A high-resolution cytogenetic map of 168 cosmid DNA markers for human chromosome 11

Integrated karyotyping of sorghum by in situ hybridization of landed BACs

The reliability of genome analysis and proficiency of genetic manipulation are increased by assignment of linkage groups to specific chromosomes, placement of centromeres, and orientation with respect to telomeres. We have endeavored to establish means to enable these steps in sorghum (Sorghum bicolor (L.) Moench), the genome of which contains ca. 780 Mbp spread across n = 10 chromosomes. Our approach relies on fluorescence in situ hybridization (FISH) and integrated structural genomic resources, including large-insert genomic clones in bacterial artificial chromosome (BAC) libraries. To develop robust FISH probes, we selected sorghum BACs by association with molecular markers that map near the ends of linkage groups, in regions inferred to be high in recombination. Overall, we selected 22 BACs that encompass the 10 linkage groups. As a prelude to development of a multiprobe FISH cocktail, we evaluated BAC-derived probes individually and in small groups. Biotin- and digoxygenin-labeled probes were made directly from the BAC clones and hybridized in situ to chromosomes without using suppressive unlabelled C0t-1 DNA. Based on FISH-signal strength and the relative degree of background signal, we judged 19 BAC-derived probes to be satisfactory. Based on their relative position, and collective association with all 10 linkage groups, we chose 17 of the 19 BACs to develop a 17-locus probe cocktail for dual-color detection. FISH of the cocktail allowed simultaneous identification of all 10 chromosomes. The results indicate that linkage and physical maps of sorghum allow facile selection of BAC clones according to position and FISH-signal quality. This capability will enable development of a high-quality molecular cytogenetic map and an integrated genomics system for sorghum, without need of chromosome flow sorting or microdissection. Moreover, transgeneric FISH experiments suggest that the sorghum system might be applicable to other Gramineae.

Restricted chromosome breakpoint sites on 11q22-q23.1 and 11q25 in various hematological malignancies without MLL/ALL-1 gene rearrangement

We analyzed 32 patients with various hematological malignancies including acute myelocytic leukemia and non-Hodgkin lymphoma with a breakpoint at 11q22-q25 of chromosome 11, but who did not have rearrangements of the MLL/ALL-1 gene. The breakpoint in each patient was identified by fluorescence in situ hybridization using 21 cosmid probes and 2 YAC probes. Breakpoints for each "rearrangement" involving translocations such as t(1;11), t(2;11), inv(11), t(11;15), and t(10;11) found in 5 of the 11 patients had breakpoints in a small region from Ccl11-430 to Ccl11-526 at 11q22-q23.1. Furthermore, breakpoints for chromosome deletions at 11q21-q23 in 10 patients were located in the same region as that of translocations. A commonly deleted region among 8 patients was identified from Ccl11-526 to Ccl11-555 at 11q23.1. Fluorescence in situ hybridization analysis revealed that breakpoints for additive chromosome [add(11)] aberrations, which had additional material of unknown origin at 11q23 to 11q25 in 11 patients, were not located at 11q23 but rather at the more telomeric site of Ccl11-503 to VIJ(2)2072 at 11q25. These results indicated that the patients had several restricted breakpoint sites, which means that these chromosomal regions have recurrent oncogenes and tumor suppressor genes for pathogenesis for leukemia and lymphoma.

Segmental jumping translocation in leukemia and lymphoma with a highly complex karyotype

In order to identify the oncogene associated with malignant transformation 141 leukemia and malignant lymphoma patients were studied by FISH. Specific chromosome regions were translocated onto structurally abnormal chromosomes, resulting in partial tri-, tetra-, or pentasomy of these regions. We designated this type of chromosomal translocation as a "segmental jumping translocation (SJT)". These SJTs were found in several chromosomal regions such as 8q24, 9q34, 11q13, 11q23, 13q14, 14q24-q32, 21q22 and 22q11. The SJT at 9q34, which involved the ABL oncogene, was found in three of nine secondary leukemia patients who were treated with anticancer drugs and radiation. Non-Hodgkin's lymphoma and acute myeloid leukemia (AML) patients had 3-7 copies of SJT at 11q13 or 11q23. SJT at 14q32 and 21q22 were predominantly detected in the acute type of adult T-cell leukemia (8 of 27 patients) and in AML (5 of 17 patients). The size of the SJT regions varied among the patients. The overlapping region within the SJT could involve oncogene(s) associated with transformation to the advanced stage in leukemia and lymphoma patients. The SJT provides evidence of a new mechanism for gene amplification and formation of unidentified marker chromosomes in the advanced disease stage.

