P1-derived Artificial Chromosome Research Articles

Epilepsy and neurological findings in 11 individuals with 1p36 deletion syndrome

The 1p36 deletion syndrome is a newly delineated multiple congenital anomalies/mental retardation syndrome characterized by mental retardation, growth delay, epilepsy, congenital heart defects, characteristic facial appearance, and precocious puberty. We analyzed 11 patients by fluorescence in situ hybridization (FISH) using commercially available bacterial artificial chromosome and P1-derived artificial chromosome genomic clones to define the chromosomal deletion responsible for the 1p36 deletion syndrome. Cytogenetic investigation revealed two cases with a terminal deletion of 1p36. Nine patients had an apparently normal karyotype with standard G-bands by trypsin using Giemsa (GTG), but FISH screening with the highly polymorphic genetic marker D1Z2, which is mapped to 1p36.3 and contains an unusual reiterated 40-bp variable number tandem repeat, revealed a submicroscopic deletion. All patients had severe to profound mental retardation. Based on the University of California Santa Cruz Genome Browser, we constructed a deletion map and analyzed the relationship between neurological findings and chromosomal deletions for the 11 cases. Six cases had intractable epilepsy and three had no seizures. The common deletion interval was about 1 million base pairs (Mbp) located between RP11-82D16 and RP4-785P20 (Rho guanine exchange factor (GEF) 16). The severity of clinical symptoms correlates with the size of the deletion. This is demonstrated by the 3 patients with at least 8 Mbp deletions that display profound mental retardation and congenital heart defects. Although haploinsufficiency of the potassium channel beta-subunit ( KCNAB2) is thought to be responsible for intractable seizures in the 1p36 deletion syndrome, this was not the case for 3 of the 11 patients in this study. Further investigation of the 1p36 region is necessary to allow identification of genes responsible for the 1p36 deletion syndrome.

Characterization of quantitative chromosomal abnormalities in renal cell carcinomas by interphase four-color fluorescence in situ hybridization

Renal cell carcinomas (RCC) in adults are histologically heterogeneous solid tumors with specific chromosomal abnormality patterns included in the World Health Organization (WHO) classification. To overcome some of the drawbacks of cytogenetic and comparative genomic hybridization (CGH) analyses, we designed a first-generation cytogenetic diagnostic test using four-color fluorescence in situ hybridization (FISH) on interphase nuclei. We selected 51 bacterial artificial chromosome and P1-derived artificial chromosome clones covering 17 chromosomal regions involved in the abnormalities of the adult RCC histologic subtypes. An initial set of probes allowed the identification of clear-cell RCC, papillary RCC, and other RCC on a single slide. A second test allowed the detection of additional chromosomal abnormalities or aberrations specific to chromophobic RCC and oncocytomas. We tested 25 cases of RCC, and the results were in agreement with those of cytogenetic techniques and/or CGH methods. The techniques appeared to be very sensitive, because small tumoral cell clones that were undetected by other cytogenetic methods were identified with this method. It was concluded that the multicolor FISH test was specific and sensitive, easy to perform, and could be part of the investigation process in RCC.

Candidate Genes in Breast Cancer Revealed by Microarray-Based Comparative Genomic Hybridization of Archived Tissue

Genomic imbalances in 31 formalin-fixed and paraffin-embedded primary tumors of advanced breast cancer were analyzed by microarray-based comparative genomic hybridization (matrix-CGH). A DNA chip was designed comprising 422 mapped genomic sequences including 47 proto-oncogenes, 15 tumor suppressor genes, as well as frequently imbalanced chromosomal regions. Analysis of the data was challenging due to the impaired quality of DNA prepared from paraffin-embedded samples. Nevertheless, using a method for the statistical evaluation of the balanced state for each individual experiment, we were able to reveal imbalances with high significance, which were in good concordance with previous data collected by chromosomal CGH from the same patients. Owing to the improved resolution of matrix-CGH, genomic imbalances could be narrowed down to the level of individual bacterial artificial chromosome and P1-derived artificial chromosome clones. On average 37 gains and 13 losses per tumor cell genome were scored. Gains in more than 30% of the cases were found on 1p, 1q, 6p, 7p, 8q, 9q, 11q, 12q, 17p, 17q, 20q, and 22q, and losses on 6q, 9p, 11q, and 17p. Of the 51 chromosomal regions found amplified by matrix-CGH, only 12 had been identified by chromosomal CGH. Within these 51 amplicons, genome database information defined 112 candidate genes, 44 of which were validated by either PCR amplification of sequence tag sites or DNA sequence analysis.

