Biomedical subjects

G Micklem

Publications and source records attributed to G Micklem.

12 recordsLinked to original sources

PubMed2005

A friendly statistics package for microarray analysis.

SUMMARY: The friendly statistics package for microarray analysis (FSPMA) is a tool that aims to fill the gap between simple to use and powerful analysis. FSPMA is a platform-independent R-package that allows efficient exploration of microarray data without the need for computer programming. Analysis is based on a mixed model ANOVA library (YASMA) that was extended to allow more flexible comparisons and other useful operations like k nearest neighbour imputing and spike-based normalization. Processing is controlled by a definition file that specifies all the steps necessary to derive analysis results from quantified microarray data. In addition to providing analysis without programming, the definition file also serves as exact documentation of all the analysis steps. AVAILABILITY: The library is available under GPL 2 license and, together with additional information, provided at http://www.ccbi.cam.ac.uk/software/psyk/software.html#fspma

Algorithms↗

PubMed1997

Regions of human chromosome 2 (2q32-q35) and mouse chromosome 1 show synteny with the pufferfish genome (Fugu rubripes).

We have isolated and sequenced a cosmid clone from the compact genome of the Japanese pufferfish (Fugu rubripes) containing portions of three genes that have the same order as in human. The gene order is microtubule-associated protein (MAP-2), myosin light chain (MYL-1), and carbamoyl phosphate synthetase (CPS III). The intron-exon organization of Fugu CPS III is identical with that of rat CPS I, although the equivalent genomic fragments of rat and Fugu CPS span 87.9 and 21 kb, respectively. This is the first report of a piscine CPS III genomic structure and predicts a close evolutionary link between CPS III and CPS I. The 8-kb intergenic region between MYL-1 and CPS gave no clear areas of transcription factor-binding sites by pairwise comparison with shark or rat CPS promoter regions. However, there was a match with the rat myosin light chain 2 (MLC-2) gene promoter and a MyoD transcription factor-binding site 874 bp upstream of the MYL-1 gene.

Amino Acid Sequence↗

PubMed1997

The relationship between chromosome structure and function at a human telomeric region.

We have sequenced a contiguous 284,495-bp segment of DNA extending from the terminal (TTAGGG)n repeats of the short arm of chromosome 16, providing a full description of the transition from telomeric through subtelomeric DNA to sequences that are unique to the chromosome. To complement and extend analysis of the primary sequence, we have characterized mRNA transcripts, patterns of DNA methylation and DNase I sensitivity. Together with previous data these studies describe in detail the structural and functional organization of a human telomeric region.

Base Sequence↗

PubMed1997

The BRC repeats are conserved in mammalian BRCA2 proteins.

The breast cancer susceptibility gene BRCA2 encodes a protein of 3418 amino acids which does not exhibit substantial sequence similarity to any other protein in the public databases. A dot matrix comparison of BRCA2 with itself revealed an eight times repeated motif in the segment of the protein encoded by exon 11. As a preliminary test of the hypothesis that these motifs are functionally significant, we have sequenced exon 11 of BRCA2 in six mammals. An alignment of the predicted protein sequences shows that, overall, the motifs have been conserved while much of the intervening sequences has diverged. These data support the notion that the BRC motifs are important in BRCA2 function. There is, however, considerable interspecies variation within certain motif units, raising the possibility of redundancy and that not all of the repeats are required for the normal function of BRCA2.

Amino Acid Sequence↗

PubMed1997

Sequence comparison of human and yeast telomeres identifies structurally distinct subtelomeric domains.

We have sequenced and compared DNA from the ends of three human chromosomes: 4p, 16p and 22q. In all cases the pro-terminal regions are subdivided by degenerate (TTAGGG)n repeats into distal and proximal sub-domains with entirely different patterns of homology to other chromosome ends. The distal regions contain numerous, short (<2 kb) segments of interrupted homology to many other human telomeric regions. The proximal regions show much longer (approximately 10-40 kb) uninterrupted homology to a few chromosome ends. A comparison of all yeast subtelomeric regions indicates that they too are subdivided by degenerate TTAGGG repeats into distal and proximal sub-domains with similarly different patterns of identity to other non-homologous chromosome ends. Sequence comparisons indicate that the distal and proximal sub-domains do not interact with each other and that they interact quite differently with the corresponding regions on other, non-homologous, chromosomes. These findings suggest that the degenerate TTAGGG repeats identify a previously unrecognized, evolutionarily conserved boundary between remarkably different subtelomeric domains.

Base Sequence↗

PubMed1996

Molecular cloning of tissue-specific transcripts of a transketolase-related gene: implications for the evolution of new vertebrate genes.

As part of a systematic search for differentially expressed genes, we have isolated a novel transketolase-related gene (TKR) (HGMW-approved symbol TKT), located between the green color vision pigment gene (GCP) and the ABP-280 filamin gene (FLN1) in Xq28. Transcripts encoding tissue-specific protein isoforms could be isolated. Comparison with known transketolases (TK) demonstrated a TKR-specific deletion mutating one thiamine binding site. Genomic sequencing of the TKR gene revealed the presence of a pseudoexon as well as the acquisition of a tissue-specific spliced exon compared to TK. Since it has been postulated that the vertebrate genome arose by two cycles of tetraploidization from a cephalochordate genome, this could represent an example of the modulation of the function of a preexisting transketolase gene by gene duplication. Thiamine defiency is closely involved with two neurological disorders, Beriberi and Wernicke-Korsakoff syndromes, and in both of these conditions TK with altered activity are found. We discuss the possible involvement of TKR in explaining the observed variant transketolase forms.