A distamycin A-inducible fragile site, FRA8E, located in the region of the hereditary multiple exostoses gene, is not involved in HPV16 DNA integration and amplification

The rare fragile site is a specific point on a chromosome that is expressed as an isochromatid gap or break under certain conditions of cell culture and is inherited in a Mendelian codominant fashion. Five folate-sensitive fragile sites were cloned, and the molecular basis of fragile site mutation was shown to be a new class of mutation, called dynamic mutation, resulting from an allelic expansion of (CCG)n repeats. The mechanism responsible for other types of rare fragile sites, i.e., distamycin A-inducible and BrdU-requiring, is unknown, although cytogenetic studies suggested that these fragile sites play a mechanistic role in breakage and recombination and may also be integration and modification sites of foreign viral DNA genomes. A distamycin A-inducible fragile site, FRA8E, is mapped to 8q24.1 in which various loci implicated in genomic instability are located. Here we identified a YAC clone spanning both FRA8E and the hereditary multiple exostosis (EXT1) gene, using fluorescence in situ hybridization (FISH) analysis of a yeast artificial chromosome (YAC) contig. By using P1 clones as probes, the FRA8E locus was further localized to a 400-kb region including the EXT1 gene. Furthermore, the integration and amplification site of human papillomavirus 16 DNA in the ASCC (argyrophil small cell carcinoma) cells were shown not to coincide with FRA8E, but to be involved in an extensively broad genomic region of 8q24.1, including the c-myc gene.

Structure and expression of two highly related genes encoding SCM-1/human lymphotactin

SCM-1/lymphotactin is a chemokine-like molecule produced selectively, if not exclusively, by activated CD8+ T cells. Here we report that there are two highly homologous SCM-1 genes, which we designate as SCM-1alpha and SCM-1beta. Both genes have three exons and two introns. The 1st intron of SCM-1alpha contains a pseudogene of the ribosomal large subunit L7a. In SCM-1beta, a 1.5-kb region including about a quarter of the L7a pseudogene is deleted from the 1st intron. Otherwise, the two genes are highly homologous including the 5' and 3' flanking regions. Both genes were mapped to human chromosome 1q23. The two genes were similarly induced in peripheral blood mononuclear cells by mitogenic stimulation. Primer extension and RNase protection revealed several transcription initiation sites. The biological activities of SCM-1alpha and SCM-1beta, which have two amino acid differences at positions 7 and 8 in the mature proteins, remain to be compared.

The Japan Society of Human Genetics Award Lecture. Application of DNA markers to clinical genetics

DNA technology using DNA sequence polymorphisms has brought a new system to the fields of medicine and forensic science, especially for the studies of genetic diseases and tumor suppressor genes, and for identification of individuals for forensic purpose. Linkage analysis based on segregation of polymorphic alleles in affected families has contributed to identification of many genetic disease. We isolated a large number of polymorphic DNA markers, called VNTR (variable number of tandem repeat) markers and identified the APC gene that is responsible for familial adenomatous polyposis (FAP) by means of a so-called "positional cloning" and characterized germline and somatic mutations of the APC gene in colorectal cancer patients. In addition, we have applied genetic information during colorectal carcinogenesis to sensitive diagnosis of lymph-node metastasis of colorectal cancer.

Cosmids and transcribed sequences from chromosome 11q23

To obtain cosmid markers and transcribed sequences from a specific chromosome region, a series of radiation-reduced hybrids (RHs) containing various regions of human chromosome 11 was prepared from microcell hybrid A9 (neo11) cells containing a normal human chromosome 11 tagged with pSV2neo at 11p11.2. Among 15 radiation hybrid clones isolated, RH(11)-9 which contains a q23 fragment in addition to the neo integration site, was used for the construction of a cosmid library. Cosmid clones having human DNA sequences were screened, and localized by Southern hybridization with the radiation hybrid panel. Fifty-nine cosmids were assigned to 11q23 and 6 cosmids to 11p11.2. Exon amplification proceeded with 23 of the 59 cosmids and 16 putative exons were cloned. Three of them were identical to those constituting a known gene which locates on q23 (ATDC), and the others were unknown. Thus, the RHs containing various subchromosomal fragments of chromosome 11 were useful for constructing region-specific DNA markers. The RH(11)-9 cells and putative exons also facilitate the positional cloning of genes in the 11q23 region.

