Assignment of human beta-, gamma-, and delta-globin genes to the short arm of chromosome 11 by chromosome sorting and DNA restriction enzyme analysis

Identification of genetic linkage group 1-linked sequences in Japanese eel (Anguilla japonica) by single chromosome sorting and sequencing

Japanese eel (Anguilla japonica) constitutes one of the most important food fish in Japan; accordingly, genome sequencing and linkage mapping have been conducted for the purpose of artificial cultivation. In the next stage, integration of genomic sequences within linkage groups (LG) is required to construct higher-resolution genetic markers for quantitative trait loci mapping and selective breeding of beneficial traits in farming. In order to identify LG1-linked scaffolds from the draft genome assembly (323,776 scaffolds) reported previously, we attempted to isolate chromosomes corresponding to LG1 by flow sorting and subsequent analyses. Initially, single chromosomes were randomly collected by chromosome sorting and subjected to whole-genome amplification (WGA). A total of 60 WGA samples were screened by PCR with primers for a known LG1-linked scaffold, and five positive WGA samples were sequenced by next-generation sequencing (NGS). Following reference mapping analysis of the NGS reads, four of the five WGA samples were found to be enriched by LG1-linked sequences. These samples were cytogenetically assigned to chromosome 5 by fluorescence in situ hybridization. Using blastn searches with 82,081 contigs constructed from the NGS reads of the four WGA samples as queries, 2323 scaffolds were identified as putative LG1-linked scaffolds from the draft genome assembly. The total length of the putative LG1-linked scaffolds was 99.0 Mb, comparable to the estimated DNA amounts of chromosome 5 (91.1 Mb). These results suggest that the methodology developed herein is applicable to isolate specific chromosome DNAs and integrate unanchored scaffold sequences onto a particular LG and chromosome even in teleost fishes, in which isolation of specific chromosomes by flow sorting is generally difficult owing to similar morphologies, sizes, and GC-contents among chromosomes in the genome. The putative LG1-linked scaffolds of Japanese eel contain a total of 6833 short tandem repeats which will be available for higher-resolution linkage mapping.

Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes

BACKGROUND

Cultivated strawberry (Fragaria × ananassa Duch.) has homoeologous chromosomes because of allo-octoploidy. For example, two homoeologous chromosomes that belong to different sub-genome of allopolyploids have similar base sequences. Thus, when conducting de novo assembly of DNA sequences, it is difficult to determine whether these sequences are derived from the same chromosome. To avoid the difficulties associated with homoeologous chromosomes and demonstrate the possibility of sequencing allopolyploids using single chromosomes, we conducted sequence analysis using microdissected single somatic chromosomes of cultivated strawberry.

RESULTS

Three hundred and ten somatic chromosomes of the Japanese octoploid strawberry 'Reiko' were individually selected under a light microscope using a microdissection system. DNA from 288 of the dissected chromosomes was successfully amplified using a DNA amplification kit. Using next-generation sequencing, we decoded the base sequences of the amplified DNA segments, and on the basis of mapping, we identified DNA sequences from 144 samples that were best matched to the reference genomes of the octoploid strawberry, F. × ananassa, and the diploid strawberry, F. vesca. The 144 samples were classified into seven pseudo-molecules of F. vesca. The coverage rates of the DNA sequences from the single chromosome onto all pseudo-molecular sequences varied from 3 to 29.9%.

CONCLUSION

We demonstrated an efficient method for sequence analysis of allopolyploid plants using microdissected single chromosomes. On the basis of our results, we believe that whole-genome analysis of allopolyploid plants can be enhanced using methodology that employs microdissected single chromosomes.

Scanning method to identify the molecular heterogeneity of delta-globin gene especially in delta-thalassemias: detection of three novel substitutions in the promoter region of the gene

A scanning strategy for the detection of delta-globin gene mutations and polymorphisms is presented. This procedure is based on the denaturing gradient gel electrophoresis (DGGE) of four different artificially amplified DNA fragments which cover the promoter, the exons, as well as IVS I of the reported gene. To estimate the efficiency and sensitivity of the proposed procedure, we analysed the appropriate controls of delta-thalassemic carriers, uncharacterised delta-thalassemias and cases with normal hematological phenotype, but slightly increased (up to 3.5%) HbA2. DGGE results permitted the identification of delta-globin gene mutations and the polymorphism -199 (T-->C). Three novel base substitutions inside the promoter region of the gene [-65 (A-->G), -55 (T-->C), -36 (C-->A)], were also revealed. These changes are either linked in cis with other mutations or are responsible for thalassemias or for positive regulatory effect in delta-globin gene expression. The proposed experimental strategy consists of an accurate, rapid, safe and inexpensive screening procedure for establishing the molecular basis of delta-globin gene defects, suitable for the application for both research and diagnostics.

CEREAL CHROMOSOME STRUCTURE, EVOLUTION, AND PAIRING

▪ Abstract  The determination of the order of genes along cereal chromosomes indicates that the cereals can be described as a single genetic system. Such a framework provides an opportunity to combine data generated from the studies on different cereals, enables chromosome evolution to be traced, and sheds light on key structures involved in cereal chromosome pairing. Centromeric and telomeric regions have been highlighted as important in these processes.

