Progress 01/01/03 to 12/31/03
Outputs
Increased Alu density has been correlated with genetic instability, which is a recognized phenomenon in the vast majority of cancer cases. Instability arises within the genome due to various genetic alterations, duplications, deletions, chromosomal translocations, chromosomal number alterations, and gene amplifications. A high level of Alu-sequence similarity ensues a strong propensity for unequal cross over events, some of which have lead to deleterious oncogenic rearrangements. In addition, it has been demonstrated that Alu insertions can introduce consensus 3' splice sites, thus facilitating alternative splicing, constitutve splicing and misplicing. Alu-mediated defective splicing has also been associated with cancer. To investigate a possible correlation between the expansion of Alu repeats associated with primate divergence and predisposition to cancer, we selected four Alu-mediated rearrangements - known to be the basis of cancer - for phylogenetic analysis of
the necessary genotype. In all four cases, we found that the different phylogenetic age of the oncogenic recombination-prone genotype could be correlated with the evolutionary history of Alus' spreading to new genomic sites.
Impacts
Once identified, genetic elements involved in human cancer could be used for predictive screening to identify ppredisposition to cancer and targeted for gene terapy. Previously, deleterious cancer causing mutations have been identified only afetr the mutation occurred, thus lacking predictive value.
Publications
- Gibbons R. & Dugaiczyk A. Phylogenetic Roots of Alu-mediated Rearrangements Leading to Cancer. (2004) J. Mol. Evol. (submitted)
- Gibbons R. & Dugaiczyk A. Phylogenetic Origins of Human Predisposition to Cancer. (2003) 68th Annual Cold Spring Harbor Symposium p. 66.
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Progress 09/01/98 to 09/30/03
Outputs
Humans and chimpanzees share some 99% of DNA and amino acid identity, yet they exhibit important biomedical, morphological, and cognitive differences, difficult to accommodate within the remaining 1% of sequence diversity. Other types of genetic variation must be responsible for the taxonomic differences. We have traced the evolution of AluYb8 repeats from a single origin at the roots of higher primates to a large increase in their number in humans. We identified 9 AluYb8 DNA repeats in the chimpanzee genome compared to over 2,200 repeats in the human, which represents a 250-fold increase in the rate of change in the human lineage and far outweighs the 99% sequence similarity between the two species. It is estimated that the average age of the human Yb8Alus is about 3.3 My; almost 10% of them are identical in sequence, and hence are of recent origin. Genomic variations of this magnitude, distinguishing humans from great apes have not been realized. This explosive Alu
expansion must have had a profound effect on the organization of our genome and the architecture of our chromosomes, inferentially altering profiles of gene expression and chromosome choreography in cell division. Additionally, we concluded that this major evolutionary process of Alu proliferation is driven by internal forces, written in the chemistry of DNA, rather than by external selection.
Impacts
The presently identified explosive expansion of AluYb8 repeats: 2,200 in the human lineage, compared to a modest 9 such events in the chimpanzee, was very unexpected. Since the repeats are at the basis of genomic rearrangements, the human genome must be a very dynamic entity, and we must be marchuing to a faster genetic drummer.
Publications
- Gibbons R. & Dugaiczyk, L. J., Girke, T., Duistermars, B., Zielinski, R. & Dugaiczyk, A. (2004) Distinguishing Humans from Great Apes with AluYb8 Repeats. J. Mol. Biol. 339; 721-729.
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Progress 01/01/02 to 12/31/02
Outputs
Over the last 60 million years, approximately one million copies of Alu DNA repeats have accumulated in the genome of primates in what appears to be an ongoing process. Humans have a significant excess of at least several thousand Alu DNA repeats, compared to other primate species. These repeats are dispersed throughout the genome, but in some regions Alu density exceeds the typical genomic distribution. Perhaps not unexpectedly, some of these Alus mediate unequal crossovers leading to genomic rearrangements which lead to genetic molecular diseases, including human cancer. Our data suggest that humans have an increased predisposition to cancer, compared to other primate species, due to deleterious Alu-mediated recombinations.
Impacts
Once identified, genetic elements involved in human cancer could be used for predictive screening to identify predisposition to cancer and targeted for gene therapy. Previously, deleterious cancer causing mutations have been identified only after the mutation occured, thus lacking predictive value.
Publications
- Rosaleen Gibbons & Achilles Dugaiczyk. Phylogenetic Origins of Human Predisposition to Cancer. (2003) 68th Annual Cold Springs Harbor Symposium. (In press)
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Progress 01/01/01 to 12/31/01
Outputs
Over the last 60 million years approximately one million copies of Alu DNA repeats have accumulated in the genome of primates, in what appears to be an ongoing process. We determined the phylogenetic distribution of specific Alu DNA repeats in the genome of several primates: human, chimp-anzee, gorilla, orangutan, baboon, rhesus, and macaque. At the population level studied, the majority of the repeats was found to be fixed in the primate species. Our data suggest that new Alu elements arise in unique, irreversible events, in a mechanism that seems to preclude precise excision and loss.The irreversible expansion of Alus introduces a vector of time into the evolutionary process, and provides realistic (rather than statistical) answers to questions on phylogenies.