Molecular classification of human gliomas using matrix-based comparative genomic hybridization

Gliomas are the most frequent primary brain tumors and comprise a group of morphologically, biologically and clinically heterogeneous neoplasms. The different glioma types are associated with distinct genetic aberrations, which may provide useful information for tumor classification as well as prediction of prognosis and response to therapy. To facilitate the molecular classification of gliomas, we established a genomic microarray that consists of bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC) clones representing tumor suppressor genes, proto-oncogenes and chromosomal regions frequently gained or lost in gliomas. In addition, reference clones distributed evenly throughout the genome in approximately 15 Mbp intervals were spotted on the microarray. These customized microarrays were used for matrix-based comparative genomic hybridization (matrix CGH) analysis of 70 gliomas. Matrix CGH findings were validated by molecular genetic analyses of candidate genes, loss of heterozygosity studies and chromosomal CGH. Our results indicate that matrix CGH allows for the sensitive and specific detection of gene amplifications as well as low-level copy number gains and losses in clinical glioma samples. Furthermore, molecular classification based on matrix CGH data closely paralleled histological classification and was able to distinguish with few exceptions between diffuse astrocytomas and oligodendrogliomas, anaplastic astrocytomas and anaplastic oligodendrogliomas, anaplastic oligodendrogliomas and glioblastomas, as well as primary and secondary glioblastomas. Thus, matrix CGH is a powerful technique that allows for an automated genomic profiling of gliomas and represents a promising new tool for their molecular classification.

Temporally controlled targeted somatic mutagenesis in skeletal muscles of the mouse

To generate temporally controlled targeted somatic mutations selectively and efficiently in skeletal muscles, we established a transgenic HSA-Cre-ER(T2) mouse line in which the expression of the tamoxifen-dependent Cre-ER(T2) recombinase is under the control of a large genomic DNA segment of the human skeletal muscle alpha-actin gene, contained in a P1-derived artificial chromosome. In this transgenic line Cre-ER(T2) is selectively expressed in skeletal muscles, and Cre-ER(T2)-mediated alteration of LoxP flanked (floxed) target genes is skeletal muscle-specific and strictly tamoxifen-dependent. HSA-Cre-ER(T2) mice should be of great value to analyze gene function in skeletal muscles, and to establish animal models of human skeletal muscle disorders.

Identification of Genomic Imbalances in AML with Complex Karyotype Using Matrix-Based Comparative Genomic Hybridization.

Approximately 10 to 15 % of acute myeloid leukemia (AML) cases exhibit complex karyotypes, i.e., three or more chromosome abnormalities without presence of a specific fusion transcript. Using chromosome banding analysis, the majority of such cases cannot be completely described due to the low resolution of this method. Comparative genomic hybridization to microarrays (matrix-CGH) is a novel technique that allows genome-wide screening for genomic imbalances at high resolution and thus may facilitate the identification of novel regions harboring potential disease-related genes. We constructed a microarray consisting of 2799 different human genomic DNA fragments cloned in bacterial artificial chromosome (BAC) or P1-derived artificial chromosome (PAC) vectors. A set of 1502 of these clones covers the whole human genome with a physical distance of approximately 2 Mb. The remaining 1297 clones either contiguously span genomic regions known to be frequently involved in hematologic malignancies (e.g., 1p, 2p, 3q, 7q, 9p, 11q, 12q, 13q, 17p, 18q) (n=610) or contain oncogenes or tumor suppressor genes (n=687). In this study 45 AML cases with complex karyotypes were analyzed. Matrix-CGH detected genomic aberrations in all cases and genomic losses were found more frequently than gains. The most frequent aberration was deletion 5q in 38 of 45 cases. Three consensus regions were delineated mapping to chromosomal bands 5q11 (23 cases), 5q34 (22 cases), and 5q35 (21 cases). Further frequent deletions affected 17p (60%); two consensus regions were identified mapping to chromosomal bands 17p13 (60%), and 17p11-q11 (33%). Other chromosomal losses affected 7q (51%), 16p (31%), 16q, 18q (29% each), 15q (24%), 10p (22%), 14q, 4p (20% each), 11q, 20q (18% each), 3p, and 12p (15% each). The most frequent genomic gain was identified at 8q (40%). Further frequent gains were detected on 11q (38%), 21q (27%), 1p, 2q (24% each), 9p (22%), 6p, 19p (20% each), 3q (18%), 7p, 20p (15% each), 13q, and 20q (13% each). Genomic amplifications were identified on chromosomal band 8q24 including the MYC gene (2 cases), 9p24 (JAK2, 2 cases), 10p15 (PRKCO, 1 case), 11q23 (MLL, 2 cases), 11q23.3 (ETS1 and FLI1, 2 cases each), 12p13 (CCND2 and FGF6, 2 cases), 13q12 (CDX2, 3 cases), 20q11.1 (BCL2L, 1 case), 21p (1 case), 21q (2 cases), and 22q (1 case). These data demonstrate the potential of matrix-CGH with regard to spatial resolution and sensitive detection of genomic imbalances. Analysis of a large series of AML cases with complex karyotype may lead to the identification of novel critical regions and pathogenetically relevant genes.

