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Biomedical subjects

O Smithies

Publications and source records attributed to O Smithies.

At least 145 records · Page 8Linked to original sources
PubMed1986

A gene deletion ending within a complex array of repeated sequences 3' to the human beta-globin gene cluster.

A DNA fragment containing the deletion junction region from an Indian individual with a type of hereditary persistence of fetal hemoglobin has been cloned. Using a probe isolated from this deletion-spanning clone, we located the 3' breakpoint of the deletion in normal DNA to a region 30 kilobase pairs (kb) downstream of the beta-globin gene. The deletion removes 48.5 kb of DNA. Sequences of the deletion junction and of the normal DNA surrounding the 3' breakpoint were determined and compared to the previously determined sequence of the normal DNA surrounding the 5' breakpoint. This comparison shows that the deletion was the result of a nonhomologous recombinational event, although there is a 5-base-pair (bp) region of local homology between the normal DNAs at their breakpoints. The 5' deletion breakpoint occurs in the Alu family repeat 3' to the A gamma-globin gene. The 3' breakpoint is located within a region that contains the following: a portion of an L1 (Kpn I) repeat, a perfect 160-bp palindrome, and a set of 41-bp direct repeats that are found elsewhere in the human genome. A variation in restriction fragment lengths was observed in this region in one family.

Chromosome Deletion↗
PubMed1986

Polymorphisms in the human haptoglobin gene cluster: chromosomes with multiple haptoglobin-related (Hpr) genes.

We have found polymorphisms for the number of tandemly arranged haptoglobin-related (Hpr) genes in the haptoglobin gene cluster of Blacks. Genomic mapping and nucleotide sequence analysis indicate that two copies of the Hpr gene first resulted from unequal but homologous crossing-over in a region 3' to the haptoglobin (Hp) and the haptoglobin-related genes. Subsequent increases in the number of Hpr loci have occurred in some chromosomes. Among 25 American Blacks studied (15 were unrelated), 2 related individuals have one extra copy of the Hpr gene and 5 unrelated individuals have more than two extra Hpr genes. None of 26 Whites and one Oriental studied have extra copies. In one of the Blacks, six tandemly arranged Hpr genes were demonstrated in one chromosome by pulsed field gradient electrophoresis. His other chromosome had one Hpr gene. The tandem Hpr genes were found in individuals with the haptoglobin genotypes Hp2/Hp2 (3 of 3 tested) and Hp2/Hp1 (4 of 11 tested), but none were found in the Hp1/Hp1 individuals (11 tested). Fibroblast cell cultures from two Hp2/Hp1 heterozygotes were fused to mouse cells to obtain cell lines retaining a human chromosome 16 on which the haptoglobin gene cluster is located. DNA analysis of the hybrid cells showed that in both individuals the tandemly arranged Hpr genes are linked to the Hp2 allele. These results suggest that the multiple copies are associated with the Hp2 gene.

Base Sequence↗
PubMed1986

Short gene conversions in the human fetal globin gene region: a by-product of chromosome pairing during meiosis?

DNA sequence comparisons of a 1200-base pair (bp) region in 14 human fetal globin genes in seven linked pairs reveal 31 nucleotide substitutions at positions where the fetal globin genes, G gamma and A gamma, usually differ. In each case, the newly substituted nucleotide is identical to the one found at the same position in the linked nonallelic gene. Most of these nucleotide substitutions are clearly the result of gene conversions, but 11 could be the result of either very short gene conversions or of point mutations. The unexpectedly frequent occurrence of these short gene conversions suggests that they may be the relics of some normal interaction between homologous but nonallelic DNA sequences, and we discuss the possibility that they result from interactions occurring between homologous sequences during the process of meiotic chromosome pairing.

Alleles↗
PubMed1986

Efficient transformation and frequent single-site, single-copy insertion of DNA can be obtained in mouse erythroleukemia cells transformed by electroporation.