Phylogenetic relationships among Brazilian howler monkeys, genus Alouatta (Platyrrhini, Atelidae), based on g1-globin pseudogene sequences

The genus Alouatta (howler monkeys) is the most widely distributed of New World primates, and has been arranged in three species groups: the Central American Alouatta palliata group and the South American Alouatta seniculus and Alouatta caraya groups. While the latter is monotypic, the A. seniculus group encompasses at least three species (A. seniculus, A. belzebul and A. fusca). In the present study, approximately 600 base pairs of the g1-globin pseudogene were sequenced in the four Brazilian species (A. seniculus, A. belzebul, A. fusca and A. caraya). Maximum parsimony and maximum likelihood methods yielded phylogenetic trees with the same arrangement: {A. caraya [A. seniculus (A. fusca, A. belzebul)]}. The most parsimonious tree had bootstrap values greater than 82% for all groupings, and strength of grouping values of at least 2, supporting the sister clade of A. fusca and A. belzebul. The study also confirmed the presence of a 150-base pair Alu insertion element and a 1.8-kb deletion in the g1-globin pseudogene in A. fusca, features found previously in the remaining three species. The cladistic classification based on molecular data agrees with those of morphological studies, with the monospecific A. caraya group being clearly differentiated from the A. seniculus group.

Synergistic enhancement of globin gene expression by activator protein-1-like proteins

DNA sequences corresponding to the four major DNase I hypersensitive sites upstream of the beta-globin gene cluster are essential for the achievement of high levels of globin gene expression and development regulation. In this study, we focused on one of these sites, hypersensitive site 2, which behaves as a powerful enhancer in transient expression and transgenic mouse experiments. We identified a tandem repeat of the activator protein 1 (AP-1) consensus sequence that binds AP-1-like proteins from nuclear extracts of K562 and HeLa cells. These proteins have the same binding properties as HeLa AP-1 but differ in the electrophoretic mobility and in functional assays. Transient-expression experiments in K562 of various deletion and point mutation constructs derived from hypersensitive site 2 indicate that the enhancer activity and the inducibility of a linked gamma-globin promoter are dependent upon the synergistic action of proteins bound to the tandem AP-1 repeat.

The role of genetic factors in the etiology of the affective disorders

Recent application of genetic linkage analysis to the affective disorders has suggested that there are at least three genotypic forms. This is an important step toward defining the genetic etiology involved, as it had previously been suggested that the complex nature of the clinical phenotype would preclude any attempt to apply such a technique. However, to date no clinical evidence exists to discriminate these genotypes at the phenotypic level. Molecular geneticists now face a formidable task of identifying the aberrant gene and relating the gene product, a protein, to the observed psychopathology. Current molecular genetic research in the affective disorders is discussed and similar work applied to the study of nonpsychiatric disorders such as cystic fibrosis and Duchenne muscular dystrophy is reviewed. The clinical value of genetic risk analysis for individuals with a family history of the affective disorders is also considered.

Human beta-globin gene expression in transgenic mice is enhanced by a distant DNase I hypersensitive site

Several lines of evidence suggest that erythroid-specific DNase I hypersensitive sites (HS) located far upstream of the human beta-globin gene are important in regulating beta-globin gene expression. We used the polymerase chain reaction technique to amplify and clone an 882-base-pair DNA fragment spanning one of these HS, designated HSII, which is located 54 kilobases upstream of the beta-globin gene. The cloned HSII fragment was linked to a human beta-globin gene in either the genomic (HSII-beta) or antigenomic (HSII-beta) orientation. These two constructs and a beta-globin gene alone (beta) were injected into fertilized mouse eggs, and expression was analyzed in liver and brain from day-16 transgenic fetuses. Five of 7 beta-transgenic fetuses expressed human beta-globin mRNA, but the level of expression per gene copy was low, ranging from 0.93 to 22.4% of mouse alpha-globin mRNA (average 9.9%). In contrast, 11 of 12 HSII-beta transgenic fetuses expressed beta-globin mRNA at levels per gene copy ranging from 31.3 to 336.6% of mouse alpha-globin mRNA (average 139.5%). Only three fetuses containing intact copies of the HSII-beta construct were produced. Two of three expressed human beta-globin mRNA at levels per gene copy of 179.2 and 387.1%. Expression of human beta-globin mRNA was tissue-specific in all three types of transgenic fetuses. These studies demonstrate that a small DNA fragment containing a single erythroid-specific HS can stimulate high-level human beta-globin gene expression in transgenic mice.

