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Complex Rearrangement (complex + rearrangement)
Selected AbstractsMolecular characterization of the spectrum of genomic deletions in the mismatch repair genes MSH2, MLH1, MSH6, and PMS2 responsible for hereditary nonpolyposis colorectal cancer (HNPCC)GENES, CHROMOSOMES AND CANCER, Issue 2 2005Heleen van der Klift A systematic search by Southern blot analysis in a cohort of 439 hereditary nonpolyposis colorectal cancer (HNPCC) families for genomic rearrangements in the main mismatch repair (MMR) genes, namely, MSH2, MLH1, MSH6, and PMS2, identified 48 genomic rearrangements causative of this inherited predisposition to colorectal cancer in 68 unrelated kindreds. Twenty-nine of the 48 rearrangements were found in MSH2, 13 in MLH1, 2 in MSH6, and 4 in PMS2. The vast majority were deletions, although one previously described large inversion, an intronic insertion, and a more complex rearrangement also were found. Twenty-four deletion breakpoints have been identified and sequenced in order to determine the underlying recombination mechanisms. Most fall within repetitive sequences, mainly Alu repeats, in agreement with the differential distribution of deletions between the MSH2 and MLH1 genes: the higher number and density of Alu repeats in MSH2 corresponded with a higher incidence of genomic rearrangement at this disease locus when compared with other MMR genes. Long interspersed nuclear element (LINE) repeats, relatively abundant in, for example, MLH1, did not seem to contribute to the genesis of the deletions, presumably because of their older evolutionary age and divergence among individual repeat units when compared with short interspersed nuclear element (SINE) repeats, including Alu repeats. Moreover, Southern blot analysis of the introns and the genomic regions flanking the MMR genes allowed us to detect 6 novel genomic rearrangements that left the coding region of the disease-causing gene intact. These rearrangements comprised 4 deletions upstream of the coding region of MSH2 (3 cases) and MSH6 (1 case), a 2-kb insertion in intron 7 of PMS2, and a small (459-bp) deletion in intron 13 of MLH1. The characterization of these genomic rearrangements underlines the importance of genomic deletions in the etiology of HNPCC and will facilitate the development of PCR-based tests for their detection in diagnostic laboratories. © 2005 Wiley-Liss, Inc. [source] A new complex rearrangement involving the ETV6, LOC115548, and MN1 genes in a case of acute myeloid leukemiaGENES, CHROMOSOMES AND CANCER, Issue 3 2004Elena Belloni A new complex rearrangement involving chromosome bands 5q13, 12p13, 22q11, and 3q12 was identified and characterized in a patient with acute myeloid leukemia. Fluorescence in situ hybridization showed the involvement of the ETV6 gene in 12p13. ETV6 primers were specifically designed for 3,- and 5,-RACE-PCR experiments, which led to the identification of the other two rearranged genes. The derivative chromosome 5 harbored a fusion of the ETV6 sequence with that of the LOC115548 gene. The two genes were placed in opposite orientation and did not encode a fusion protein. On the derivative chromosome 12, ETV6 was fused to the MN1 gene on chromosome 22. Also in this case, the insertion, within the MN1 sequence, of a portion of chromosome 3 prevented the formation of a fusion protein. Finally, the derivative chromosome 22 contained the 3, portions of both LOC115548 and MN1, and no fusion transcript with coding potential could be predicted. In conclusion, all chromosome breakpoints led to the truncation of the three involved genes in the absence of predicted fusion proteins. This study lends further support to the hypothesis that gene disruption resulting in either loss of function or haploinsufficiency may be relevant in acute myeloid leukemia pathogenesis. © 2004 Wiley-Liss, Inc. [source] Semilobar holoprosencephaly prenatal diagnosis: an unexpected complex rearrangement in a de novo apparently balanced reciprocal translocation on karyotypePRENATAL DIAGNOSIS, Issue 3 2007S. Kanafani Abstract We report a semilobar holoprosencephaly (HPE) in a post-intracytoplasmic-sperm-injection pregnancy. It was suggested by ultrasonography (US), documented on karyotype, identified with magnetic resonance imaging (MRI), established after birth and confirmed on post-mortem autopsy. An amniocentesis revealed a de novo apparently balanced reciprocal translocation 46,XY, t(7;8) (q31.3;q12). Fluorescence in situ hybridization (FISH) identified a deletion in the region of the Sonic Hedgehog gene (SHH) on der(8); nevertheless, the subtelomeric regions for chromosomes 7 and 8 were present. The parents decided to continue the pregnancy; a boy was born and survived for 3 days. The brain autopsy confirmed the semilobar HPE