Comparative mapping of human claudin-1 (CLDN1) in great apes

The gene encoding claudin-1 (CLDN1) has been mapped to human chromosome 3 (HSA3; 3q28→q29) using a radiation hybrid panel. Employing fluorescence in situ hybridization (FISH) we here show that a human P1-derived artificial chromosome (PAC) containing CLDN1 detects the orthologous sites in chromosomes of the great apes, chimpanzee, gorilla, and orangutan. Furthermore, the chromosomal position of CLDN1 was determined in mouse chromosomes by FISH. The position of fluorescent signals is confined to a single chromosomal site in both great apes and mouse and in each case maps to the chromosomal region that has conserved synteny with HSA3 (PTR2q28, GGO2q28, PPY2q38 and MMU16B1). Using a gene-specific probe our results are consistent with reports of the striking similarity of great ape and human genomes as illustrated previously by chromosome painting.

Selecting transpositions using phage P1 headful packaging: new markerless transposons for functionally mapping long-range regulatory sequences in bacterial artificial chromosomes and P1-derived artificial chromosomes

New Tn10 minitransposons were constructed to functionally map long-range transcription regulatory sequences in bacterial artificial chromosomes (BACs) and P1-derived artificial chromosomes (PACs). Each contained a wild-type loxP site but, significantly, contained no mammalian or bacterial genes and/or promoter elements within the transposed portion of DNA. In contrast to loxP transposons described previously, the new ones do not introduce transcription regulatory elements capable of interfering with those endogenous to the BAC clone in functional mapping studies. Progressive deletions from the loxP end of genomic DNA were efficiently generated using these transposons, and a series of truncations generated in a green fluorescence protein (GFP)–BAC fusion clone unambiguously identified three new long-range enhancer sequences functionally in the Nkx2-5 gene in transgenic mice. Insertions of these new transposons lacking antibiotic resistance genes into a BAC or PAC were indirectly selected by their ability to delete enough DNA from the clone so as to enable its packaging within a P1 phage head with both loxP sites intact for subsequent recovery of the large plasmid. The outcome of such an indirect mode of selection is both desirable and undesirable. First, because the screen is not antibiotic resistance marker dependent, the same transposon can be used to generate nested deletions efficiently in both BACs and PACs. Second, deletions through intrainsert recombinations unrelated to loxP/Cre also get packaged and recovered, and size analyses of the BAC/PAC vector band after NotI digestion is indispensable to identify authentic loxP/Cre deletions. The procedure nevertheless offers a potential approach to map recombinogenic sequences in BACs and PACs.