Mapping by chromosome sorting of several gene probes, including c-myc, to the derivative chromosomes of a 3;8 translocation associated with familial renal cancer

In eight members of a single family a constitutional translocation t(3;8) (p14.2;q24.1) is associated with the development of renal cancer. Chromosomes isolated from a cell line established from a subject with this translocation were analysed in flow with a fluorescence-activated cell sorter (FACS II). Nearly six million chromosomes from the flow karyotype region containing the der(8) and 5.5 million from the region containing the der(3) were sorted, the DNA extracted, digested with EcoRI, size fractionated by electrophoresis, and transferred to nitrocellulose. Hybridization with gene probes for c-mos, which has been localized to 8q11-q22 and somatostatin, which has been mapped to 3q28, confirmed that the sorted fractions contained, respectively, the der(8) and der(3) chromosomes. The cellular oncogenes c-raf-1 (3p25) and c-myc (8q24) were found to be translocated to the der(8) and der(3) chromosomes, respectively. The possible role that the relocation of c-myc might have on the development of renal carcinoma in carriers of this 3;8 translocation was further studied by analysis of the region surrounding the c-myc gene. By the use of cosmid cloning, no rearrangement 31 Kb 5'(or 19 Kb 3') of the translocated gene was found, indicating that the break-point is not immediately adjacent to c-myc. In an associated study, the DNA fragment D3S2 from chromosome 3 was found to map to 3p14.2-pter. This assignment in conjunction with published somatic cell hybrid data enabled D3S2 to be mapped more precisely to the interval 3p14.2-3p21.

Detecting abnormal human chromosome constitutions by dual laser flow cytogenetics

Our custom dual laser chromosome sorter has been used to characterize and isolate metaphase human chromosomes rapidly for gene mapping purposes. Herein, we tested how well this system could detect unknown abnormal human chromosome constitutions. These results were compared to those of conventional cytogenetic analyses by banding and photomicrography. The sorter was used to analyze each cell line stained with two different stain pairs: DIPI-chromomycin and Hoechst-chromomycin. In 20 min, two histograms representing 2 X 10(5) chromosomes each were collected for each stain pair. A blind study of 11 samples by flow analysis demonstrated excellent concordance between the abnormal chromosomes detected and the diagnoses of Giemsa-banded karyotypes. Aneuploidy was identified by changes in the number of chromosomes in each histogram peak, while rearrangements such as deletions and translocations caused shifts in the histogram peak positions. The direction and distance of histogram peak shifts are directly related to alterations in chromosome size and banding pattern. We conclude that dual-laser flow analysis may provide a rapid approach to the screening and diagnosis of chromosome abnormalities.

Cloning and chromosomal location of the alpha- and beta-globin genes from a marsupial

The cDNA sequences encoding the adult alpha- and beta-globin polypeptides of a marsupial, the native cat Dasyurus viverrinus, have been cloned and their nucleotide sequences have been determined. Using these cDNA clones we have determined the chromosomal location of the native cat alpha- and beta-globin genes by in situ hybridization to fixed metaphase chromosomes and by hybridization to DNA extracted from chromosomes purified by a fluorescence-activated cell sorter. Using two independent methods of gene assignment we have shown the alpha- and beta-globin-like gene sequences to be asyntenic in the native cat, the alpha-globin-like sequences being on chromosome 2 and the beta-globin-like sequences being on chromosome 4.

Human ferritin light chain gene sequences mapped to several sorted chromosomes

The iron storage ferritin light-chain gene exhibits multiple restriction enzyme fragments which have been mapped by analyzing sorted human chromosomes. A dual laser chromosome sorter was used to construct spot-blot filter panels representing 22 chromosome fractions. Hybridization of radiolabeled human ferritin-L gene probe to spot-blot panels revealed the ferritin-L gene on more than one chromosome. Miniaturized restriction enzyme analysis was used to map each of the ferritin-L restriction fragments uniquely to one of three chromosomes. This combination of sorted chromosome analyses provides a rapid method to map homologous DNA sequences located on more than one chromosome.

Gene order on the short arm of human chromosome 11: regional assignment of the LDH A gene distal to catalase in two translocations

Leukemic cells with reciprocal translocations involving 11p13 and 14q13 were obtained from two patients with T-cell acute lymphoblastic leukemia and fused with mouse Ltk- cells. DNA from independent hybrid clones was screened by Southern blot and hybridization to molecular probes for the human catalase and Ha-ras-1 genes. Several clones showed segregation of these two genes, indicating the presence of either the der11 or der14 human chromosomes. When DNA from these hybrid clones was examined for the presence of the human genes for calcitonin and gamma-globin, both genes were found to segregate with the Ha-ras-1 gene and the der14 chromosome indicating that they lie distal to catalase. When the hybrid clones were examined for the presence of human lactate dehydrogenase A (LDH A) activity, only those clones containing the der14 chromosome expressed activity indicating that the LDH A gene is also distal to catalase on the short arm of chromosome 11.

Random association of Epstein-Barr virus genomes with host cell metaphase chromosomes in Burkitt's lymphoma-derived cell lines

The random association of Epstein-Barr virus DNA with host cell metaphase chromosomes of all sizes in Burkitt's lymphoma-derived cell lines was demonstrated by two substantially different techniques, namely fluorescence-activated chromosome sorting and in situ hybridization. The nature and potential importance of this association are discussed.

