Publications by authors named "Dugaiczyk A"

There are over a million Alu repetitive elements dispersed throughout the human genome, and a high level of Alu-sequence similarity ensures a strong propensity for unequal crossover events, some of which have lead to deleterious oncogenic rearrangements. Furthermore, Alu insertions introduce consensus 3' splice sites, which potentially facilitate alternative splicing. Not surprisingly, Alu-mediated defective splicing has also been associated with cancer.

View Article and Find Full Text PDF

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. Here we trace the evolution of AluYb8 repeats from a single origin at the roots of higher primates to a large increase in their number in humans.

View Article and Find Full Text PDF

When viewed from the perspective of time, human genetic disorders give new insights into their etiology and evolution. Here, we have correlated a specific set of Alu repetitive DNA elements, known to be the basis of certain genetic defects, with their phylogenetic roots in primate evolution. From a differential distribution of Alu repeats among primate species, we identify the phylogenetic roots of three human genetic diseases involving the LPL, ApoB, and HPRT genes.

View Article and Find Full Text PDF

Differential gene expression lies at the heart of biology and is responsible for all developmental processes, including the growth and differentiation of cells. Perhaps even speciation could be defined as a change in differential gene expression over evolutionary time. The present work is a phylogenetic study of four Alu elements known to have gene regulatory functions in the human.

View Article and Find Full Text PDF

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 observations of evolutionary changes within a single line (human) of evolutionary descent.

View Article and Find Full Text PDF

Over the past 60 million years, or so, 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 (and other) DNA repeats in the genome of several primates: human, chimpanzee, 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.

View Article and Find Full Text PDF

The serum albumin gene family is composed of four members that have arisen by a series of duplications from a common ancestor. From sequence differences between members of the gene family, we infer that a gene duplication some 580 Myr ago gave rise to the vitamin D-binding protein (DBP) gene and a second lineage, which reduplicated about 295 Myr ago to give the albumin (ALB) gene and a common precursor to alpha-fetoprotein (AFP) and alpha-albumin (ALF). This precursor itself duplicated about 250 Myr ago, giving rise to the youngest family members, AFP and ALF.

View Article and Find Full Text PDF

The nucleotide sequence of the human alpha-albumin gene, including 887 bp of the 5'-flanking region and 1311 bp of the 3-flanking region (24,454 in total), was determined from three overlapping lambda phage clones. The sequence spans 22,256 bp from the cap site to the polyadenylylation site, revealing a gene structure of 15 exons separated by 14 introns. The methionine initiation codon ATG is within exon 1; the termination codon TGA is within exon 14.

View Article and Find Full Text PDF

The albumin gene family is comprised of four genes encoding: serum albumin (ALB), alpha-fetoprotein (AFP), alpha-albumin (ALF), and vitamin D-binding protein (DBP; also known as GC). The genes are regulated developmentally, expressed in the liver, and the proteins are secreted into the bloodstream. The GC gene, and the tandemly linked ALB and AFP genes, have been previously localized to human chromosome 4q11-13.

View Article and Find Full Text PDF

The chimpanzee (Pan troglodytes) alpha-fetoprotein (AFP)-encoding gene (AFP) spans 18,867 bp from the transcription start point to the polyadenylation site, and the nucleotide (nt) sequence reveals that the gene is composed of 15 exons, which are symmetrically placed within three domains of AFP. In addition, we report 3121 bp of 5'-flanking sequence and 4886 bp of 3'-flanking sequence. The entire 26,874 bp of contiguous DNA reported here was determined from three overlapping lambda phage clones.

View Article and Find Full Text PDF

The closely related serum albumin, alpha-fetoprotein, and vitamin D-binding proteins are derived from a common ancestor, which itself was the result of a triplication of an ancestral gene. We have aligned the sequences of these proteins against themselves to assess the degree to which the ancestral 3-fold symmetry has been retained; in a dot plot, relics of the molecular symmetry appear as a series of alignments parallel to the main diagonal. The decay of internal symmetry reflects the rate of change of a gene in a single line of evolutionary descent.

View Article and Find Full Text PDF

As part of our efforts to construct a high-resolution physical map of human chromosome 4, we developed a systematic approach for efficiently generating large numbers of chromosome-specific sequence-tagged sites (STSs). In this paper, we describe how rate-limiting steps in our STS development were identified and overcome, and detail our current development strategy. We present information for 822 new human chromosome 4-specific STSs, including PCR amplification conditions and subchromosomal localization data, obtained by analysis of the STS with somatic cell hybrids containing different portions of human chromosome 4.

