCFA oxidation in the liver and in the fibroblasts depends on CPT I, while it depends on CPT II in the muscle.

Human genes for glutathione S-transferases

The tissue distribution of different glutathione S-transferases (GST) is analysed by electrophoresis. The existence of GST"e" (erythrocyte), GST3, GST1, and GST2 is confirmed. GST"e" the fastest and most thermolabile of different GST analysed is observed only in erythrocyte cells. GST3 which migrates more slowly than GST"e" is present in all tissues and cells analysed, excepted for erythrocyte cells in which only GST"e" is observed. GST1 presents a polymorphism with four phenotypes, 1, 1/2, 2, and 0 controlled by three alleles 1, 2, and 0 (null). With the sample of 56 livers analysed the different frequencies obtained are 9%, 5%, 43%, 43% for the phenotypes 1, 1/2, 2, and 0 respectively and 0.074 (p), 0.279 (q), 0.647 (r) for the alleles, 1, 2, and 0 (null). GST2 presents variant patterns due probably, in the majority of cases, to post-synthetic modifications rather than allelic variation. Two new GST are described, GST4 and GST5. GST4 abundant in muscle tissue is a dimeric protein. GST4 forms with GST1 a heterodimeric band. GST5 is observed in brain homogenates. For the chromosome localization the results obtained by man (leucocytes)-mouse somatic cell hybrid analysis indicate that the gene for leucocytes GST is on chromosome 11. This gene is the structural GST3 gene.

[Epidemiological and genetic study of 3 congenital cardiopathies with neonatal disclosure]

A familial study was undertaken on 382 probands with transposition of the great vessels, 348 with coarctation of the aorta and 143 with hypoplastic left heart syndrome. It allowed to assess in sibs the frequency of identical congenital heart diseases (respectively 0.15, 0.42 and 3.41%) and of all 7.32%). The epidemiological study did not provide further data worth noting. At the origin of the transposition of the great vessels, tetratogenetic factors are added to genetic factors, whose part is of little importance; hypoplastic left heart syndromes are heterogeneous (recessive autosomal transmission, chromosome abnormalities, sporadic cases). Coarctations of the aorta, which are dependent on different mechanisms are also heterogeneous. It is possible that common factors, whether hereditary or not, play a part on one hand in hypoplastic left heart syndromes and coarctations of the aorta, and, on the other hand, in some congenital heart diseases.

Coreactivation of four inactive X genes in a hamster x human hybrid and persistence of late replication of reactivated X chromosome

Hamster-human hybrids which contained an inactive human X chromosome were treated by 5-azacytidine. Hypoxanthine guanine phosphoribosyltransferase derepressed hybrids were selected and derepression of three other loci, phosphoglycerate kinase, alpha-galactosidase, and glucose-6-phosphate dehydrogenase were studied. Among 32 hybrids selected for hypoxanthine guanine phosphoribosyltransferase, two were found to be reactivated at four X loci. The independence or nonindependence of the reactivation events will be discussed. No correlation was found between the time of replication and the expression or nonexpression of the X chromosome genes: X chromosomes reactivated at four loci remained late replicating; conversely early replication can exist without the expression of some X genes.

Congenital lactic acidosis, alpha-ketoglutaric aciduria and variant form of maple syrup urine disease due to a single enzyme defect: dihydrolipoyl dehydrogenase deficiency

A 6-month-old girl with vomiting, hypotonia and motor retardation was found to have elevated blood lactate, pyruvate, and branched chain amino acids associated with ketoglutaric aciduria. The combination of a congenital lactic acidosis with a variant form of maple syrup urine disease and ketoglutaric aciduria suggested a defect of a single component, common to pyruvate dehydrogenase, to branched chain ketoacid dehydrogenase, and to alpha-ketoglutarate dehydrogenase. Dihydrolipoyl dehydrogenase is the common component (E3). The three enzyme activities and the E3 component activity were found to be reduced in liver and cultured fibroblasts, thus confirming that a single defect of this component can result in a multiple deficiency involving several oxidative decarboxylation reactions.

Biochemical evidence for the non-inactivation of the steroid sulfatase locus in human placenta and fibroblasts

Steroid sulfatase activities are significantly higher in placentas obtained after the birth of girls than after the birth of boys, and also in female fibroblasts compared to male strains. This constitutes biochemical evidence for the non-inactivation of the X-linked sulfatase locus. No hydrolytic activity is found in the fibroblasts of ichthyotic boys. Heterozygosity is demonstrated in the fibroblasts of the four mothers studied, as they have steroid sulfatase activity of less or equivalent to the normal male value.

