Biomedical subjects

H Lehrach

Publications and source records attributed to H Lehrach.

At least 109 records · Page 6Linked to original sources

PubMed1998

Gridded genomic libraries of different chordate species: a reference library system for basic and comparative genetic studies of chordate genomes.

The use of genomic libraries maintained in arrayed format is becoming a more and more popular tool for the analysis of molecular evolution and comparative molecular development. Being able to use already existing reference libraries considerably reduces the work load, and if results are made publicly available, it will facilitate in silica experiments in the future. Here we describe the construction and preliminary characterization of six cosmid libraries of different chordate species, Ciona intestinalis (Hemichordate), Branchiostoma floridae (Cephalochordate), Lampetra fluviatilis (Cyclostoma), Xiphophorus maculatus, and Danio rerio (Osteichthyes) in Lawrist7 and Fugu rubripes in Lawrist4.

Animals↗

PubMed1998

Gene mapping in zebrafish using single-strand conformation polymorphism analysis.

To exploit fully the power of the zebrafish system as a model for vertebrate development, it will be necessary to develop efficient tools for genomic analysis. In this report we have tested whether single-strand conformation polymorphism analysis (SSCP) can be utilized for gene mapping in zebrafish. Over 100 primer pairs derived from noncoding regions of known genes and partially characterized cDNAs were analyzed, and a polymorphism frequency of approximately 50% was detected in zebrafish strains used for genetic mapping studies. A subset of these polymorphic cDNAs was localized on the zebrafish map. SSCP thus represents an efficient strategy for mapping transcribed sequences with a high resolution in the zebrafish genome, which will facilitate the integration of existing zebrafish framework maps, the generation of a zebrafish EST map, and the application of alternative gene localization strategies such as comparative mapping.

3' Untranslated Regions↗

PubMed1998

Huntingtin aggregation monitored by dynamic light scattering.

An initial stage of fibrillogenesis in solutions of glutathione S-transferase-huntingtin (GST-HD) fusion proteins has been studied by using dynamic light scattering. Two GST-HD systems with poly-L-glutamine (polyGln) extensions of different lengths (20 and 51 residues) have been examined. For both systems, kinetics of z-average translation diffusion coefficients (Dapp) and their angular dependence have been obtained. Our data reveal that aggregation does occur in both GST-HD51 and GST-HD20 solutions, but that it is much more pronounced in the former. Thus, our approach provides a powerful tool for the quantitative assay of GST-HD fibrillogenesis in vitro.

Glutathione Transferase↗

PubMed1998

Comparative gene expression profiling by oligonucleotide fingerprinting.

The use of hybridisation of synthetic oligonucleotides to cDNAs under high stringency to characterise gene sequences has been demonstrated by a number of groups. We have used two cDNA libraries of 9 and 12 day mouse embryos (24 133 and 34 783 clones respectively) in a pilot study to characterise expressed genes by hybridisation with 110 hybridisation probes. We have identified 33 369 clusters of cDNA clones, that ranged in representation from 1 to 487 copies (0.7%). 737 were assigned to known rodent genes, and a further 13 845 showed significant homologies. A total of 404 clusters were identified as significantly differentially represented (P < 0.01) between the two cDNA libraries. This study demonstrates the utility of the fingerprinting approach for the generation of comparative gene expression profiles through the analysis of cDNAs derived from different biological materials.

Animals↗

PubMed1998

HAP1-huntingtin interactions do not contribute to the molecular pathology in Huntington's disease transgenic mice.

HAP1 (huntingtin associated protein) has previously been found to interact with huntingtin (htt) in a glutamine length dependent manner and has been proposed to play a role in the cell specific neurodegeneration observed in Huntington's disease (HD). We have isolated mouse HAP1 (hap1) and have shown that expression is not enriched in areas specifically affected in HD. We have used the yeast two hybrid system to demonstrate that htt amino acids 171-230 are necessary for the hap1-htt binding and that hapl does not interact with the transgene exon 1 protein in a transgenic model of HD.

Amino Acid Sequence↗

PubMed1998

A cosmid and cDNA fine physical map of a human chromosome 13q14 region frequently lost in B-cell chronic lymphocytic leukemia and identification of a new putative tumor suppressor gene, Leu5.