View Article and Find Full Text PDF

The sequence of the human Gc gene, including 4228 base pairs of the 5'-flanking region and 8514 base pairs of the 3' flanking region (55,136 in total), was determined from five overlapping lambda phage clones. The sequence spans 42,394 base pairs from the cap site to the polyadenylation site, and it reveals that the gene is composed of 13 exons, which are symmetrically placed within the three domains of the Gc protein. The first exon is partially untranslated, as is exon 12, which contains the termination codon TAG.

View Article and Find Full Text PDF

We have identified four genetic novelties that are fixed in specific primate lineages and hence can serve as phylogenetic time markers. One Alu DNA repeat is present in the human lineage but is absent from the great apes. Another Alu DNA repeat is present in the gorilla lineage but is absent from the human, chimpanzee, and orangutan.

View Article and Find Full Text PDF

The sequence of the gorilla alpha-fetoprotein gene, including 869 base pairs of the 5' flanking region and 4892 base pairs of the 3' flanking region (24,607 in total), was determined from two overlapping lambda phage clones. The sequence extends 18,846 base pairs from the Cap site to the polyadenylation site, and it reveals that the gene is composed of 15 exons, which are symmetrically placed within three domains of alpha-fetoprotein. The deduced polypeptide chain is composed of a 19-amino-acid leader peptide, followed by 590 amino acids of the mature protein.

View Article and Find Full Text PDF

We discovered the presence of an Alu and an Xba repetitive DNA element within introns 4 and 7, respectively, of the human alpha-fetoprotein (AFP) gene; these elements are absent from the same gene in the gorilla. The Alu element is flanked by 12-base-pair direct repeats, AGGATGTTGTGG ..

View Article and Find Full Text PDF

We have identified a structural defect in the serum albumin gene in human analbuminemia. Sequence determination of 1.1 kilobases (kb) of the 5' regulatory region and of 6 kb across exonic regions revealed a single AG-to-GG mutation within the 3' splice site of intron 6 in the defective gene of an analbuminemic individual.

View Article and Find Full Text PDF

We have recently determined complete DNA sequences for the human albumin and alpha-fetoprotein [AFP] genes and thus have identified their detailed structures. Each is composed of three domains of four exons, three of which are internal and one of which is a domain-linking exon. Equivalent exons in each domain show sufficient sequence and structural similarity to be considered homologous; additional unique exons at each end of the gene show no similarity to the internal triplicated structures.

View Article and Find Full Text PDF

The human alpha-fetoprotein gene spans 19,489 base pairs from the putative "Cap" site to the polyadenylation site. It is composed of 15 exons separated by 14 introns, which are symmetrically placed within the three domains of alpha-fetoprotein. In the 5' region, a putative TATAAA box is at position -21, and a variant sequence, CCAAC, of the common CAT box is at -65.

View Article and Find Full Text PDF

The human albumin-alpha-fetoprotein genomic domain contains 13 repetitive DNA elements randomly distributed throughout the symmetrical structures of these genes. These repeated sequences are located at different sites within the two genes. The human albumin gene contains five Alu elements within four of its 14 intervening sequences.

View Article and Find Full Text PDF

The human albumin gene spans 16,961 nucleotides from the putative "Cap" site to the first poly(A) addition site. It is split into 15 exons by 14 intervening sequences which are symmetrically placed within the three domains of albumin. The 5' region is highly conserved up to position -250 and contains the putative TATA (-32) and CAT (-88) boxes.

View Article and Find Full Text PDF

We conducted the present study in an attempt to correlate function with the rate of molecular evolution for serum albumin and alpha-fetoprotein. We found a high rate of silent substitution (between 5 X 10(-9) and 7 X 10(-9)/site/year) for both the albumin and alpha-fetoprotein genes, perhaps the highest so far reported for an expressed nuclear gene. The rates of effective substitution and amino acid changes were also very high, but in contrast to silent substitutions, they are higher for alpha-fetoprotein than for albumin by approximately 70%.

View Article and Find Full Text PDF

By in situ hybridization of cloned human alpha-fetoprotein cDNA to human mitotic chromosome preparations, the alpha-fetoprotein gene was localized within the q11-22 region on the long arm of human chromosome 4. In addition, the human alpha-fetoprotein gene was isolated from a genomic phage library. The gene is split into 15 exons and 14 introns, and the entire structure is contained within two large (9.

View Article and Find Full Text PDF

The human serum albumin gene was analyzed by restriction endonuclease mapping of chromosomal DNA isolated from a patient with congenital analbuminemia. Following digestion with a variety of restriction endonucleases, the DNA from this individual produced the same fragments with homology to a serum albumin cDNA probe as did a control DNA specimen. Therefore, the genetic condition of congenital analbuminemia is not caused by any gross structural rearrangement or deletion of the gene itself, but may result from an abnormality in the gene's fine structure, perhaps affecting regulation or processing of the primary RNA transcript.

View Article and Find Full Text PDF