Biomedical subjects

A A Dempsey

Publications and source records attributed to A A Dempsey.

9 recordsLinked to original sources

PubMed2004

First comprehensive mapping of cartilage transcripts to the human genome.

We present the first comprehensive transcriptome-to-genome mapping for human cartilage. First, we determined that the cartilage transcriptome represents between 13,200 and 15,800 unique genes. Next, a subset of approximately 10,000 of the best characterized cartilage-expressed transcripts (CETs) was selected and mapped to the human genome. The distribution of CETs across the genome was found to be significantly different compared to the expected distribution. Furthermore, clusters of adjacent coordinately transcribed genes, as well as numerous "hot spots" and "cold spots" for transcription in cartilage, were identified. We propose that transcriptional control in cartilage can be exerted over genomic domains containing as few as four neighboring genes. Our findings, which are consistent with recent "chromatin domain" models of transcription, are further supported by our identification of CETs that putatively encode components of the HDAC- and Swi/SNF-mediated chromatin remodeling pathways. Our study illustrates the value of comprehensive high-resolution scans to detect transcription patterns within the human genome.

Cartilage↗

PubMed2001

Organization of human cardiovascular-expressed genes on chromosomes 21 and 22.

The recent availability of the sequenced and annotated DNA sequences of chromosomes 21 and 22 has initiated the next phase in the human genome project: the application of this resource. One facet of these data is that they provide a list of ordered genes along the chromosome that can be capitalized upon to determine gene position effects. Specifically, the physical position and distribution of genes along the chromosomes may be related to gene expression in specific organs or organ systems. In this report we index the subset of genes constituting the human "cardiovascular genome" on chromosomes 21q and 22q as well as report the identification of several "cardiovascular gene" clusters. These gene clusters are suggestive of a higher order of tissue-specific gene regulation at the chromosomal level.

Cardiovascular System↗

PubMed2001

Cardiovascular genomics: estimating the total number of genes expressed in the human cardiovascular system.

The number of genes encoded by the human genome has long sought to be determined. With the recent publications of the complete sequence of the human genome, the number of genes encoded by the human genome has now been estimated to be approximately 32,000-38,000. Now the next step will be to determine which of these genes are expressed in a given cell, tissue or organ. Using three unique approaches taking advantage of our current cardiovascular EST database and the complete nucleotide sequence of human chromosomes 21 and 22 as well as cDNA microarray hybridization, we estimate that between 20,930-27,160 genes are expressed in the cardiovascular system.

Cardiovascular System↗

PubMed2000

Identification of differentially expressed genes in cardiac hypertrophy by analysis of expressed sequence tags.

Cardiac hypertrophy is an adaptive response to chronic hemodynamic overload. We employed a whole-genome approach using expressed sequence tags (ESTs) to characterize gene transcription and identify new genes overexpressed in cardiac hypertrophy. Analysis of general transcription patterns revealed a proportional increase in transcripts related to cell/organism defense and a decrease in transcripts related to cell structure and motility in hypertrophic hearts compared to normal hearts. Detailed comparison of individual gene expression identified 64 genes potentially overexpressed in hypertrophy, of 232 candidate genes derived from a set of 77,692 cardiac ESTs, including 47,856 ESTs generated in our laboratory. Of these, 29 were good candidates (P < 0.0002) and 35 were weaker candidates (P < 0.005). RT-PCR of a number of these candidate genes demonstrated correspondence of EST-based predictions of gene expression with in vitro levels. Consistent with an organ under various stresses, up to one-half of the good candidates predicted to exhibit differential expression were genes potentially involved in stress response. Analyses of general transcription patterns and of single-gene expression levels were also suggestive of increased protein synthesis in the hypertrophic myocardium. Overall, these results depict a scenario compatible with current understanding of cardiac hypertrophy. However, the identification of several genes not previously known to exhibit increased expression in cardiac hypertrophy (e.g., prostaglandin D synthases; CD59 antigen) also suggests a number of new avenues for further investigation. These data demonstrate the utility of genome-based resources for investigating questions of cardiovascular biology and medicine.

Adult↗

PubMed2000

A cardiovascular EST repertoire: progress and promise for understanding cardiovascular disease.

The application of expressed sequence tag (EST) technology has proven to be an effective tool for gene discovery and the generation of gene expression profiles. The generation of an EST resource for the cardiovascular system has revealed significant insights into the changes in gene expression that guide heart development and disease. Furthermore, an important genetic resource has been developed for cardiovascular biology that is valuable for data mining and disease gene discovery.

Animals↗

PubMed2000

Identification, characterization, and mapping of expressed sequence tags from an embryonic zebrafish heart cDNA library.