Mutually exclusive recombination of wild-type and mutant loxP sites in vivo facilitates transposon-mediated deletions from both ends of genomic DNA in PACs

Recombination of wild-type and mutant loxP sites mediated by wild-type Cre protein was analyzed in vivo using a sensitive phage P1 transduction assay. Contrary to some earlier reports, recombination between loxP sites was found to be highly specific: a loxP site recombined in vivo only with another of identical sequence, with no crossover recombination either between a wild-type and mutant site; or between two different mutant sites tested. Mutant loxP sites of identical sequence recombined as efficiently as wild-type. The highly specific and efficient recombination of mutant loxP sites in vivo helped in developing a procedure to progressively truncate DNA from either end of large genomic inserts in P1-derived artificial chromosomes (PACs) using transposons that carry either a wild-type or mutant loxP sequence. PAC libraries of human DNA were constructed with inserts flanked by a wild-type and one of the two mutant loxP sites, and deletions from both ends generated in clones using newly constructed wild-type and mutant loxP transposons. Analysis of the results provides new insight into the very large co-integrates formed during P1 transduction of plasmids with loxP sites: a model with tri- and possibly multimeric co-integrates comprising the PAC plasmid, phage DNA, and transposon plasmid(s) as intermediates in the cell appears best to fit the data. The ability to truncate a large piece of DNA from both ends is likely to facilitate functionally mapping gene boundaries more efficiently, and make available precisely trimmed genes in their chromosomal contexts for therapeutic applications.

Cre recombinase-mediated gene targeting of mesenchymal cells.

Loss-of-function approaches by the Cre/loxP technology have provided powerful tools for functional analyses of genes of interest expressed preferentially in a particular tissue. Here we describe the generation of transgenic mouse lines expressing Cre recombinase under the control of the promoter/enhancer unit of the gene for the alpha2 chain of collagen type I (Col1alpha2). As an expression vector, we used a P1-derived artificial chromosome (PAC), which harbors approximately 100 kb carrying the col1alpha2 gene. The improved coding sequence of the Cre recombinase was introduced to replace the first exon of col1alpha2. Cre expression was determined by immunohistochemistry and Cre-mediated onset of beta-galactosidase expression in ROSA26R-Cre reporter mice. In four analyzed transgenic lines, Cre recombinase was efficiently expressed during embryogenesis and in adult animals in cells of mesenchymal origin, such as dermal fibroblasts, mesenchymal cells of blood vessel walls, and cells in fibrous connective tissues surrounding internal organs.

Dorsal telencephalon-specific expression of Cre recombinase in PAC transgenic mice.

The ability to restrict gene expression or disruption to specific regions of the brain would enhance understanding of the molecular basis for brain development and function. For this purpose, brain region-restricted promoters are essential. Here we report the isolation of a DNA fragment containing the Emx1 gene promoter, which is responsible for dorsal telencephalon-specific expression. The Cre recombinase gene was inserted into a mouse PAC (P1-derived artificial chromosome) Emx1-locus clone (PAC-Emx1#1 clone) and utilized to generate three transgenic mouse lines. In all three lines, especially Tg3, Cre-mediated recombination was highly restricted to Emx1-expressing cell lineages, from embryonic stages to adulthood. Immunohistochemical analyses showed that Cre protein is expressed in the dorsal telencephalon in all three lines in adulthood. Thus, the PAC-Emx1#1 clone contains essentially all regulatory elements necessary for Emx1 gene expression. Our results suggest that Emx1-Cre Tg3 mice and the PAC-Emx1#1 clone constitute powerful tools for dorsal telencephalon-specific gene manipulation.

Use of Fimers to eliminate polymerase chain reaction and primer-dimer artifacts and to increase yield in BAC-sequencing reactions.

Specificity of primer-based amplification reactions depends on the specificity of primer hybridization. Ideally, under the elevated temperatures used in a typical amplification, the primers should hybridize only to the target sequence. However, there is a relatively narrow range of conditions (temperature, concentrations of ions and denaturing agents) for specific annealing of an oligonucleotide to its complementary target, and often it does not coincide with other requirements of the cycle-sequencing reaction. The discrimination between specific and nonspecific hybridization is most challenging when DNA template is bacterial artificial chromosome (BAC), P1-derived artificial chromosome, yeast artificial chromosome, or other long DNA with a large number of potential nonspecific priming sites. A similar situation occurs when DNA contains perfect or nonperfect repeats. As a result, amplification of nonspecific primer extension products can compete with amplification of the desired target sequences and can significantly decrease the efficiency of the amplification of the desired sequence ().