B-cell chronic lymphocytic leukemia (B-CLL) is a human hematological neoplastic disease often associated with the loss of a chromosome 13 region between RB1 gene and locus D13S25. A new tumor suppressor gene (TSG) may be located in the region. A cosmid contig has been constructed between the loci D13S1168 (WI9598) and D13S25 (H2-42), which corresponds to the minimal region shared by B-CLL associated deletions. The contig includes more than 200 LANL and ICRF cosmid clones covering 620 kb. Three cDNAs likely corresponding to three different genes have been found in the minimally deleted region, sequenced and mapped against the contigged cosmids. cDNA clone 10k4 as well as a chimeric clone 13g3, codes for a zinc-finger domain of the RING type and shares homology to some known genes involved in tumorigenesis (RET finger protein, BRCA1) and embryogenesis (MID1). We have termed the gene corresponding to 10k4/13g3 clones LEU5. This is the first gene with homology to known TSGs which has been found in the region of B-CLL rearrangements.

Amino Acid Sequence↗

PubMed1998

A gridded genomic library of the honeybee (Apis mellifera): a reference library system for basic and comparative genetic studies of a hymenopteran genome.

We present a gridded genomic library of the honey-bee (Apis mellifera) for comparative and basic genetic study of the honeybee genome. The library will be established as a "Reference Library" system, and clones as well as data will be shared with the entire scientific community. This will accelerate the molecular level of honeybee genetics, combining the efforts of different laboratories. Because of male haploidy and the high rate of recombination, the honeybee is becoming a model organism for genomic studies of naturally occurring traits and behavioral genetics. The library consists of about 110,000 clones spotted at high density onto four filter membranes, representing 22 genome equivalents. Preliminary analysis using single-copy sequences revealed a positive clone number of the same order. The techniques for library generation and preliminary analysis as well as library access are described.

Animals↗

PubMed1998

Cloning of a novel human putative type Ia integral membrane protein mapping to 21q22.3.

The distal part of human chromosome 21q22.3 is exceptionally gene rich and contains several loci that have been linked to hereditary disorders. In the course of constructing an extensive transcript map for chromosome 21, we have isolated numerous coding segments in 21q22.3 that represent potential candidate genes in this region. Following this approach, we have cloned a novel single-copy gene (C21orf3) (HGMW-approved symbol C21orf1) expressed as a unique 2.69-kb mRNA in a wide range of tissues. We have precisely mapped C21orf3 by fiber FISH distal to marker D21S171. The C21orf3 gene encodes a predicted protein of 180 residues that does not share any sequence homology with other known proteins. C21orf3 harbors predicted structural features of a type Ia integral membrane protein and contains a tetrapeptide motif (YXRF) observed in several cell surface proteins involved in signal transduction. Although the function of C21orf3 is still unknown, this novel gene may play an important role in a cell trafficking mechanism.

Amino Acid Sequence↗

PubMed1998

Transcriptional map of the 2.5-Mb CBR-ERG region of chromosome 21 involved in Down syndrome.

The region of chromosome 21 between genes CBR and ERG (CBR-ERG region), which spans 2.5 Mb on 21q22.2, has been defined by analysis of patients with partial trisomy 21. It contributes significantly to the pathogenesis of many characteristics of Down syndrome, including morphological features, hypotonia, and mental retardation. Cosmid contigs covering 80% of the region were constructed and EcoRI maps produced. These cosmids were used for exon trapping and cDNA selection from three cDNA libraries (fetal brain, fetal liver, and adult skeletal muscle). Isolated exons and cDNAs were mapped on the EcoRI map, organized into contigs, sequenced, and used as probes for Northern blot analysis of RNA from fetal and adult tissues. We identified 27 genuine or highly probable transcriptional units evenly distributed along the CBR-ERG region. Eight of the transcriptional units are known genes.

Chromosome Mapping↗

PubMed1998

CAG/CTG and CGG/GCC repeats in human brain reference cDNAs: outcome in searching for new dynamic mutations.