The generation of expressed sequence tags (ESTs) has proven to be a rapid and economical approach by which to identify and characterize expressed genes. We generated 5102 ESTs from a 3-d-old embryonic zebrafish heart cDNA library. Of these, 57.6% matched to known genes, 14.2% matched only to other ESTs, and 27.8% showed no match to any ESTs or known genes. Clustering of all ESTs identified 359 unique clusters comprising 1771 ESTs, whereas the remaining 3331 ESTs did not cluster. This estimates the number of unique genes identified in the data set to be approximately 3690. A total of 1242 unique known genes were used to analyze the gene expression patterns in the zebrafish embryonic heart. These were categorized into seven categories on the basis of gene function. The largest class of genes represented those involved in gene/protein expression (25.9% of known transcripts). This class was followed by genes involved in metabolism (18.7%), cell structure/motility (16.4%), cell signaling and communication (9.6%), cell/organism defense (7.1%), and cell division (4.4%). Unclassified genes constituted the remaining 17.91%. Radiation hybrid mapping was performed for 102 ESTs and comparison of map positions between zebrafish and human identified new synteny groups. Continued comparative analysis will be useful in defining the boundaries of conserved chromosome segments between zebrafish and humans, which will facilitate the transfer of genetic information between the two organisms and improve our understanding of vertebrate evolution.

Animals↗

PubMed1998

Identification of sequence-tagged transcripts differentially expressed within the human hematopoietic hierarchy.

Hematopoiesis is regulated by a complex gene expression program. To gain further insight into the molecular mechanisms underlying this process in humans, we sampled the transcriptional activity of the CD34+ hematopoietic progenitor line KG1a by single-pass sequencing the 5' ends of 1018 clones from a unidirectional cDNA library. Searches of public databases with the resulting expressed sequence tags (ESTs) identified 101 clones that showed no sequence similarity to any of the existing entries and that were therefore considered to derive from previously undescribed genes. Of the remaining 917 ESTs, 553 (a total of 485 distinct transcripts) corresponded to known genes. A further 279 KG1a ESTs matched or exhibited sequence similarity to ESTs or genomic sequences from humans and other species. Among the latter were putative human orthologs of developmental and cell cycle control genes from Caenorhabditis elegans, Drosophila, and yeast, as well as genes whose predicted amino acid sequences showed similarity to mammalian transcription factors. Hybridization of selected novel KG1a ESTs to globally amplified cDNAs prepared from single primary human hematopoietic precursors and homogeneous populations of terminally maturing hematopoietic cells revealed transcripts that are expressed preferentially at a specific stage or in a particular lineage within the hematopoietic hierarchy. Thus, included in the KG1a EST dataset are candidates for new human genes that may play roles in hematopoietic differentiative progression and lineage commitment.

Animals↗

PubMed1997

Identification and primary structure of five human NADH-ubiquinone oxidoreductase subunits.

The multi-subunit NADH-ubiquinone oxidoreductase (complex I) is the first enzyme complex in the electron transport chain of mitochondria. A small number of NADH-ubiquinone oxidoreductase subunits are the products of mitochondrial genes (subunits 1-7), while the remainder are nuclear encoded and imported from the cytoplasm. We have isolated and sequenced five subunits of the human complex I from a human heart lambda ZAP Express cDNA library. Comparison of the deduced amino acid sequences of the human subunits with the corresponding bovine sequences revealed greater than 80% amino acid identity. The high degree of similarity between human and bovine sequences suggests functional conservation of these subunits in the complex I. In silico Northern analysis revealed that two of the subunits were expressed ubiquitously while the remainder may have more restricted patterns of expression.

Amino Acid Sequence↗

PubMed1997

A genome-based resource for molecular cardiovascular medicine: toward a compendium of cardiovascular genes.

BACKGROUND: Large-scale partial sequencing of cDNA libraries to generate expressed sequence tags (ESTs) is an effective means of discovering novel genes and characterizing transcription patterns in different tissues. To catalogue the identities and expression levels of genes in the cardiovascular system, we initiated large-scale sequencing and analysis of human cardiac cDNA libraries. METHODS AND RESULTS: Using automated DNA sequencing, we generated 43,285 ESTs from human heart cDNA libraries. An additional 41,619 ESTs were retrieved from public databases, for a total of 84,904 ESTs representing more than 26 million nucleotides of raw cDNA sequence data from 13 independent cardiovascular system-based cDNA libraries. Of these, 55% matched to known genes in the Genbank/EMBL/DDBJ databases, 33% matched only to other ESTs, and 12% did not match to any known sequences (designated cardiovascular system-based ESTs, or CVbESTs). ESTs that matched to known genes were classified according to function, allowing for detection of differences in general transcription patterns between various tissues and developmental stages of the cardiovascular system. In silico Northern analysis of known gene matches identified widely expressed cardiovascular genes as well as genes putatively exhibiting greater tissue specificity or developmental stage specificity. More detailed analysis identified 48 genes potentially overexpressed in cardiac hypertrophy, at least 10 of which were previously documented as differentially expressed. Computer-based chromosomal localizations of 1048 cardiac ESTs were performed to further assist in the search for disease-related genes. CONCLUSIONS: These data represent the most extensive compilation of cardiovascular gene expression information to date. They further demonstrate the untapped potential of genome research for investigating questions related to cardiovascular biology and represent a first-generation genome-based resource for molecular cardiovascular medicine.

Blotting, Northern↗