Applications of interspersed repeat sequence polymerase chain reaction.

Analysis of complex genomes includes characterization of complete large-insert genomic libraries comprising several hundreds of thousands of clones. Conventional methods to screen large-insert clone libraries for specific clones within a defined chromosomal interval are polymerase chain reaction (PCR) based using microsatellite markers. This strategy is labor- and cost-intensive and requires the PCR amplification of several thousands of DNA samples and verification of the PCR products via agarose gel electrophoresis. The number of PCR reactions is significantly reduced by the pooling of library clones in a three-dimensional (3D) pooling system. Nevertheless, several hundred PCR reactions are necessary to screen a P1-derived artificial chromosome (PAC) or bacterial artificial chromosome (BAC) library for one individual microsatellite marker. The application of high-density clone arrays, spotted robotically on nylon filters, offers the possibility of screening several tens of thousands of clones in a single working step. A new hybridization-based marker system has been established in the department of Hans Lehrach at the Max-Planck Institute for Molecular Genetics (Berlin, Germany). The interspersed repetitive sequence (IRS) markers are generated by amplification of genomic sequences that are located between two repetitive short interspersed repetitive elements (SINE) elements and are evenly distributed over the whole genome. IRS-PCR strategies have been applied to various species using the SINE sequences in human (Alu repeat), mouse (B1 repeat), rat (ID repeat), and zebrafish (DANA/mermaid repeat).

Physical maps and recombination frequency of six rice chromosomes.

We constructed physical maps of rice chromosomes 1, 2, and 6-9 with P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) clones. These maps, with only 20 gaps, cover more than 97% of the predicted length of the six chromosomes. We submitted a total of 193 Mbp of non-overlapping sequences to public databases. We analyzed the DNA sequences of 1316 genetic markers and six centromere-specific repeats to facilitate characterization of chromosomal recombination frequency and of the genomic composition and structure of the centromeric regions. We found marked changes in the relative recombination rate along the length of each chromosome. Chromosomal recombination at the centromere core and surrounding regions on the six chromosomes was completely suppressed. These regions have a total physical length of about 23 Mbp, corresponding to 11.4% of the entire size of the six chromosomes. Chromosome 6 has the longest quiescent region, with about 5.6 Mbp, followed by chromosome 8, with quiescent region about half this size. Repetitive sequences accounted for at least 40% of the total genomic sequence on the partly sequenced centromeric region of chromosome 1. Rice CentO satellite DNA is arrayed in clusters and is closely associated with the presence of Centromeric Retrotransposon of Rice (CRR)- and RIce RetroElement 7 (RIRE7)-like retroelement sequences. We also detected relatively small coldspot regions outside the centromeric region; their repetitive content and gene density were similar to those of regions with normal recombination rates. Sequence analysis of these regions suggests that either the amount or the organization patterns of repetitive sequences may play a role in the inactivation of recombination.

Identification of a BAC clone overlapping the t(6p12.3) breakpoint in the cell line ESS-1 derived from an endometrial stromal sarcoma

A major subgroup of endometrial stromal sarcomas (ESS) is characterized by translocations involving chromosome 6 with consistent breakpoints at 6p11∼p21. As part of an ongoing positional cloning effort to identify the genes affected by these translocations, this article reports on the delineation of the 6p breakpoint in the cell line ESS-1 derived from an ESS. The G- and 4′,6-diamidino-2-phenylindole–banded karyotypes showed an unbalanced translocation described originally as der(3)t(3;6) (q29;p21.1). Fluorescence in situ hybridization using probes derived from contigous yeast artificial chromosome, bacterial artificial chromosome (BAC), and P1-derived artificial chromosome clones specific to 6p12.3∼p21.1 located the breakpoint at 6p to the BAC clone RP11-337K13 mapping to 6p12.3. The DNA sequence of the breakpoint region contained in RP11-337K13 will serve as a candidate locus for further molecular genetic analyses to isolate the gene(s) altered in ESS with 6p rearrangement.

Genetic susceptibility in type 1 diabetes and its associated autoimmune disorders.