Electroporation has recently been shown to have advantages over the commonly used method of calcium phosphate precipitation for obtaining DNA-mediated transformation of certain types of cells. Although mouse erythroleukemia cells and other cells of hematopoietic origin are not transformed at useful frequencies by calcium phosphate-DNA precipitation methods, we obtained high frequencies of transformation (approximately 10(-5)) of these cells with electroporation. Even higher transformation frequencies (approximately 10(-3)) were obtained with human fibroblasts. Another advantage of electroporation was found when analysis of Southern blots of DNA from 243 transformed erythroleukemia cell colonies indicated that, under appropriate conditions, about 79% of the transformed cells had the exogenous DNA integrated in single copies at single sites. Under conditions of higher DNA and lower cell concentrations using fibroblasts, cotransformation was obtained with two plasmids that confer HAT or G418 resistance when integrated into cellular DNA. About 23% of the transformed cells developed both types of resistance. We describe a simple, inexpensive apparatus for carrying out electroporation.

Animals↗
PubMed1985

Nucleotide sequence of 16-kilobase pairs of DNA 5' to the human epsilon-globin gene.

We have determined the nucleotide sequence of a 16-kilobase pair (kb) region of DNA on the 5' side of the human embryonic globin gene (epsilon). This sequence, when combined with previously published sequences, gives an uninterrupted sequence of 21 kb extending from approximately 19.5 kb upstream of the epsilon-globin gene to 0.3 kb 3' to its poly(A)-addition site. Computer-assisted analysis of this DNA reveals no large regions of self-homology but it shows the presence of seven members of the Alu family of repeated DNA, two very short members of the Kpn family of repeated DNA, one unusual direct repeat of 39 base pairs, and two potential stem and loop structures. The overall frequencies of mono- and dinucleotides within the 21 kb approximate those found in the total human genome but the distribution of (G + C)-rich regions signal many sequences of interest. The occurrences of some of the polynucleotides and polydinucleotides also differ appreciably from randomness, and the region contains several large stretches of these simple sequences. We found no evidence of strand asymmetry in the region. Homology between the nucleotide sequences of the human epsilon- and G gamma-globin genes extends only 100 base pairs 5' to the genes. One region, about 10 kb upstream of the gene, shows an apparent clustering of unusual sequence features. We discuss our sequence data in relation to the studies by others of DNAase hypersensitive sites and 5' transcription endpoints in this part of the beta-globin gene cluster.

Base Sequence↗
PubMed1985

A Chinese G gamma + (A gamma delta beta)zero thalassemia deletion: comparison to other deletions in the human beta-globin gene cluster and sequence analysis of the breakpoints.

A clone was isolated that contains the deletion junction region from an individual with a deletion associated with Chinese G gamma + (A gamma delta beta)zero thalassemia. A clone containing the normal DNA corresponding to the 3' breakpoint of this deletion was also isolated. Portions of these two clones were sequenced and compared to the region in the A gamma-globin gene where the 5' breakpoint occurs. This comparison reveals that the breakage and reunion event was nonhomologous and that it probably involved the insertion of 36-41 bases of DNA belonging to the L1 (KpnI) family of repetitive DNA. Genomic mapping revealed that the DNA on the 3' side of this deletion is closely linked in normal DNA to the 3' breakpoints of two different large deletions that are associated with hereditary persistence of fetal hemoglobin (HPFH). We cloned and mapped 35 kbp of normal DNA from this region (greater than 45 kbp downstream of the human beta-globin gene) that contains the 3' breakpoints of the Chinese thalassemia and the two HPFH deletions. An endogenous retrovirus-like element and several other repetitive sequences are located within this region. We show that the Chinese thalassemia deletion is greater than 80 kbp in length and differs in size from the two HPFH deletions by less than 6%. We also show that the Chinese thalassemia deletion is at least 40 kbp larger than several other deletions associated with a very similar phenotype.

Base Sequence↗
PubMed1985

Differential RNA splicing and post-translational cleavages in the human salivary proline-rich protein gene system.

