A map of 75 human ribosomal protein genes

Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human

BACKGROUND

Knowledge of the amount of gene order and synteny conservation between two species gives insights to the extent and mechanisms of divergence. The vertebrate Fugu rubripes (pufferfish) has a small genome with little repetitive sequence which makes it attractive as a model genome. Genome compaction and synteny conservation between human and Fugu were studied using data from public databases.

METHODS

Intron length and map positions of human and Fugu orthologues were compared to analyse relative genome compaction and synteny conservation respectively. The divergence of these two genomes by genome rearrangement was simulated and the results were compared to the real data.

RESULTS

Analysis of 199 introns in 22 orthologous genes showed an eight-fold average size reduction in Fugu, consistent with the ratio of total genome sizes. There was no consistent pattern relating the size reduction in individual introns or genes to gene base composition in either species. For genes that are neighbours in Fugu (genes from the same cosmid or GenBank entry), 40-50% have conserved synteny with a human chromosome. This figure may be underestimated by as much as two-fold, due to problems caused by incomplete human genome sequence data and the existence of dispersed gene families. Some genes that are neighbours in Fugu have human orthologues that are several megabases and tens of genes apart. This is probably caused by small inversions or other intrachromosomal rearrangements.

CONCLUSIONS

Comparison of observed data to computer simulations suggests that 4000-16 000 chromosomal rearrangements have occurred since Fugu and human shared a common ancestor, implying a faster rate of rearrangement than seen in human/mouse comparisons.

Gene organization and sequence of the region containing the ribosomal protein genes RPL13A and RPS11 in the human genome and conserved features in the mouse genome

We have determined the organization and sequence of the region containing two ribosomal protein (rp) genes in the human and mouse genomes. The two genes, human RPL13A and RPS11, and mouse Rpl13a and Rps11, are tandemly located in both genomes with an interval of only 4.6kb in the case of the human genes and 1.6kb in the case of the mouse genes. The human RPL13A and RPS11 are 4236bp and 3254bp in length and comprise eight and five exons respectively, whereas the mouse Rps11 is 1951bp long and has five exons. Structural comparison of these genes, including previously reported mouse Rpl13a, revealed a significant conservation of sequences in the promoter regions. Although most rp genes are dispersed throughout the human genome, the conserved features and adjacent localization indicate possible coordinate transcription of the two genes. Furthermore, we have found that four small nucleolar RNA (snoRNA) genes are located in the introns of the two rp genes, both human and mouse. U32, U33, and U34 snoRNAs are encoded in introns 2, 4, and 5 of RPL13A respectively, and U35 in the sixth intron of RPL13A and the third intron of RPS11. The same organization of these snoRNA genes was also observed in the case of the mouse genes.

Chromosomal, in silico and in vitro expression analysis of cardiovascular-based genes encoding zinc finger proteins

Three hundred and sixty expressed sequence tags (ESTs) from human heart cDNA libraries corresponding to one hundred and twenty six unique zinc finger proteins (ZFPs) were annotated and classified into seven types of ZFPs as reported previously. Among these 126 cvbZFPs (cardiovascular-based ZFPs), the C(2)H(2)-type and the C(2)C(2)-type are the two major ZFP types which account for more than 80% of ZFP genes present in the cardiovascular system. The expression patterns of 11 randomly selected ZFP genes (at least one for each type) in normal fetal, adult and hypertrophic adult hearts, respectively, were determined using reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. The results suggest that ZFPs may be involved in the processes of either developmental control (downregulated or upregulated expression) or basic cellular functional regulation (constant expression). Interestingly, PAF-1 (peroxisome assembly factor-1), a C(3)HC(4)-type ZFP (RING domain-containing ZFP) showing a downregulated expression pattern in normal tissues was found to be upregulated in hypertrophic adult heart, suggesting a possible role for this fetal gene in the pathogenesis of cardiac hypertrophy. In silico Northern analysis of 15 tissues showed that over 90% of cvbZFPs demonstrate widespread tissue distribution, suggesting the vast majority of ZFPs are functionally shared among tissues. The potential importance of transcriptional repressors in cardiovascular development and disease, such as HFHZ, was supported by the observation that one-third (39 of 126) of cvbZFPs possess this function. Of these, 26 are C(2)H(2)-type and the remaining 13 included 8 C(2)C(2)-type, 1 C(3)HC(4)-type, 1 C(2)HC(4)C(HD)-type, 2 C(3)H-type and 1 combination type. Of particular interest was the observation that ZFPs which contain a KRAB domain are the major subtype present (51. 3% of the total repressors in cvbZFPs). Chromosomal distribution analysis showed that mapping loci of cvbZFP genes are concentrated on chromosomes 1, 3, 6, 8, 10, 11, 12, 19 and X. In particular, chromosome 19 appears to be enriched in ZFP genes with C(2)H(2)-type as the predominant type present. Overall, this report provides a fundamental initial step toward understanding the potential role of ZFPs in regulating cadiac development and disease.

The gene encoding ribosomal protein S19 is mutated in Diamond-Blackfan anaemia

Diamond-Blackfan anaemia (DBA) is a constitutional erythroblastopenia characterized by absent or decreased erythroid precursors. The disease, previously mapped to human chromosome 19q13, is frequently associated with a variety of malformations. To identify the gene involved in DBA, we cloned the chromosome 19q13 breakpoint in a patient with a reciprocal X;19 chromosome translocation. The breakpoint occurred in the gene encoding ribosomal protein S19. Furthermore, we identified mutations in RPS19 in 10 of 40 unrelated DBA patients, including nonsense, frameshift, splice site and missense mutations, as well as two intragenic deletions. These mutations are associated with clinical features that suggest a function for RPS19 in erythropoiesis and embryogenesis.

A physical map of 30,000 human genes

A map of 30,181 human gene-based markers was assembled and integrated with the current genetic map by radiation hybrid mapping. The new gene map contains nearly twice as many genes as the previous release, includes most genes that encode proteins of known function, and is twofold to threefold more accurate than the previous version. A redesigned, more informative and functional World Wide Web site (www.ncbi.nlm.nih.gov/genemap) provides the mapping information and associated data and annotations. This resource constitutes an important infrastructure and tool for the study of complex genetic traits, the positional cloning of disease genes, the cross-referencing of mammalian genomes, and validated human transcribed sequences for large-scale studies of gene expression.