Animal models of type 1 diabetes There are several animal models of type 1A diabetes (immune mediated). The first inbred animal model evolved from the discovery of diabetic animals in an outbred colony of Wistar rats maintained at the Bio Breeding Research Laboratories in Ottawa, Canada. The Bio Breeding (BB) rat develops spontaneous immune-mediated diabetes with at least four loci contributing to disease: the major histocompatibility complex (MHC, iddm2) on rat chromosome 20; the lymphopenic locus iddm1 on rat chromosome 4 [1], iddm3 on rat chromosome 2 [2], and a fourth locus on rat chromosome 15. The lymphopenic phenotype (iddm1 or lyp) locus has been mapped to a syntenic region of rat chromosome 4 [1,3]. Mutation at this locus in a homozygous state produces a severe T cell lymphopenia. Hornum and co-workers have mapped the gene to a 0.3-cM region between markers D4Got59 and Abp1 and constructed a 550-kb P1-derived artificial chromosome (PAC) contig covering the region [4]. They found a frameshift mutation in Immune-Associated Nucleotide4 (Ian4) gene which encodes a GTP-binding protein localized in the outer mitochondrial membrane [5]. This mutation results in a truncated gene product that lacks twothirds of the total protein. They hypothesized that Ian 4 is involved in the regulation of T-cell apoptosis, making it an excellent candidate for iddm1. The Ian4 gene product is anchored to the outer mitochondrial membrane, and this organelle is an important site for the regulation of cell death [6]. The same mutation was found by MacMurray and co-workers but they termed the gene Ian5 [7]. Some Ian genes are expressed in mature T cells and switched on during thymic T-cell development [8–10]. The Komeda diabetes-prone (KDP) rat [11], a diabetesprone substrain of the Long-Evans Tokushima lean (LETL) rat is characterized by autoimmune destruction of pancreatic β cells [12], rapid onset of overt diabetes with no sex difference, and no significant T cell lymphopenia. The gene Cblb (Casitus B-lineage lymphoma b, also known as Cas-Br-M murine ectropic retroviral transforming sequence b) was a potential candidate given its influence on immune function. Yokoi et al. [13] confirmed a C → T homozygous nonsense mutation (arginine to a stop at codon 455, Arg455X) that removes 484 amino acids, including the proline-rich region and leucine zipper domain. The mutation is specific to the KDP rat and its original LETL strain. Approximately 80% of the Iddm/kdp1 homozygous mutant animals develop diabetes with severe insulitis, and most of the remainder showed mild to moderate insulitis. Neither heterozygous nor wildtype animals developed diabetes. They demonstrated that Cblb is a important regulator of autoimmunity and Cblb is a major susceptibility gene for rat type 1 diabetes [14]. The non-obese diabetic mouse is the best studied spontaneous animal model of type 1 diabetes. Diabetes susceptibility in the NOD is polygenic, with a major influence of genes within the MHC. Linkage analyses have identified at least 19 susceptibility loci (Idd1-Idd19) that contribute to disease pathogenesis [15,16]. Lymphocytes mediate the specific destruction of insulin-producing β cells. These loci can either confer susceptibility or resistance to expression of insulin autoantibodies, insulitis and or disease development. Idd1 has been mapped to the MHC locus on mouse chromosome 17 [17,18]. Idd1 mapped to class II I-A and I-E regions as a gene complex [19], but the incidence of the disease is strongly affected by a gene or genes outside of this segment (Idd16). Variants of the beta-2 microglobulin gene is one of the first non-MHC genes to by clearly identified. Though neither the insulin 2 gene on chromosome 7 nor the insulin 1 gene on chromsome 19 show linkage to diabetes, in crosses with normal mouse strains, knockouts of either of these genes greatly influences the development of diabetes. Several new mouse models of human type 1 diabetes have been developed using transgenic mice. We found

Construction of a 1.2-Mb BAC/PAC Contig of the Porcine Gene RYR1 Region on SSC 6q1.2 and Comparative Analysis with HSA 19q13.13