Fluorescent in situ hybridization of a bacterial artificial chromosome

Fluorescent in situ hybridization (FISH) of a 130 kilobase cotton (Gossypium hirsuitum L.) bacterial artificial chromosome (BAC) clone containing a high proportion of single-copy DNA produced a large pair of FISH signals on the distal end of the long arm of a pair of chromosomes of the D-genome species G. raimondii Ulbr. and produced a fainter pair of signals on a small submetacentric pair of chromosomes of the A-genome species G. herbaceum L. The signals were synthetic with a nucleolar organizer region in G. raimondii and G. herbaceum. Signal pairs were easily recognized in interphase and metaphase cells either with or without suppression of repetitive sequences with unlabeled G. hirsutum C0t-1 DNA. High quality FISH results were consistently obtained and image analysis was not required for viewing or photography. Results indicate that FISH of BAC clones is an excellent tool for the establishment of new molecular cytogenetic markers in plants and will likely prove instrumental in the development of useful physical maps for many economically important crop species.

Application of fluorescence in situ hybridization in genome analysis of the mouse

Fluorescence in situ hybridization (FISH) is an effective technique for localizing cloned DNA probes directly onto metaphase chromosomes. Human genome mapping using FISH has been significantly enhanced by the development of new techniques, especially high-resolution gene mapping with direct R-banding FISH and physical gene ordering with multi-color FISH. By contrast, FISH techniques have not been put to practical use for the analysis of the mouse genome compared with the human. We have developed and modified FISH techniques for use in mouse genome analysis. In this article we summarize and review our recent results with FISH analyses in the following studies: (i) high-resolution gene mapping with the direct R-banding FISH, (ii) analysis of chromosomal rearrangement with multi-color FISH, (iii) establishment of centromere mapping with the major satellite DNA probe, (iv) analysis of chromatin structure in meiotic cells, and (v) application of FISH in cytogenetic studies of genetic variation in the mouse, showing that these applications of FISH are very useful for mouse genome analysis.

High-resolution cytogenetic mapping of the short arm of chromosome 1 with newly isolated 411 cosmid markers by fluorescence in situ hybridization: the precise order of 18 markers on 1p36.1 on prophase chromosomes and "stretched" DNAs

A high-resolution cytogenetic map of the short arm of chromosome 1 with newly isolated 411 cosmid markers was constructed by fluorescence in situ hybridization (FISH). These markers were scattered throughout chromosome 1p, but they were preferentially concentrated on R-band dominant regions such as 1p36, 1p34, 1p32, 1p22, and 1p13. Among these markers, 197 were localized on chromosome band 1p36, a region frequently deleted in neuroblastoma. Of these, 18 were precisely ordered on 1p36.1 by multicolor FISH of prophase chromosomes and "stretched" DNAs as follows: 1pter-163-41-11-1-226-586-568-614-631-665-451-199-190-561-241-74-1 76-652-1cen. The high-density map of chromosome 1p constructed here can provide useful landmarks for constructing a contig map of the short arm of chromosome 1 with YACs and cosmid clones and will expedite the identification of breakpoints and/or tumor suppressor gene(s) associated with several types of malignant tumors that frequently exhibit chromosomal aberrations or deletions of chromosome 1p.

Sequence tagged sites of microclones obtained by microdissection of a human chromosomal region 11q23 and isolation of yeast artificial chromosomes

A human chromosomal region 11q23-specific DNA library has been constructed by means of microdissection-microcloning method with polymerase chain reaction (PCR) technique (Seki et al., Genomics 16: 1993). DNA sequences were determined for 25 microclones that contained approximately 300-500 bp insert and gave a unique (single copy) signal in Southern blot analysis. The sequence tagged site (STS) was designed and appropriate condition for PCR was determined for each unique microclone. Twelve STSs were established and used for PCR-screening of human genomic libraries constructed with yeast artificial chromosome (YAC). Thirteen YAC clones have been isolated from eight STSs. These chromosomal region-specific STSs and YAC clones will be useful in the positional cloning of disease-related genes localized to the q23 region of chromosome 11.