The nucleotide sequences of cDNAs coding for human salivary proline-rich proteins (PRPs) were determined. Clones cP1 and cP2 contain repetitive regions in which sites for the restriction enzyme HaeIII occur repeatedly; they code for the precursors of acidic PRPs. Clones cP3 to cP7 contain repetitive regions in which BstNI sites occur repeatedly; they code for precursors of basic and glycosylated PRPs. The clones cP3, cP4, and cP5 are identical except that cP4 and cP5 are missing 399 and 459 base pairs, respectively, from the repetitive region of cP3. The sequences at these deletion end points are homologous to the consensus sequences of RNA splicing donor and acceptor sites. This strongly suggests that all three cDNAs are derived from the transcript of a single gene via differential RNA splicing. All of the precursor proteins share a feature--the N-terminal region, following the signal peptide, is acidic, while the remainder of the molecule, made of proline-rich repeats of about 21 amino acids, is basic. Each precursor can generate multiple PRPs by various post-translational cleavages on the carboxylic side of specific arginine residues. The data show how differential RNA splicing and post-translational cleavages could generate a large number of proteins, such as those found in saliva, from a much smaller number of genes.

Animals↗
PubMed1985

(A gamma delta beta)0-Thalassaemia in Blacks is due to a deletion of 34 kbp of DNA.

DNA from members of 10 Black families with conditions considered to be G gamma (delta beta)0-thalassaemia or G gamma (delta beta)0-HPFH were studied by using restriction enzyme analysis. One or more affected members from each family were shown to have the same deletion of 34 kbp of DNA in the human beta-globin gene cluster. A clone spanning the deletion was isolated from the DNA of one such person and studied in detail. The deletion removed part of the A gamma and all of the psi beta, delta and beta-globin genes and is different from the four previously identified deletions which caused a condition presently known as (A gamma delta beta)0-thalassaemia.

Adolescent↗
PubMed1984

Two novel arrangements of the human fetal globin genes: G gamma-G gamma and A gamma-A gamma.

We describe two novel arrangements of the human fetal globin gene region: one chromosome with two linked A gamma genes (A gamma-A gamma) and two chromosomes with two linked G gamma genes (G gamma-G gamma). The gamma genes of these three chromosomes were cloned and the unusual 5' A gamma gene and one of the unusual 3' G gamma genes were partially sequenced. Both of these unusual genes differ from the genes normally found at their respective locations by a nucleotide substitution at the site of the single coding region difference between normal G gamma and A gamma genes. In both cases, the substitution is identical to the nucleotide found at that position in the normal neighboring gene. The unusual 3' G gamma gene also differs from normal A gamma genes at two other nucleotide positions, but both differences appear to be "private" or exclusive to this particular gene. These unusual fetal globin gene arrangements could have arisen from point mutations or from gene conversions of limited extent, the boundaries of which have been determined for all three chromosomes.

Base Sequence↗
PubMed1984

A comprehensive set of sequence analysis programs for the VAX.

The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system. The programs available and the conditions for transfer are described.

Base Sequence↗
PubMed1984

Homologous recombination between plasmids in mammalian cells can be enhanced by treatment of input DNA.

We have used the eukaryotic-prokaryotic shuttle vector pSV2Neo to demonstrate that cultured mammalian somatic cells have the enzymatic machinery to mediate homologous recombination and that the frequency of this recombination can be enhanced by pretreatment of the input DNA. Two nonoverlapping deletion mutants of pSV2Neo were constructed, each affecting the bacterial aminoglycoside 3'-phosphorylase gene (the neo gene), which confers resistance to aminoglycoside antibiotics on bacteria and resistance to the antibiotic G418 on mammalian cells. Mammalian cells transfected with either deletion plasmid alone yield no G418 -resistant colonies. Cells cotransfected with both deletion plasmids yield G418 -resistant colonies with high frequency. We show that these resistant colonies result from recombination involving homologous crossing-over or gene conversion between the deletion plasmids by rescuing from the resistant cells both types of reciprocal recombinant, full-length plasmids, and doubly deleted plasmids. Cutting one of the input plasmids to generate a double-stranded gap in the neo gene considerably enhances the frequency of homologous recombination within the gene. This suggests that targeting exogenous DNA to specific sites in mammalian chromosomes could be facilitated by suitable pretreatment of the DNA.

