Identification and characterization of a novel human brain-specific gene, homologous to S. scrofa tmp83.5, in the chromosome 10q24 critical region for temporal lobe epilepsy and spastic paraplegia.

We describe the structure, genomic organization, and some transcription features of a human brain-specific gene previously localized to the genomic region involved in temporal lobe epilepsy and spastic paraplegia on chromosome 10q24. The gene, which consists of six exons disseminated over 16 kb of genomic DNA, is highly homologous to the porcine tmp83.5 gene and encodes a putative transmembrane protein of 141 amino acids. Unlike its porcine homolog, from which two mRNAs with different 5'-sequences are transcribed, the human gene apparently encodes three mRNA species with 3'-untranslated regions of different sizes. Mutation analysis of its coding sequence in families affected with temporal lobe epilepsy or spastic paraplegia linked to 10q24 do not support the involvement of this gene in either diseases.

Characterization of 16 novel human genes showing high similarity to yeast sequences.

The entire set of open reading frames (ORFs) of Saccharomyces cerevisiae has been used to perform systematic similarity searches against nucleic acid and protein databases: with the aim of identifying interesting homologies between yeast and mammalian genes. Many similarities were detected: mostly with known genes. However: several yeast ORFs were only found to match human partial sequence tags: indicating the presence of human transcripts still uncharacterized that have a homologous counterpart in yeast. About 30 such transcripts were further studied and named HUSSY (human sequence similar to yeast). The 16 most interesting are presented in this paper along with their sequencing and mapping data. As expected: most of these genes seem to be involved in basic metabolic and cellular functions (lipoic acid biosynthesis: ribulose-5-phosphate-3-epimerase: glycosyl transferase: beta-transducin: serine-threonine-kinase: ABC proteins: cation transporters). Genes related to RNA maturation were also found (homologues to DIM1: ROK1-RNA-elicase and NFS1). Furthermore: five novel human genes were detected (HUSSY-03: HUSSY-22: HUSSY-23: HUSSY-27: HUSSY-29) that appear to be homologous to yeast genes whose function is still undetermined. More information on this work can be obtained at the website http://grup.bio.unipd.it/hussy

Fine mapping and genomic structure of ACTN2, the human gene coding for the sarcomeric isoform of alpha-actinin-2, expressed in skeletal and cardiac muscle.

The present paper reports on the fine mapping of the ACTN2 gene and on the reconstruction of its genomic structure. By radiation hybrid mapping, the gene was located about 912 cR from the 1p-telomere. ACTN2 was placed between the marker WI-9317 (alias D1S2421) and the marker AFMA045ZC5, within the chromosomal band 1q43. The gene was detected in YAC 955 c 12. This YAC was used as template DNA for long-distance and Alu-PCR, using a set of putative exonic primers, designed on the cDNA sequence of alpha-actinin-2, in order to characterize the ACTN2 intron-exon boundaries. The entire genomic structure of the gene was reconstructed. The ACTN2 gene contained 21 exons, in a segment spanning about 40 kb of genomic DNA. Only the proximal part of the gene shows a high conservation through evolution, whereas in the remaining part a divergence from the genomic organization of C. elegans and D. melanogaster was noticed. A series of intronic primers was specifically designed and produced, to amplify all the exons of ACTN2, directly from genomic DNA. This will enable mutation screening in patients affected with hereditary diseases linked to the marker CA4F/R, a polymorphism in the last intron of the alpha-actinin-2 gene.

A comprehensive, high-resolution genomic transcript map of human skeletal muscle.

We present the Human Muscle Gene Map (HMGM), the first comprehensive and updated high-resolution expression map of human skeletal muscle. The 1078 entries of the map were obtained by merging data retrieved from UniGene with the RH mapping information on 46 novel muscle transcripts, which showed no similarity to any known sequence. In the map, distances are expressed in megabase pairs. About one-quarter of the map entries represents putative novel genes. Genes known to be specifically expressed in muscle account for <4% of the total. The genomic distribution of the map entries confirmed the previous finding that muscle genes are selectively concentrated in chromosomes 17, 19, and X. Five chromosomal regions are suspected to have a significant excess of muscle genes. Present data support the hypothesis that the biochemical and functional properties of differentiated muscle cells may result from the transcription of a very limited number of muscle-specific genes along with the activity of a large number of genes, shared with other tissues, but showing different levels of expression in muscle. [The sequence data described in this paper have been submitted to the EMBL data library under accession nos. F23198-F23242.]

ARVD4, a new locus for arrhythmogenic right ventricular cardiomyopathy, maps to chromosome 2 long arm.