Impacts
Molecular forces driving the evolutionary process are rather poorly understood. One can never tell whether two taxa share a nucleotide state by descent or chance. This is because individual nucleotides change multiple times in their evolutionary past. We show that transpositions of Alus obey different molecular rules. Individual Alus came to existence in unique events, and hence are identical (in two lineages) by descent rather than by chance.
Publications
- Martinez, J., Dugaiczyk, L.J., Zielinski, R. and Dugaiczyk, A. 2001. Human Genetic Disorders, a Phylogenetic Perspective. J. Mol. Biol. 308: 587-596.
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Progress 01/01/00 to 12/31/00
Outputs
Four Alu DNA elements, known to have gene regulatory functions in the human, were found to be differentially distributed among seven primate species (human, chimpanzee, gorilla, orangutan, baboon, rhesus, and macaque), in away that is congruent with an accepted phylogeny of these species. The four elements regulate the parathyroid hormone gene, the hematopoietic receptor gene, the CNS-specific nicotinic acetylcholine receptor gene, and the T-cell-specific CD8-alpha gene. The results establish a link between gene regulation and the divergence of primates.
Impacts
Differential gene expression lies at the heart of biology and is responsible for all developmental processes, including the growth and differentiation of cells. The evolutionary variation in gene regulation suggests a novel experimental system to study gene regulation.
Publications
- Hamdi, H.K., Nishio, H., Tavis, J., Zielinski, R. and Dugaiczyk, A. 2000. Alu-mediated Phylogenetic Novelties in Gene Regulation and Development. J. Mol. Biol. 299: 931-939.
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Progress 01/01/99 to 12/31/99
Outputs
The albumin gene family arose in a series of duplication events which gave rise to symmetry in its structure. The four genes are tandemly linked on human chromosome 4q in the order: 5'ALB-5'AFP-5'ALF-5'DBP-centromere, and their introns display a symmetrical and repetitive pattern that is shared by members of the gene family. These repetitive motifs provide an internal reference, allowing observation of evolutionary changes within a single line (human) of evolutionary descent. The four genes and intergenic regions between them increase in size, forming a gradient of genomic expansion, pointing in the centromeric direction. It is not strictly a linear gradient, but nevertheless there is a clear directionality to the expansion. An invasion by multiple repetitive DNA elements may account, in part, for this expansion.
Impacts
The dynamics of genomic changes is rather poorly understood, and pertinent questions are more difficult to formulate, as compared to questions about individual genes. The present study shows that genomic changes can be observed from the deterioration of elements of symmetry within the structure of a gene family.
Publications
- Nishio, H., Hamdi, H.K. and Dugaiczyk, A. 1999. Genomic Expansion Across the Albumin Gene Family on Human Chromosome 4q Is Directional. Biol. Chem. 380: 1431-1434.
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Progress 01/01/98 to 12/01/98
Outputs
In chromosome walking experiments from the ends of previously existing clones, we obtained a contig of overlapping lambda clones, spanning over 120 kilo bases of human genomic DNA. After restriction mapping of lambda ALF 9 and Southern hybridization to an ALF cDNA clone, we found that a 7.9 kilo bases EcoRI fragment of lambda 9 was the most 5' located fragment that hybridized to the cDNA probe. Sequencing from the 5'-end of this 7.9 kb DNA revealed the presence of exon 1 of the human ALF gene and thus established its tandem (5'AFP3'---5'ALF3') linkage with the AFP gene. This arrangement of the human AFP and ALF genes is very similar to that in the rat, although the human intergenic distance between the two genes is larger than that in the rat. The linkage between the ALF and the GC gene has been established by hybridization of fluorescently labeled lambda probes to mechanically stretched chromosomes and extended DNA fibers. These two genes are also linked in tandem:
5'ALF3'---5'GC3'). Thus, the entire gene family is tandemly linked: 5'ALB3'---5'AFP3'---5'ALF3'---5'GC3') and it is transcribed in the same, centromeric direction.