Alternative Splicing↗

PubMed1995

Comparative sequence analysis of the human and pufferfish Huntington's disease genes.

The Huntington's disease (HD) gene encodes a novel protein with as yet no known function. In order to identify the functionally important domains of this protein, we have cloned and sequenced the homologue of the HD gene in the pufferfish, Fugu rubripes. The Fugu HD gene spans only 23 kb of genomic DNA, compared to the 170 kb human gene, and yet all 67 exons are conserved. The first coding exon, the site of the disease-causing triplet repeat, is highly conserved. However, the glutamine repeat in Fugu consists of just four residues. We also show that gene order may be conserved over longer stretches of the two genomes. Our work describes a detailed example of sequence comparison between human and Fugu, and illustrates the power of the pufferfish genome as a model system in the analysis of human genes.

Amino Acid Sequence↗

PubMed1994

The sequence complexity of exons trapped from the mouse genome.

BACKGROUND: A central issue in genome analysis is the identification and characterization of coding regions. Estimating the coding complexity of vertebrate genomes by measuring the kinetic complexity of mRNA populations and by sequence analysis of cDNAs is limited by the fact that any given source of mRNA represents a very biased sample of all genes. Exon trapping is a method that enables the identification of genes irrespective of their transcriptional status. RESULTS: Exons were trapped from the entire mouse genome, and the resulting fragments cloned. About 7% of a random sample of exons taken from this library have significant structural homology or sequence similarity to previously sequenced genes. Using cDNAs derived from several stages of mouse development, evidence for expression of about 62% of this sample of exons was found. These data suggest that the great majority of 'exons' in the library are derived from genes. We estimate that the fraction of the genome contained in trapped exons is 2.4%; this corresponds to a sequence complexity of about 72 megabases. CONCLUSIONS: The library of exons trapped from the entire mouse genome probably represents one of the least biased and most comprehensive libraries of mouse coding regions, and should therefore prove very useful for finding genes during genome mapping and sequencing.

Amino Acid Sequence↗

PubMed1994

Dissecting the temporal requirements for homeotic gene function.

Homeotic genes confer identity to the different segments of Drosophila. These genes are expressed in many cell types over long periods of time. To determine when the homeotic genes are required for specific developmental events we have expressed the Ultrabithorax, abdominal-A and Abdominal-Bm proteins at different times during development using the GAL4 targeting technique. We find that early transient homeotic gene expression has no lasting effects on the differentiation of the larval epidermis, but it switches the fate of other cell types irreversibly (e.g. the spiracle primordia). We describe one cell type in the peripheral nervous system that makes sequential, independent responses to homeotic gene expression. We also provide evidence that supports the hypothesis of in vivo competition between the bithorax complex proteins for the regulation of their down-stream targets.

Animals↗

PubMed1993

Yeast origin recognition complex is involved in DNA replication and transcriptional silencing.

The HMR E silencer represses transcription of silent mating-type genes in the budding yeast Saccharomyces cerevisiae and contains three redundant regulatory elements A, E and B (ref. 1). The A element contains the 11 base pair consensus sequence that is essential for the firing of DNA replication origins. A multisubunit protein called the origin recognition complex (ORC) binds specifically to this consensus sequence within yeast origins in vitro and in vivo. We isolated mutants in A element-mediated silencing and report here that one of the genes we identified, RRR1, encodes ORC2, the 72K subunit of ORC. RRR1/ORC2 is an essential gene, but the rrr1-316 allele, which is viable, is defective in the replication of nuclear DNA and the maintenance of the 2-microns episomal DNA. This is, to our knowledge, the first genetic evidence that ORC is involved in DNA replication and silencing.

Amino Acid Sequence↗

PubMed1987

A yeast silencer contains sequences that can promote autonomous plasmid replication and transcriptional activation.

Repression of the yeast silent mating type loci requires cis-acting sequences located over 1 kb from the regulated promoters. One of these sites, a "silencer," exhibits enhancer-like distance- and orientation-independence. The silencer demonstrates both autonomous replication sequence (ARS) activity and a centromere-like segregation function, suggesting roles for DNA replication and segregation in transcriptional repression. Here we identify three sequences (A, E, and B) involved both in repression and in either ARS or segregation activity. The sequences are functionally redundant: no one is essential for complete transcriptional control, but mutations in any two inactivate the silencer. Surprisingly, elements E and B can each activate transcription from heterologous promoters, and E shows striking homology to several yeast upstream activation sequences. Therefore, sequences individually involved in replication, segregation, and transcriptional activation can, at the silencer, efficiently repress transcription.

Base Sequence↗

PubMedDate not supplied

Identification of the breast cancer susceptibility gene BRCA2.

In Western Europe and the United States approximately 1 in 12 women develop breast cancer. A small proportion of breast cancer cases, in particular those arising at a young age, are attributable to a highly penetrant, autosomal dominant predisposition to the disease. The breast cancer susceptibility gene, BRCA2, was recently localized to chromosome 13q12-q13. Here we report the identification of a gene in which we have detected six different germline mutations in breast cancer families that are likely to be due to BRCA2. Each mutation causes serious disruption to the open reading frame of the transcriptional unit. The results indicate that this is the BRCA2 gene.

Amino Acid Sequence↗