Spot-blot analysis of sorted chromosomes assigns a fructose intolerance disease locus to chromosome 9

The aldolase B gene was mapped to chromosome 9 using a rapid gene mapping system. This system uses a dual-laser sorter to identify and separate metaphase human chromosomes stained with either DIPI-chromomycin or Hoechst-chromomycin. Chromosome panels were constructed from a normal cell line by sorting 22 chromosome fractions directly onto nitrocellulose filters. Twelve labeled gene probes hybridized to the sorted chromosomal DNA fractions predicted by previous chromosome assignments. Eighteen newly cloned genes have been mapped using the same protocol.

The LLNL high-speed sorter: design features, operational characteristics, and biological utility

This report describes a dual-beam, high-speed sorter (HiSS) with a droplet production rate of 220,000 s-1 now in routine use at the Lawrence Livermore National Laboratory. The system can process and sort objects at rates in excess of 20,000 s-1. We report here on the development of HiSS, describe its operational characteristics, and evaluate its utility for analysis and purification of human chromosomes, human erythrocytes, and living Chinese hamster ovary cells.

Cloned DNA probes regionally mapped to human chromosome 21 and their use in determining the origin of nondisjunction

A number of unique sequence recombinant DNA clones were isolated from a recombinant DNA library constructed from DNA enriched for chromosome 21 by flow sorting. Of these, five were mapped to chromosome 21 using a somatic cell hybrid. Regional mapping of these probes and of a probe previously assigned to chromosome 21, was carried out with the aid of chromosome 21 rearrangements using both chromosome sorting and a somatic cell hybrid. Three probes were shown to be located on either side of the breakpoint 21q21.2. Two of the probes were shown to identify restriction fragment length polymorphisms (RFLPs) with high rare-allele frequencies (0.46 and 0.43). A Bgl II RFLP revealed the parental origin of non-disjunction in three of ten families with Down's syndrome.

Mapping parathyroid hormone, beta-globin, insulin, and LDH-A genes within the human chromosome 11 short arm by spot blotting sorted chromosomes

Rearranged human chromosomes carrying segments of chromosome 11 were separated from the normal chromosome 11 by high-resolution chromosome sorting. Sorted chromosomes were tested with parathyroid hormone, beta-globin, insulin, and LDH-A gene-specific probes to determine the genes carried by each chromosome segment. Based on the gene content and karyotypes of these abnormal chromosomes, the parathyroid hormone, beta-globin, insulin, and LDH-A genes and the unique restriction fragment ADJ-762 are all located on the terminal band of the short arm of human chromosome 11 (band 11p15), with LDH-A proximal to the other loci.

Germ-line chromosomal localization of genes in chromosome 11p linkage: parathyroid hormone, beta-globin, c-Ha-ras-1, and insulin

The chromosomal localization of genes for parathyroid hormone (PTH), beta-globin cluster, c-Ha-ras-1, and insulin, all of which have previously been assigned to the short arm of chromosome 11, generated considerable interest because of their association with development of disease states. Furthermore, the availability of recombination data from family studies made the determination of their physical location on the chromosome necessary. Several investigators have attempted this; however, controversy has arisen concerning the location of beta-globin, insulin, and c-Ha-ras-1 genes. Thus, while the results of some investigators suggested that all three genes are situated in the 11p15 region, data of other investigators placed the beta-globin and insulin genes close to the centromere and c-Ha-ras-1 in a more proximal region than 11p15. The subchromosomal position of the PTH gene remains to be determined. We have performed in situ hybridization of meiotic pachytene bivalents with 3H-labeled cloned genomic probes of PTH, beta-globin, and insulin genes and find their germ-line positions to be the following: PTH at 11p11.21, beta-globin at 11p11.22, and insulin at 11p14.1. These data, when considered with our recent germ-line assignment of the c-Ha-ras-1 gene to 11p14.1, indicate the following relative order on 11p: cen-PTH-beta-globin-c-Ha-ras-insulin or cen-PTH-beta-globin-insulin-c-Ha-ras. The former order is consistent with genetic evidence from linkage analysis of DNA polymorphisms adjacent to these genes segregating in families.

Chromosomes for molecular hybridization. Assignment of repetitive and single copy genes using a rapid filter-fixation method

Specific recombinant DNA sequences (5S rRNA, B1, albumin) were assigned to flow sorted chromosomes of the Chinese hamster cell line CHV79. For this purpose, a rapid protocol was developed using filterbound chromosomal DNA and probing with various nucleic acids, that allows sequence identification in chromosomes. A flow histogram and a flow karyogram of the CHV79 cell line were established by flow analysis in order to calculate the amount of DNA per CHV79 cell and their chromosomes. Subsequently, metaphase chromosomes or chromosomal groups were fractionated by electronic sorting and a defined number of chromosomes was directly bound to nitrocellulose filters for sequence homology analysis by a dot blot hybridization procedure. This procedure not only allows the assigning of specific DNA sequences to particular chromosomes, it is also applicable to studies of changes in karyotypes, for example translocations of given sequences.

High-resolution chromosome sorting and DNA spot-blot analysis assign McArdle's syndrome to chromosome 11

A rapid gene-mapping system uses a high-resolution, dual-laser sorter to identify genes from separate human chromosomes prepared with a new stain combination. This system was used to sort 21 unique chromosome types onto nitrocellulose filter papers. Several labeled gene probes hybridized to the sorted chromosomal DNA types predicted by their previous chromosome assignments. The skeletal muscle glycogen phosphorylase gene was then mapped to a portion of chromosome 11 by spot blotting normal and translocated chromosomes.