Characterization of a cosmid library from flow-sorted chromosomes 11

A cosmid library specific for human chromosome 11 has been constructed from flow-sorted chromosomes. The flow-purified chromosomes were prepared from the hamster/human hybrid line J1 which contains chromosome 11 as the only human chromosome. Individual clones were sampled in 187 microtitre plates, resulting in a total of 17,952 colonies. Hybridization analysis revealed that 83.7% of these clones were of human and 10.4% of hamster origin. The average insert size was estimated at 33.6 kb, and only 2.4% of insert fragments appear to be rearranged. This should result in 494,487 kb of cloned human DNA representing 3.5 chromosome 11 equivalents. We have prepared high-density nylon membranes of the arrayed library containing 1,536 single colonies per filter. We have demonstrated the usefulness of the library in the molecular genetic analysis of human chromosome 11 by testing for the presence of possibly polymorphic simple repeat motifs, by identifying cosmids that contain inserts from the telomeric ends of chromosome 11 and by assessing the potential of the library for rapid chromosome walking.

A high-resolution cytogenetic map of human chromosome 12: localization of 195 new cosmid markers by direct R-banding fluorescence in situ hybridization

We have constructed a high-resolution cytogenetic map of human chromosome 12 with 195 newly isolated cosmids by direct R-banding fluorescence in situ hybridization. The fluorescent signals of 195 clones were evenly distributed throughout chromosome 12, but sublocalized preferentially to R-positive bands. This high-resolution cytogenetic map with an average map distance of 0.73 Mb on bands can, in conjunction with a genetic linkage map, facilitate the analysis of chromosomal and molecular aberrations in genetic diseases and cancers. Moreover, the cytogenetic mapping data provide starting points for establishing contig maps with cosmid clones and yeast artificial chromosomes.

Integrating maps of human chromosome 11

The past year has seen major advances in our understanding of chromosome structure, driven by technology that allows the rapid construction of physical and genetic maps. Information on the structure and organization of human chromosome 11 is rapidly being accumulated as a result of these developments.

Interstitial deletion of the long arm of chromosome 11 determined by fluorescence in situ hybridization

An interstitial deletion, del(11)(q14q22), found in a female infant was examined by fluorescence in situ hybridization with cosmid DNA markers mapped on the long arm of chromosome 11. Three cosmids mapped on 11q14.1-11q22.1 region were not hybridized to the del(11) chromosome, while all the other DNA markers mapped on 11cen-11q14.1 and 11q23.1-11qter region gave hybridization signals on the del(11) chromosome. Cytogenetic analysis after R-banding confirmed an apparent deletion of 11q14-q22, but containing a small R-negative band, a part of 11q22.3 and/or 11q14.1, in the middle part of del(11) chromosome. The karyotype thus was determined to be 46,XX,del(11)(q14.1q22.3).

Physical ordering of three polymorphic DNA markers spanning the regions containing a tumor suppressor gene of renal cell carcinoma by three-color fluorescent in situ hybridization

Fluorescent in situ hybridization (FISH) is a powerful technique for gene mapping and multi-color FISH allows us to determine directly the order of two or more probes on both metaphase and interphase chromosomes. We report the physical ordering of three DNA markers by three-color FISH using two fluorochrome dyes, fluorescein isothiocyanate (FITC; green) and rhodamine (red). The third color was visualized as a pseudo-color (yellow) generated by optical interference with FITC and rhodamine. Using this system we could rapidly determine the order of three polymorphic DNA markers located on the 3p23-p21.2 bands which span a tumor suppressor gene for renal cell carcinoma, lung carcinoma, and several other types of tumors.

A high-resolution cytogenetic map of human chromosome 3: localization of 291 new cosmid markers by direct R-banding fluorescence in situ hybridization

We localized 291 new cosmid markers (including 65 RFLPs) on human chromosome 3 by direct R-banding fluorescence in situ hybridization. This system, which is based on fluorescence in situ hybridization combined with replicated prometaphase R-bands, allows the direct visualization of signals on R-banded prometaphases stained with propidium iodide and provides a more rapid and efficient method for genome mapping of cosmid clones. The signals of 291 markers examined here were localized preferentially to R-positive bands throughout chromosome 3. The detailed map positions of 366 clones and the characterization of 142 RFLPs, including the preliminary data reported by Yamakawa et al. (1991, Genomics 9: 536-543; and 11: 565-572), are summarized. This high-resolution cytogenetic map (average distance of 0.58 Mb), in conjunction with a genetic linkage map, can facilitate the analysis of chromosomal and molecular aberrations in genetic diseases and cancers. Furthermore, these mapping data will provide many useful landmarks for the construction of contig maps of chromosome 3.