CAG and CGG expansion is associated with 10 inherited neurological diseases and is thought to be involved in other human genetic diseases. To identify new candidate genes, we have undertaken a large-scale screening project for CAG/CTG ([CAG]n) and CGG/GCC ([CGG]n) repeats in human brain reference cDNAs. Here, we present the final classification for 597 cDNAs selected by CAG and CGG hybridization from two libraries (100,128 clones) and the updated characterization of [CAG]n- and [CGG]n-positive cDNAs (repeat polymorphism and cDNA localization). We have selected 124 CAG and 83 CGG hybridization-positive clones representing new genes, from which 49 CAG and 7 CGG repeats could be identified. New [CAG]n and [CGG]n with more than seven to nine units were rare (1/2000), and perfect [CAG]n 9 were more likely polymorphic. Overall, highly polymorphic to monomorphic new [CAG]n > 9 and [CGG]n > 7 were characterized. The comparison of our data with other [CAG]n and [CGG]n resources suggests that the screening of reference cDNAs leads to unique sources of new [CAG]n and [CGG]n and will enhance the study of enlarged triplet repeats in human genetic diseases.

Brain↗

PubMed1998

IXDB, an X chromosome integrated database.

The integrated X chromosome database (IXDB) is a repository for physical mapping data of the human X chromosome. Its current content is the result of a strict integration of data stemming from many different sources. The main features of IXDB include a flexible and extendible schema, a comfortable and fully cross-referenced WWW interface (http://ixdb.mpimg-berlin-dahlem.mpg.de ) and a graphical map viewer implemented in JAVA. The database stores objects used in physical mapping as well as the maps resulting from this work, but a strong emphasis is placed on recording experiments that connect objects together. This should greatly contribute to fulfilling one of the major goals of the database: to support the construction of an integrated physical, genetic, transcript and sequence map of the human X chromosome.

Chromosome Mapping↗

PubMed1998

AmphiBMP2/4, an amphioxus bone morphogenetic protein closely related to Drosophila decapentaplegic and vertebrate BMP2 and BMP4: insights into evolution of dorsoventral axis specification.

Amphioxus AmphiBMP2/4 appears to be a single gene closely related to vertebrate BMP2 and BMP4. In amphioxus embryos, the expression patterns of AmphiBMP2/4 suggest patterning roles in the ectodermal dorsoventral axis (comparable to dorsoventral axis establishment in the ectoderm by Drosophila decapentaplegic and vertebrate BMP4). In addition AmphiBMP2/4 may be involved in somite evagination, tail bud growth, pharyngeal differentiation (resulting in club-shaped gland morphogenesis), hindgut regionalization, differentiation of olfactory epithelium, patterning of the anterior central nervous system, and establishment of the heart primordium. One difference between the developmental role of amphioxus AmphiBMP2/4 and vertebrate BMP4 is that the former does not appear to be involved in the initial establishment of the dorsoventral polarity of the mesoderm.

Amino Acid Sequence↗

PubMed1998

Structure of the human CD94 C-type lectin gene.

The genomic structure of the human CD94 gene was obtained by analyzing genomic clones obtained from two different libraries. The CD94 gene contains six exons separated by five introns. The carbohydrate-recognition domain (CRD) is encoded by three exons, and the conservation of intron positions within the CRD indicated that CD94 is closely related to group V of C-type lectins. Primer extension and S1 nuclease protection assays showed that initiation of transcription in the CD94 gene is heterogeneous, but restricted to a 60 base pair region around the major initiation site enclosed within a putative initiator element (TTA+1TTCA). The study of the promoter region of CD94 may help to understand the selective expression of this C-type lectin glycoprotein on NK cells and subsets of cytotoxic T cells.

Antigens, CD↗

PubMed1998

The genomic organization of NKG2C, E, F, and D receptor genes in the human natural killer gene complex.