Localization of the beta-globin gene by chromosomal in situ hybridization

A 3.7-kilobase (kb) genomic clone of the human beta-globin gene, including 1.5-kb upstream and approximately 0.5-kb downstream, was utilized in chromosomal in situ hybridization for precise mapping of the beta-globin locus on peripheral blood lymphocyte-derived metaphases from a normal male, and for further evaluation of a clonal t(7;11) (q22;p15) translocation on bone marrow-derived metaphases from a 46-year-old male with erythroleukemia. Analyses of 205 midmetaphases from a normal male hybridized with the tritium-labeled beta-globin probe and stained with quinacrine mustard dihydrochloride revealed approximately 12% of spreads to have silver-grain deposition over the p15 band of chromosome 11. Of the 365 silver grains observed to be located on or beside chromosomes, 25 (approximately 7%) grains were localized in band p15. Karyotype analysis of a bone marrow specimen from the patient with erythroleukemia revealed hypodiploidy with various unidentified marker chromosomes as well as a presumably balanced translocation between 7q and 11p . Chromosomal in situ hybridization showed localization of silver grains at the junction between chromosomes 7 and 11 as well as to the normal chromosome 11, indicating that the beta-globin locus had not been translocated in the chromosomal rearrangement. This case demonstrates the value of chromosomal in situ hybridization in the definition of chromosome rearrangements and provides further evidence for the localization of the beta-globin gene to 11p15 .

Separation and analysis of human chromosomes by combined velocity sedimentation and flow sorting applying single- and dual-laser flow cytometry

Human chromosomes were separated on basis of size by velocity sedimentation at 52g in a specially designed sedimentation chamber. The chamber has been constructed in such a way that large numbers of chromosomes can be fractionated on a sucrose gradient while wall sedimentation, streaming, and swirling movements of the gradient during centrifugation are eliminated. Flow deflectors in the chamber allow undisturbed introduction and fractionation of the density gradient. The different chromosomal fractions obtained are highly enriched for the various human chromosomes. Individual chromosomes were subsequently sorted to purity by fluorescence activated flow sorting using a FACS IV flow sorter equipped with a 4-W argon-ion laser. Following this procedure, the sorting rate for specific chromosomes can be speeded up by a factor of 5-10 when the preenriched chromosomal fractions are used as starting material. A high chromosome resolution could be obtained by a few simple modifications of the FACS IV. By applying fluorochromes with different DNA-base specificity the sorting possibilities of individual human chromosomes can be improved. In addition, the chromosomal fractions were analysed by dual-laser flow cytometry after staining the chromosomes with Hoechst 33258 and chromomycin A3. In this way the enrichment of virtually all individual human chromosomes in the different chromosomal fractions can be visualized.

Thalassemic hemoglobinopathies

Hemoglobinopathies are due to changes in the normal amino acid sequence of globin. Thalassemias result from imbalance in the normal coordinated synthesis of the globin subunits that make up the hemoglobin tetramer. It is now apparent that a single globin gene can have coding region mutations which simultaneously produce a structural defect (hemoglobinopathy) and a biosynthetic defect (thalassemia). It is likely that two distinct mutations within the same gene can occur and produce a hemoglobinopathy with features of thalassemia. In this review the authors discuss such disorders and include the Hb Lepore and Constant Spring variants, hyper-unstable globins, mutations which create alternative sites for mRNA splicing, and amino acid substitutions likely to be associated with an additional thalassemia lesion within the same gene.

Direct hybridization of sorted human chromosomes: localization of the Y chromosome on the flow karyotype

A method is described for directly hybridizing a small number of sorted chromosomes with specific DNA probes. The chromosomes are analyzed by flow cytometry and sorted by deflecting the droplets containing the desired chromosomes onto a nitrocellulose filter. By using probes specific for the human Y chromosome, it has been possible to unambiguously identify the peak corresponding to the Y chromosome in the flow karyotypes of a variety of male cell lines. The position of this peak was found to vary significantly from individual to individual, correlating with the heterochromatin chromosomal polymorphism of the human Y chromosome. The sensitivity of the hybridization was such that, with a probe for a male-specific repetitive sequence, only 2,500 sorted chromosomes were enough to obtain a clear, positive signal; 10,000 were needed with a probe specific for a weakly repeated (maximum, 3-fold) sequence of Y chromosome. With this new method, chromosome sorting may be a rapid and efficient way to assign DNA sequences to chromosomes.