Impacts
(N/A)
Publications
- HAMDI, H. Intersparsed repetitive DNA elements: Temporal markers in the history of humans and primates. PhD Thesis, University of
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Progress 06/01/94 to 12/01/97
Outputs
We have determined the complete structure of the chimpanzee alpha-fetoprotein gene and analyzed the structure in the light of the known gene structures of the human and gorilla alpha-fetoprotein genes. The conclusions are: (1) The DNA sequence of the chimpanzee AFP gene spans 18,867 bp from the transcription start point to the polyadenylation site, and the gene is split into 15 exons by 14 intervening sequences. (2) The deduced amino acid sequence is composed of a 19-amino acid leader peptide, followed by 590 amino acids of the mature protein. (3) The gene is composed of three homologous globular domains which are interrupted by 14 introns in a symmetrical and alternating pattern. (4) A comparison of DNA repeats with orthologous human and gorilla sites revealed two human-specific DNA transpositions which constitute the most prominent distinction in the AFP gene structure between human and the other primates. (5) At the protein level, there are 6 single amino acid
differences between human and chimpanzee, 4 single amino acid differences between human and gorilla, and 8 single amino acid differences between chimpanzee and gorilla. It appears tat these amino acid differences represent neutral changes with no biological consequences to the three primate species. (6) The data were used to reexamine the rate constancy of the molecular evolutionary clock. It was concluded that the molecular clock runs at different rates among closely related members of a gene family.
Impacts
(N/A)
Publications
- NISHIO, H., GIBBS, P.E.M., MINGHETTI, P.P., ZIELINSKI, R. and DUGAICZYK, A. (1995) The chimpanzee alpha-fetoprotein-encoding gene shows structural similarity to that of gorilla but distinct differences from that of human. Gene 162; 213-220.
- NISHIO, H. (1996) Structure and Evolution of the Serum Albumin Gene Family; Comparison of the Individual Genes Within and Between Primate Species..PhD Thesis, University of California, Riverside.
- NISHIO, H., HEISKANEN, M., PALOTIE, A., BELANGER, L. and DUGAICZYK, A.(1996) Tandem Arrangement of the Human Serum Albumin Multigene Family in the Sub-centromeric Region of 4q: Evolution and Chromosomal Direction of Transcription. J. Mol.
- GIBBS, P.E.M., WITKE, W.F. and DUGAICZYK, A. (1998) The Molecular Clock Runs at Different Rates Among Closely Related Members of a Gene Family. J. Mol. Evol. 46; 552-561.
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Progress 01/01/96 to 12/30/96
Outputs
We have determined the complete structure of the chimpanzee alpha-fetoprotein gene (the second aim of the project), and analyzed the structure in the light of the known gene structures of the human and gorilla alpha-fetoprotein genes. The conclusions are: (1) The DNA sequence of the chimpanzee AFP gene spans 18,867 bp from the transcription start point to the polyadenylation site, and the gene is split into 15 exons by 14 intervening sequences. (2) The deduced amino acid sequence is composed of a 19-amino acid leader peptide, followed by 590 amino acids of the mature protein. (3) The gene is composed of three homologous globular domains which are interrupted by 14 introns in a symmetrical and alternating pattern. (4) A comparison of DNA repeats with orthologous human and gorilla sites revealed two human-specific DNA transpositions which constitute the most prominent distinction in the AFP gene structure between human and the other primates. (5) At the protein level,
there are 6 single amino acid differences between human and chimpanzee, 4 single amino acid differences between human and gorilla, and 8 single amino acid differences between chimpanzee and gorilla. It appears that these amino acid differences represent neutral changes with no biological consequences to the three primate species.
Impacts
(N/A)
Publications
- NISHIO, H., GIBBS, P.E.M., MINGHETTI, P.P., ZIELINSKI, R. and DUGAICZYK, A. (1995) The chimpanzee alpha-fetoprotein-encoding gene shows structural similarity to that of gorilla but distinct differences from that of human. Gene 162; 213-220.
- NISHIO, H. (1996) Structure and Evolution of the Serum Albumin Gene Family; Comparison of the Individual Genes Within and Between Primate Species..PhD Thesis, University of California, Riverside.
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Progress 01/01/95 to 12/30/95
Outputs
The first aim of the project was to screen a chimpanzee genomic library constructed in a phage lambda cloning vector. Using restriction DNA fragments from a gorilla alpha-fetoprotein gene as probes, we have successfully screened a chimpanzee genomic library and isolated the desired clones that encompass the 5 prime end of the chimpanzee alpha-fetoprotein gene. Restriction DNA fragments from these lambda clones were subcloned in a plasmid (pBLUESCRIPT) vector for sequences analysis. We have also determined the complete structure of the chimpanzee alpha-fetoprotein gene, thus completing the second objective of the project. The intron/exon structure of the chimpanzee gene was found to be the same as the intron/exon structure of the human and gorilla alpha-fetoprotein genes. However, based on the presence of repetitive DNA elements, the chimpanzee alpha-fetoprotein gene shows structural similarities to that of gorilla but distinct differences from that of human.
Impacts
(N/A)
Publications
- NISHIO, H., GIBBS, P.E.M., MINGHETTI, P. P., ZIELINSKI, R. and DUGAICZYK, A. (1995) The chimpanzee alpha-fetoprotein-encoding gene shows structural similarity to that of differences gorilla but distinct from that of human. Gene 162; 213-220.
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