Animals↗
PubMed1984

Clones from the human gene complex coding for salivary proline-rich proteins.

The salivary protein gene complex consists of a series of loci coding for related but distinct proline-rich proteins (PRPs) found chiefly in saliva. We have screened a library of human genomic DNA fragments in bacteriophage lambda Charon 4A with a PRP cDNA synthesized and cloned from rat parotid gland mRNA. Two phages (PRP1 and PRP2) hybridizing to the rat probe under moderately stringent conditions contain related but not identical DNAs. Preliminary nucleotide sequence data indicate that both DNAs include regions comprised of nearly identical tandemly repeated sequences, each able to code for about 21 amino acids. The decoded consensus repeat sequence is homologous to the repeating amino acid units found by others in human PRPs. This and other features demonstrate that these two clones are members of the PRP gene family. Polymorphic differences between the DNAs of different individuals were observed after probing digests of human genomic DNA with a HinfI fragment from PRP1. These DNA polymorphisms reflect size differences, possibly caused by frequent unequal crossing-over between the repeated units in the PRP genes.

Amino Acid Sequence↗
PubMed1983

Unexpected relationships between four large deletions in the human beta-globin gene cluster.

Two independent gamma delta beta-thalassemias are each associated with large deletions. We show, by comparing DNA sequences, that the deletions are due to non-homologous DNA exchanges. The 5' breakpoints are located approximately the same distance apart and in the same order along the DNA as their 3' breakpoints. Two independent cases of hereditary persistence of fetal hemoglobin, also involving large deletions, show the same unexpected relationship between their 5' and 3' breakpoints. This relationship is most simply explained if, within each pair, the deletions are of approximately the same length. The results suggest that the four deletions were generated by a common mechanism. Perhaps their 5' and 3' breakpoints are physically close in the nucleus, although far apart on the linear DNA.

Base Sequence↗
PubMed1983

Coordinate modulation of transfected HSV thymidine kinase and human globin genes.

We have shown that high-frequency phenotypic switching of a transfected gene is associated with alterations in chromatin structure. To examine this phenomenon further, a plasmid containing HSV thymidine kinase and human alpha- and gamma-globin genes was transfected into mouse L cells. All three genes were expressed through utilization of their individual promoters. One of these cell lines was capable of switching to its TK- phenotype at high frequencies (8%-10%). The revertants (TK-) had no TK or globin transcripts, while the rerevertants (TK+) expressed all three genes at their original levels. We conclude that genes introduced into cells by ligated cotransfection can be regulated coordinately and that the unit of this regulated expression can be at least 20 kb long.

Animals↗
PubMed1983

Recombination and balanced chromosome polymorphism suggested by DNA sequences 5' to the human delta-globin gene.

Two types of chromosome (R and T) were found by cloning from six human individuals the 3.1-kilobase-pair EcoRI fragment that contains the bipolar Alu family repeat 5' to the delta-globin gene. Two type T fragments were identical in nucleotide sequence. Two type R fragments were identical except for one base. Both types are found in whites, blacks, and orientals. The differences between R and T sequences (16 base substitutions and two deletions) were mostly in the 5' domain of the fragment (0.91% difference in 1.7 kilobases), which contains the bipolar Alu repeat, whereas the 3' domain of the fragment was more conserved (0.14% difference in 1.4 kilobases). To help understand the history of this human polymorphism, the equivalent fragment from a chimpanzee was cloned and its sequence was determined. The chimpanzee sequence differed from both human sequences at 39 positions distributed almost uniformly along the whole 3.1-kilobase-pair fragment. Assuming that humans and chimpanzees diverged 4 to 5 million years ago, the data indicate that the divergence of the two types of human chromosome started about 3 million years ago but about 0.4 million years ago an interchromosomal recombination rendered the two types of human chromosome alike in their 3' domains. The two chromosomes have since remained discrete and have persisted in several populations. These observations suggest that factors are operating to maintain a balanced chromosomal polymorphism in this region 5' to the human delta-globin gene.

Animals↗