The c-Ha-ras1, insulin and beta-globin loci map outside the deletion associated with aniridia-Wilms' tumour

The localization of protooncogenes on human chromosomes may coincide with chromosome breakpoints of consistent translocations in leukaemias or lymphomas, suggesting a direct involvement of oncogenes in carcinogenesis. For example, in Burkitt's lymphoma consistent translocations may be associated with rearrangements of c-myc. Our assignment of the c-Harvey-ras1 oncogene to chromosome 11, precisely to region 11p11 leads to p15 (ref. 5; not 11p13 as stated in ref. 6), has raised the possibility that this oncogene might have a role in the predisposition to nephroblastoma (Wilms' tumour, WT) seen in the aniridia-WT association (AWTA) that is frequently caused by an interstitial deletion of band 11p (ref. 8). We have now studied the organization and copy number of sequences at three loci mapped to 11p: c-Ha-ras1, insulin and gamma-globin in cells from four individuals with structural rearrangements of the short arm of chromosome 11. Our results reported here rule out a close physical linkage between c-Ha-ras1 and the genes responsible for AWTA, and suggest a more distal localization of the beta-globin cluster than currently assumed.

Human parathyroid hormone gene (PTH) is on short arm of chromosome 11

The human gene for parathyroid hormone (PTH) was chromosomally mapped using human-rodent hybrids and Southern filter hybridization of cell hybrid DNA. A recombinant DNA probe containing human PTH cDNA insert (pPTHm122) hybridized to a 3.7-kb fragment in human DNA cleaved with the restriction enzyme EcoRI. By correlating the presence of this fragment in somatic cell hybrid DNA with the human chromosomal content of the hybrid cells, the PTH gene was mapped to the short arm of the chromosome 11.

Flow karyotype analysis and fluorescence-activated sorting of Burkitt-lymphoma-associated translocation chromosomes

Flow karyotype analysis was performed to assess the feasibility of fluorescence-activated sorting of Burkitt lymphoma (BL)-associated translocation chromosomes. The typical 14q+ chromosome in the t(8;14) and the two "variant translocations", the 2q+ in the t(2;8) and the small 22q- in the t(8;22), could be identified as single peaks within the flow karyotypes of metaphase chromosomes isolated from several different BL-lines for each translocation. The translocation chromosomes could be separated with a high degree of purity and in quantities suitable for biochemical analysis. The same analytical and preparative technique was also successfully applied to the identification and sorting of the Philadelphia (Ph1) chromosome in a 9;22 translocation-carrying CML-derived line and a familial (11;22) translocation.

Hemolytic disease of the newborn caused by a new deletion of the entire beta-globin cluster

We describe a new type of gamma delta beta-thalassemia in four generations of a family of Scotch-Irish descent. The proposita presented with hemolytic disease of the newborn, which was characterized by a microcytic anemia. Initial restriction endonuclease analysis of the DNA showed no grossly abnormal patterns, but studies of polymorphic restriction sites and gene dosage revealed an extensive deletion that removed all the beta- and beta-like globin genes from the affected chromosome. In situ hybridization of chromosome preparations with radioactive beta-globin gene probes showed that only one 11p homolog contained the beta-globin gene cluster in the affected family members.

Recombination within and between the human insulin and beta-globin gene loci

We detected a large number of polymorphic insulin restriction fragments in black Americans. These different size fragments were probably generated by unequal recombination on both sides of the human insulin gene. Population genetic analysis indicates that recombination occurred 33 times more frequently than expected to generate this large number of polymorphic fragments. Specific properties of the unique repeated 14- to 16-base-pair sequences 5' to the insulin gene suggest that this sequence would promote increased unequal recombination. Additional pedigree analysis showed that the recombination rate between the structural insulin and beta-globin gene loci was 14% with strong evidence for linkage. Since both insulin and beta-globin have been mapped to the short arm of human chromosome 11, this study establishes that the genetic map distance between these genes is 14.2 centimorgans.

Chromosome sorting and DNA sequence localization

This article focuses on current techniques and possible future developments in chromosome isolation and sorting, and DNA analysis of sorted chromosomes. The strategy of subchromosomal gene mapping by chromosome sorting is outlined and a list of cell lines containing translocated chromosomes is provided which may be used to map genes to a single chromosome with a standard fluorescence activated cell sorter. The usefulness of this and other gene mapping methods for localizing unique DNA sequences and characterizing recombinant DNA libraries constructed from sorted chromosomal DNA is also discussed.

Design and operation of a dual laser chromosome sorter

We describe the design and operation of a dual laser fluorescence activated chromosome sorter that can analyze and sort chromosome suspensions stained with two complementary DNA stains. We used two 18-watt argon-ion lasers to provide maximal excitation of the DNA-specific stains Hoechst 33258 and chromomycin A3. The lasers are focused onto the sample stream by independent optics permitting optimal focusing of any pair of laser wavelengths. We incorporated beam expanders to decrease the energy density on the optics and improve the focal spot uniformity. Adjustable focusing lens holders are used to set the optimal focal spot size. The redesigned sorter separates suspensions of normal human fibroblast chromosomes into 21 fractions and can reliably sort more pure chromosome fractions than was previously possible.