Interactions of natural killer cell receptors with their cognate ligands play a major role in regulating NK cell function. The NKG2 gene family encodes several highly similar proteins, which are known to form heterodimers with the CD94 receptor. These dimers play a role in the inhibition as well as the activation of NK cells. We have analyzed the gene structures of the NKG2C, D, E, and F genes, and determined their genomic organization. Restriction mapping and sequencing revealed the four genes to be closely linked to one another, and of the same transcriptional orientation. An exon duplication within the NKG2C and E genes was identified, although the duplicated version of this exon has not yet been found in mRNA sequences. The NKG2C, E, and F genes, despite being highly similar, are variable at their 3' ends. We show that NKG2C consists of six exons, whereas NKG2E has seven, and the splice acceptor site for the seventh exon occurs in an Alu repeat. NKG2F consists of only four exons and part of exon IV is in some cases spliced to the 5' end of the NKG2D transcript. NKG2D has only a low similarity to the other NKG2 genes.

Base Sequence↗

PubMed1998

IRS-PCR-based genetic mapping of the huntingtin interacting protein gene (HIP1) on mouse chromosome 5.

Huntington's disease (HD) is a devastating central nervous system disorder. Even though the gene responsible has been positionally cloned recently, its etiology has remained largely unclear. To investigate potential disease mechanisms, we conducted a search for binding partners of the HD-protein huntingtin. With the yeast two-hybrid system, one such interacting factor, the huntingtin interacting protein-1 (HIP-1), was identified (Wanker et al. 1997; Kalchman et al. 1997) and the human gene mapped to 7q11.2. In this paper we demonstrate the localization of the HIP1 mouse homologue (Hip1) into a previously identified region of human-mouse synteny on distal mouse Chromosome (Chr) 5, both employing an IRS-PCR-based mapping strategy and traditional fluorescent in situ hybridization (FISH) mapping.

Animals↗

PubMed1998

Complex probes for high-throughput parallel genetic mapping of genomic mouse BAC clones.

We describe a novel approach for the identification and mapping of polymorphic markers. Amplicons are generated by ligation of double-stranded adaptor molecules to genomic DNA cleaved with a restriction enzyme. Using primers that extend beyond the restriction site, reduced-complexity subsets of fragments are generated by PCR. Differences in the composition of complex probes generated from DNA of different strains are revealed through hybridization against high-density filter grids of large-insert genomic clones. Genetic mapping of genomic clones is achieved by hybridizing complex probes derived from backcross animals against the polymorphic clones. The mouse was chosen as a model system to test the feasibility of this technique because of the general availability of backcross resources and genomic libraries. Nevertheless, we would expect the method to be of particular use to generate markers for species that have not yet been extensively studied, because a substantial number of easy-to-use markers can be recruited in a relatively short period of time.

Animals↗

PubMed1998

Refined radiation hybrid map of mouse chromosome 17.

We have made a radiation hybrid map of mouse Chromosome (Chr) 17 with 75 microsatellite markers, including those from McCarthy et al. (Genome Res 7, 1153-1161, 1997). Seventy-four of the markers are linked at LOD > 9, and all link at LOD > 5. A LOD 3 framework of 18 markers was used to construct a placement map. The order obtained is in good agreement with genetic maps, and distance estimates give an idea of how recombination rates vary across the chromosome. Recombination is remarkably low with respect to RH break frequency in the region from the centromere to the end of H2. This is similar in interspecific and intersubspecific crosses despite the inversion of a substantial part of this region in Mus spretus with respect to Mus musculus.

Animals↗

PubMed1998

SH3GL3 associates with the Huntingtin exon 1 protein and promotes the formation of polygln-containing protein aggregates.

The mechanism by which aggregated polygins cause the selective neurodegeneration in Huntington's disease (HD) is unknown. Here, we show that the SH3GL3 protein, which is preferentially expressed in brain and testis, selectively interacts with the HD exon 1 protein (HDex1p) containing a glutamine repeat in the pathological range and promotes the formation of insoluble polyglutamine-containing aggregates in vivo. The C-terminal SH3 domain in SH3GL3 and the proline-rich region in HDex1p are essential for the interaction. Coimmunoprecipitations and immunofluorescence studies revealed that SH3GL3 and HDex1p colocalize in transfected COS cells. Additionally, an anti-SH3GL3 antibody was also able to coimmunoprecipitate the full-length huntingtin from an HD human brain extract. The characteristics of the interaction between SH3GL3 and huntingtin and the colocalization of the two proteins suggest that SH3GL3 could be involved in the selective neuronal cell death in HD.

Adaptor Proteins, Signal Transducing↗