[Lysinuric protein intolerance: a severe hyperammonemia secondary to l-arginine deficiency (author's transl)]]

Lysinuric protein intolerance is an autosomal recessive disease, due to a defect in intestinal, renal and hepatic dibasic amino acid transport. Two new cases in the same family are reported. The disease appears progressively during the first months of life with failure to thrive, anorexia, vomiting, diarrhea, hepatosplenomegaly, muscular weakness, osteoporosis, anemia, leukothrombocytopenia, hyperammonemia and orotic aciduria after a high-protein intake. Hyperdibasicamino-aciduria was associated with subnormal plasma concentrations of the same aminoacids. Oral l-arginine, l-ornithine, l-lysine, and lysyl-glycine loads confirmed the diagnosis. The supplementation of the diet with l-citrulline resulted in normal levels of blood ammonia. However, hepatosplenomegaly, muscular weakness, osteoporosis remained unchanged and growth was not improved. These may be due to lysine deficiency.

Neonatal glutaric aciduria type II: an X-linked recessive inherited disorder

A new case of neonatal glutaric aciduria type II is reported. Neonatal acidosis, hypoglycemia, and hyperammonemia were characteristic. The baby died at four days of age. Organic acid analysis revealed massive glutaric aciduria with elevated concentrations of butyric, isobutyric, n-butyric, and isovaleric acid in his urine. The baby's pedigree suggested strongly an X-linked recessive mode of inheritance. Clinically, biochemically, and genetically glutaric aciduria type II is an heterogeneous disorder. The neonatal form is an X-linked inherited disorder which presents early in life, and is associated with metabolic acidosis, hypoglycemia, and hyperammonemia, and leads to death in the neonatal period. The mild form is an autosomal recessive inherited disease which may present even in adults, and is associated with recurrent hypoglycemia without ketosis and usually improves. Nevertheless the same unusual organic acid pattern is observed in both forms. The basic biochemical defect must be distinct and has not been elucidated.

Inheritance in the etiology of convergent squint

From a study of 195 unselected cases of idiopathic squint, the authors distinguish three types of squint (simple, accommodative, and with amblyopia). Both sexes are equally affected, the age of onset is later in accommodative squint than in the other two types. The percentage of familial cases (65.4%) is comparable whatever the type of squint involved, the sex of the subjects or the age of onset. The family study and the complex segregation studies show that the hypothesis of dominant autosomal inheritance with incomplete penetrance is the most probable for the three types, but they do not affirm that three distinct entities are involved.

[Risk of recurrence of several congenital malformations: anencephaly, spina bifida, cleft palate and cleft lip]

Recurrence risks were estimated for some congenital malformation from a multifactorial model according to the method given by Smith (1971). Risks were estimated for cleft lip with or without cleft palate, cleft palate alone, anencephaly and spina bifida from data on frequency and heritability collected in France. Results are given in tables representing risks for some 180 specific family histories.

Mutation theory of carcinogenesis in retinoblastoma

To test Knudson's hypothesis that two successive mutations are involved in retinoblastoma, we studied the data on 899 cases. Some of the findings appeared to differ from those that might be expected if Knudson's hypothesis were correct. Certain criticisms of Knudson's methodology and model were suggested. Alternative explanations proposed were 1) the role of the sequence in which mutations occur, and 2) the possibility of three mutational events.

[Prevalence of etinoblastoma in the Midi-Pyrenées area]

The frequency of retinoblastoma was estimated in southwest France (Midi-Pyrénées) during the 1950-1969 period. Twenty-three cases were detected among 507 157 liveborns. After correcting for the probability of ascertainment of patient, the estimated frequency is 1 per 15 849 births. The proportion of unilateral cases is estimated 91 percent after correcting for the higher probability of ascertaining bilateral cases.

[Frequency of birth defects. Study of a maternity hospital in Paris]

A retrospective study of 20,591 live born babies and still birth was made in order to estimate the incidence of congenital malformations total and by type diagnosed at birth. The total incidence is 1,74 p. 100. The sex ratio, the mean birth rank and parental ages were computed for the different types of malformation and in the control group. The birth weight was low in case of severe malformation. It was found that malformations were associated with significantly raised abortions and still birth rates among previous pregnancies.