Autosomal dominant arrhythmogenic right ventricular dysplasia (ARVD; MIM 107970) is a genetically heterogeneous cardiomyopathy, which often causes sudden death in juveniles and athletes. Two disease loci were previously mapped respectively to 14q23-q24 (ARVD1) and to 1q42-q43 (ARVD2). A third possible locus was assigned to 14q12-q22. We report here on a linkage study performed on three independent families with recurrence of ARVD characterized by localized involvement of the left ventricle. In these families the disease appears to be transmitted with three polymorphic DNA markers of the chromosome 2 long arm, showing a maximum lod score of 3.46 at theta = 0 for the marker D2S152. The multipoint linkage analysis suggests that the novel ARVD locus, provisionally named ARVD4, maps to 2q32. 1-q32.3, within the chromosomal region including markers D2S152, D2S103, and D2S389.

The preliminary transcript map of a human skeletal muscle.

By sequencing 11,405 individual expressed sequence tags (ESTs) from a cDNA library of a human skeletal muscle, we identified 1945 individual transcripts, 725 of which showed no correspondence with known human genes. We report here the chromosomal localization of 267 of these, obtained by radiation hybrid (RH) mapping. The map position of additional 242 ESTs from the same library, corresponding to known human genes, is also reported. The resulting information provides a preliminary genomic transcriptional profile of a human muscle. Several genes occur in clusters on different chromosomes. Moreover, chromosomes 17, 19, 21 and X appear to be significantly rich in muscle ESTs. By analysing several collections of ESTs from different tissues, we observed significant deviations in the distribution of ESTs by chromosome in fetal heart, adult brain and adult retina, supporting the hypothesis that a non-random localization of genes expressed in specific tissues might not be uncommon. The selective concentration of expressed genes in some chromosomes and in specific chromosomal subregions in a given tissue might reflect the existence of batteries of genes under the same control mechanisms, regulating tissue-specific gene expression.

Chromosome assignment of 115 expressed sequence tags (ESTs) from human skeletal muscle.

The chromosome assignment of 115 expressed sequence tags (ESTs) from human skeletal muscle, 101 of which identify unknown human genes, is reported. The ESTs were selected among over 4,000 obtained from systematic sequencing of a skeletal muscle cDNA library containing 3' portions of the mRNAs. Chromosome assignments were obtained by PCR amplification of two panels of human x rodent somatic cell hybrids. Analysis of these preliminary data suggests a nonrandom distribution of muscle ESTs in the human chromosome complement. The unexpected occurrence of multiple chromosome localizations for some ESTs is discussed.

Fine mapping of five human skeletal muscle genes: alpha-tropomyosin, beta-tropomyosin, troponin-I slow-twitch, troponin-I fast-twitch, and troponin-C fast.

In this paper the chromosomal localization of the human skeletal muscle genes Troponin-I slow-twitch (TNNI1), Troponin-I fast-twitch (TNNI2), and Troponin-C fast (TNNC2) and the refinement of the position for alpha-Tropomyosin (TPM1) and beta-Tropomyosin (TPM2) are reported. By radiation hybrid mapping, TPM1 was assigned to chromosome 15q22.1, TPM2 to chromosome 9p13.2-p13.1, TNNI1 to chromosome 1q31.3, TNNI2 to chromosome 11p15.5, and TNNC2 to chromosome 20q12-q13.11. The genomic distribution of these genes is discussed, with particular emphasis on the cluster organization of the Troponin genes.

Chromosomal localization of four MAPK signaling cascade genes: MEK1, MEK3, MEK4 and MEKK5.

The mitogen-activated protein kinase (MAPK) signaling cascade is one of the most important mechanisms for the cytoplasmic transduction of extracellular signals. We report the chromosomal localization of the human MEK1, MEK3, MEK4 and MEKK5 genes, involved in the MAPK cascade. Using radiation hybrid mapping, MEK1 was assigned to chromosome 15q22.1 --> q22.33, MEK3 to chromosome 17q11.2, MEK4 to chromosome 17p12, and MEKK5 to chromosome 6q22.33.

Chromosomal localization of the human genes, CPP32, Mch2, Mch3, and Ich-1, involved in cellular apoptosis.

Members of the ICE/CED-3 protease family appear to play an essential role in programmed cell death process. In this paper the chromosomal localization of the human genes CPP32, Mch2, Mch3 and Ich-1 is reported, obtained by Radiation Hybrid Mapping. CPP32 was assigned to chromosome 4q33-q35.1, Mch2 to chromosome 4q25-q26, Mch3 to chromosome 10q25.1-q25.2 and Ich-1 to chromosome 7q35. Ich-1 was found to map very close to the marker WI-9353. The possible overlapping of the two independent locus assignments is considered. The genomic distribution of these genes is discussed, with particular reference to the co-location with some human genetic diseases all characterized by autosomal dominant inheritance and by similar malformative features.