General method for cloning amplified DNA by differential screening with genomic probes

Mutant Syrian hamster cell lines resistant to N-(phosphonacetyl)-L-aspartate, a potent and specific inhibitor of aspartate transcarbamylase, have amplified the gene coding for the multifunctional protein (CAD) that includes this activity. The average amount of DNA amplified is approximately 500 kilobases per gene copy, about 20 times the length of the CAD gene itself. A differential screening method which uses genomic DNAs as probes was developed to isolate recombinant phage containing fragments of amplified DNA. One probe was prepared by reassociating fragments of total genomic DNA from 165-28, a mutant cell line with 190 times the wild-type complement of CAD genes, until all of the sequences repeated about 200 times were annealed and then isolating the double-stranded DNA with hydroxyapatite. This DNA was highly enriched in sequences from the entire amplified region, whereas the same sequences were very rare in DNA prepared similarly from wild-type cells. After both DNAs were labeled by nick translation, highly repeated sequences were removed by hybridization to immobilized total genomic DNA from wild-type cells. A library of cloned DNA fragments from mutant 165-28 was screened with both probes, and nine independent fragments containing about 165 kilobases of amplified DNA, including the CAD gene, have been isolated so far. These cloned DNAs can be used to study the structure of the amplified region, to evaluate the nature of the amplification event, and to investigate gene expression from the amplified DNA. For example, one amplified fragment included a gene coding for a 3.8-kilobase, cytoplasmic, polyadenylated RNA which was overproduced greatly in cells resistant to N-(phosphonacetyl)-L-aspartate. The method for cloning amplified DNA is general and can be used to evaluate the possible involvement of gene amplification in phenomena such as drug resistance, transformation, or differentiation. DNA fragments corresponding to any region amplified about 10-fold or more can be cloned, even if no function for the region is known. The method for removing highly repetitive sequences from genomic DNA probes should also be of general use.

Hemoglobin Parchman: double crossover within a single human gene

Structural analysis of a new variant hemoglobin revealed tryptic peptides with the amino acid composition of normal delta-globin, except for two internal peptides, which had the compositions of normal beta-globin. The most likely explanation for these findings is that a double, nonhomologous crossover between the delta-and beta-globin genes had occurred.

Gene for glutathione S-transferase-1 (GST1) is on human chromosome 11

The glutathione S-transferases (GST) are a group of related enzymes that can detoxify potentially carcinogenic electrophiles by conjugating them with reduced glutathione (GSH). The chromosomal location of one of the enzyme forms, GST1, reported recently to be polymorphic, was determined utilizing man-mouse somatic cell hybrids segregating human chromosomes. The expression of GST1 by hybrid clones was compared with that of 34 enzyme markers representing 23 chromosomes, and karyotypes of selected cell hybrids were analyzed. The evidence indicated that GST1 is assigned to chromosome 11 in humans. Utilizing and X/11 translocation segregating in hybrids, GST1 was localized to the p13 leads to qter region of chromosome 11.

Assignment of snRNA gene sequences to the large chromosomes of rat kangaroo and chinese hamster isolated by flow cytometric sorting

Chromosomes from a rat kangaroo (Potorous tridactylus) cell line (PtK2) and from a Chinese hamster (Cricetulus griseus) cell line (CHV79) were isolated by means of fluorescence activated flow cytometric sorting. DAPI (4'-6-diamino-2-phenylindole) was used as the DNA specific fluorescent dye. The karyotype of the PtK2 cells which exhibits 13 chromosomes was separated into 6, and the 22 chromosomes of the CHV79 cells were resolved into 11 fractions. DNA extracted from these chromosomal fractions was used for restriction enzyme digestion and blotting on nitrocellulose filters. The blots were challenged with gene probes corresponding to ribosomal RNA (18S and 28S) and small nuclear RNA (U1-snRNA) genes. The rRNA genes were exclusively assigned to chromosomes containing the nucleolus organizing region (in PtK2: X chromosome; in CHV79: chromosomes 4, 5, 6, and 11). - Solely the largest chromosomes in both cell lines hybridized with U1-snRNA indicating that these gene sequences are located on those chromosomes only. Further possible genetic and biochemical applications of this experimental system are discussed.

The developmental change in the G gamma and A gamma globin. Proportions in hemoglobin F

The proportions of G gamma and A gamma globins in hemoglobin F were determined in fetuses around the 20th week of gestation, newborns, and children 3 weeks to 5 months of age. In the last group, the G gamma/G gamma + A gamma ratio decreased continously; there was a good correlation between the decline of G gamma with respect to total gamma and the decline of Hb F (r = 0.88). In contrast, there was virtually no difference in the gamma globin composition of Hb F between the fetuses and the newborns, i.e. in late pregnancy, the decrease in the synthesis of both gamma globins appears to be proportionate. The G gamma and A gamma globin genes may be inactivated in a sigmoidal fashion with time, thus producing a G gamma/G gamma + A gamma ratio which at first changes only slightly and then declines linearily.

Flow cytometric characterization of a Chinese hamster X man hybrid cell line retaining the human Y chromosome

A Chinese hamster X man hybrid cell line (CH-Y-VII) was established which retains a free human Y chromosome. Exponentially growing CH-Y-VII cells were arrested with colcemid; metaphase chromosomes were isolated and stained with 33258 Hoechst (HO) plus Chromomycin A3 (CA3), or with ethidium bromide (EB). The HO/CA3-stained chromosomes were measured in a dual beam flow cytometer, and bivariate HO/CA3 flow karyotypes and univariate HO and CA3 flow karyotypes were established. EB-stained chromosomes were analyzed in a modified Becton Dickinson FACS-Sorter. For all three stains used, the human Y chromosome forms a separate peak in univariate flow karyotypes; the optimum resolution was obtained for the HO distribution. In the bivariate HO/CA3 flow karyotype, the peak for the human Y chromosome is completely separated from the Chinese hamster chromosomes.