We screened a porcine bacterial artificial chromosome (BAC) and a P1 derived artificial chromosome (PAC) library to construct a sequence-ready ∼ 1.2-Mb BAC/PAC contig of the ryanodine receptor-1 gene ( RYR1) region on porcine chromosome (SSC) 6q1.2. This genomic segment is of special interest because it harbors the locus for stress susceptibility in pigs and a putative quantitative trait locus for muscle growth. Detailed physical mapping of this gene-rich region allowed us to assign to this contig 17 porcine genes orthologous to known human chromosome 19 genes. Apart from the relatively well-characterized porcine gene RYR1, the other 16 genes represent novel chromosomal assignments and 14 genes have been cloned for the first time in pig. Comparative analysis of the porcine BAC/PAC contig with the human chromosome (HSA) 19q13.13 map revealed a completely conserved gene order of this segment between pig and human. A detailed porcine–human–mouse comparative map of this region was constructed.

Rice Genome Organization: the Centromere and Genome Interactions

Over the last decade, many varied resources have become available for genome studies in rice. These resources include over 4000 DNA markers, several bacterial artificial chromosome (BAC) libraries, P-1 derived artificial chromosome (PAC) libraries and yeast artificial chromosome (YAC) libraries (genomic DNA clones, filters and end-sequences), retrotransposon tagged lines, and many chemical and irradiated mutant lines. Based on these, high-density genetic maps, cereal comparative maps, YAC and BAC physical maps, and quantitative trait loci (QTL) maps have been constructed, and 93 % of the genome has also been sequenced. These data have revealed key features of the genetic and physical structure of the rice genome and of the evolution of cereal chromosomes. This Botanical Briefing examines aspects of how the rice genome is organized structurally, functionally and evolutionarily. Emphasis is placed on the rice centromere, which is composed of long arrays of centromere-specific repetitive sequences. Differences and similarities amongst various cereal centromeres are detailed. These indicate essential features of centromere function. Another view of various kinds of interactive relationships within and between genomes, which could play crucial roles in genome organization and evolution, is also introduced. Constructed genetic and physical maps indicate duplication of chromosomal segments and spatial association between specific chromosome regions. A genome-wide survey of interactive genetic loci has identified various reproductive barriers that may drive speciation of the rice genome. The significance of these findings in genome organization and evolution is discussed.

A microinjected COL7A1-PAC vector restores synthesis of intact procollagen VII in a dystrophic epidermolysis bullosa keratinocyte cell line.

Dystrophic epidermolysis bullosa (DEB) comprises a family of inherited blistering skin disorders for which no corrective therapy currently exists. In the most severe form, the Hallopeau-Siemens subtype (RDEB-HS), the epidermal adhesion protein collagen VII is absent from the skin as a consequence of null mutations in the COL7A1 gene. In order to develop an ex vivo gene therapy approach for DEB, we aimed to restore expression of intact procollagen VII in RDEB-HS keratinocytes. The entire human COL7A1 locus in a P1-derived artificial chromosome (PAC) was transferred to RDEB-HS keratinocytes by microinjection, after which sustained biosynthesis and secretion of procollagen VII was detected for 1 year in vitro. Protein chemical analysis demonstrated that the chain composition, domain structure, N-glycosylation and protein folding of the newly produced procollagen VII were similar, if not identical, to its authentic counterpart, indicating that transgenic procollagen VII was structurally normal. These data demonstrate a "proof of principle" for genomic DNA vectors as a means of restoring collagen VII production in RDEB-HS skin and help develop future gene therapy protocols.

Physical mapping of the major histocompatibility complex class II and class III regions of the rat

A contig of overlapping bacterial and P1-derived artificial chromosome (BAC, PAC) clones derived from the inbred rat strain BN was constructed that encompasses the class II and the class III regions of the rat MHC (RT1 complex). The genomic structure of the rat, human, and mouse class II and class III regions is highly similar. However, different from human and mouse, a copy of the C4, Cyp21, and Stk19 genes is found that maps to the class II region in the rat. Gene trees constructed from human, rat, and mouse C4, Cyp21, and Stk19 sequences show species-specific clustering of the duplicated genes. The class II/III contig reported here links two previously published PAC contigs of the BN rat that contain the centromeric and the telomeric class I regions, RT1-A and RT1-C/E/M, respectively. Thus, the MHC of the rat is now completely mapped in a single contig of BAC/PAC clones derived from a single RT1 haplotype and encompasses about 3.7 Mb.