Application of the BrdU/thymidine method to flow cytogenetics: differential quenching/enhancement of Hoechst 33258 fluorescence of late-replicating chromosomes

Discrimination between many types of isolated mammalian chromosomes can be accomplished by dual-beam flow cytometry following DNA staining with Hoechst 33258 (HO) and Chromomycin A3 (CA3). In this report, we show that the bivariate discrimination of selected late-replicating Chinese hamster M3-1 chromosomes can be improved by appropriate treatment of the cells with 5-bromo-2'-deoxyuridine (BrdU) prior to chromosome isolation and staining. Two labeling schemes are reported. In one scheme the chromosomes are collected from cells labeled with BrdU only during late S phase. The Hoechst fluorescence of the 10, 11, M2, and Y chromosomes is substantially quenched by the incorporated BrdU, thus improving their discrimination. In the other scheme, chromosomes are collected from cells labeled with thymidine (dT) during late S phase following 20 h of growth in BrdU-containing medium. The Hoechst fluorescence of the 10, 11, M2, and Y chromosomes is quenched less than the other chromosomes, again improving their discrimination. Y chromosomes from chromosome suspensions of untreated controls, of cells labeled with BrdU during late S phase, and of cells labeled with dT during late S phase following 20 h growth in BrdU were separated by dual-parameter sorting. While the purity of the sorted Y chromosome was 15% in untreated controls, it was 70-75% using the BrdU/dT labeling protocols.

General method for cloning amplified DNA by differential screening with genomic probes

Mutant Syrian hamster cell lines resistant to N-(phosphonacetyl)-L-aspartate, a potent and specific inhibitor of aspartate transcarbamylase, have amplified the gene coding for the multifunctional protein (CAD) that includes this activity. The average amount of DNA amplified is approximately 500 kilobases per gene copy, about 20 times the length of the CAD gene itself. A differential screening method which uses genomic DNAs as probes was developed to isolate recombinant phage containing fragments of amplified DNA. One probe was prepared by reassociating fragments of total genomic DNA from 165-28, a mutant cell line with 190 times the wild-type complement of CAD genes, until all of the sequences repeated about 200 times were annealed and then isolating the double-stranded DNA with hydroxyapatite. This DNA was highly enriched in sequences from the entire amplified region, whereas the same sequences were very rare in DNA prepared similarly from wild-type cells. After both DNAs were labeled by nick translation, highly repeated sequences were removed by hybridization to immobilized total genomic DNA from wild-type cells. A library of cloned DNA fragments from mutant 165-28 was screened with both probes, and nine independent fragments containing about 165 kilobases of amplified DNA, including the CAD gene, have been isolated so far. These cloned DNAs can be used to study the structure of the amplified region, to evaluate the nature of the amplification event, and to investigate gene expression from the amplified DNA. For example, one amplified fragment included a gene coding for a 3.8-kilobase, cytoplasmic, polyadenylated RNA which was overproduced greatly in cells resistant to N-(phosphonacetyl)-L-aspartate. The method for cloning amplified DNA is general and can be used to evaluate the possible involvement of gene amplification in phenomena such as drug resistance, transformation, or differentiation. DNA fragments corresponding to any region amplified about 10-fold or more can be cloned, even if no function for the region is known. The method for removing highly repetitive sequences from genomic DNA probes should also be of general use.

Construction and characterization of genomic libraries from specific human chromosomes

Highly purified fractions of human chromosomes 21 and 22 were isolated from a suspension of metaphase chromosomes stained with ethidium bromide by using a fluorescence-activated cell sorter (FACS II). Two recombinant DNA libraries, representing chromosomes 21 and 22, were constructed by complete digestion of DNA from these fractions with EcoRI and insertion into the vector lambda gtWES lambda B. Twenty clones selected at random from the chromosome 22 library hybridized to EcoRI-digested human DNA, and five of these clones hybridized to single bands identical in size to the phage inserts. These five single-copy sequences and a clone coding for an 8S RNA isolated by screening the chromosome 22 library for expressed sequences were characterized in detail. Hybridization of all six clones to a panel of sorted chromosomes and hybrid cell lines confirmed the assignment of the sequences to chromosome 22. The sequences were localized to regions of chromosome 22 by hybridization to translocated chromosomes sorted from a cell line having a balanced translocation t(17;22)(p13;q11) and to hybrid cell lines containing the various portions of another translocation t(X;22)(q13;q112). Five clones reside on the long arm of chromosome 22 between q112 and pter, while one clone and an 18S rRNA gene isolated from the chromosome 22 library reside pter and g112. The construction of chromosome-specific libraries by this method has the advantage of being direct and applicable to nearly all human chromosomes and will be important in molecular analysis of human genetic diseases.