previously noted on US and MRI. Further, band-specific FISH revealed, in addition to SHH deletion, the presence of an inversion in the 7q translocated material on der(8). The parents' karyotypes were normal. An unexpected complex rearrangement was present in a de novo apparently balanced reciprocal translocation in a semilobar HPE. Copyright © 2007 John Wiley & Sons, Ltd. [source] Structural characterization of unphosphorylated STAT5a oligomerization equilibrium in solution by small-angle X-ray scatteringPROTEIN SCIENCE, Issue 4 2009Pau Bernadó Abstract Signal transducer and activator of transcription (STAT) proteins play a crucial role in the activation of gene transcription in response to extracellular stimuli. The regulation and activity of these proteins require a complex rearrangement of the domains. According to the established models, based on crystallographic data, STATs convert from a basal antiparallel inactive dimer into a parallel active one following phosphorylation. The simultaneous analysis of small-angle X-ray scattering data measured at different concentrations of unphosphorylated human STAT5a core domain unambiguously identifies the simultaneous presence of a monomer and a dimer. The dimer is the minor species but could be structurally characterized by SAXS in the presence of the monomer using appropriate computational tools and shown to correspond to the antiparallel assembly. The equilibrium is governed by a moderate dissociation constant of Kd , 90 ,M. Integration of these results with previous knowledge of the N-terminal domain structure and dissociation constants allows the modeling of the full-length protein. A complex network of intermolecular interactions of low or medium affinity is suggested. These contacts can be eventually formed or broken to trigger the dramatic modifications in the dimeric arrangement needed for STAT regulation and activity. [source] A Transgenic Insertional Inner Ear Mutation on Mouse Chromosome 1,THE LARYNGOSCOPE, Issue 4 2000Rick A. Friedman MD Abstract Objectives/Hypothesis To clone and characterize the integration site of an insertional inner ear mutation, produced in one of fourteen transgenic mouse lines. The insertion of the transgene led to a mutation in a gene(s) necessary for normal development of the vestibular labyrinth. Study Design Molecular genetic analysis of a transgene integration site. Methods Molecular cloning, Southern and northern blotting, DNA sequencing and genetic database searching were the methods employed. Results The integration of the transgene resulted in a dominantly inherited waltzing phenotype and in degeneration of the pars superior. During development, inner ear fluid homeostasis was disrupted. The integration consisted of the insertion of a single copy of the transgene. Flanking DNA was cloned, and mapping indicated that the genomic DNA on either side of the transgene was not contiguous in the wild-type mouse. Localization of unique markers from the two flanks indicated that both were in the proximal region of mouse chromosome 1. However, in the wild-type mouse the markers were separated by 6.3 cM, indicating a sizable rearrangement. Analysis of the mutant DNA indicated that the entire region between the markers was neither deleted nor simply inverted. Conclusions These results are consistent with a complex rearrangement, including at least four breakpoints and spanning at least 6.3 cM, resulting from the integration of the transgene. This genomic rearrangement disrupted the function of one or more genes critical to the maintenance of fluid homeostasis during development and the normal morphogenesis of the pars superior. [source] Translocation,excision,deletion,amplification mechanism leading to nonsyntenic coamplification of MYC and ATBF1,GENES, CHROMOSOMES AND CANCER, Issue 2 2006Nadine Van Roy Despite oncogene amplification being a characteristic of many tumor types, the mechanisms leading to amplicon formation have remained largely unresolved. In this study, we used a combinatorial approach of fluorescence in situ hybridization and single-nucleotide polymorphism chip gene copy number analyses to unravel the mechanism leading to nonsyntenic coamplification of MYC and ATBF1 in SJNB-12 cells. To explain our findings, we propose a complex series of events consisting of multiple double-strand breaks, accompanied (or triggered) by the formation of a reciprocal translocation t(8;16), as well as excisions and deletions near the translocation breakpoints. This study provides evidence for a translocation,excision,deletion,amplification sequence of events rather than a breakage,fusion,bridge model, which has been more frequently proposed to explain proto-oncogene amplification. Furthermore, it illustrates the power of presently available tools for detailed analysis of the complex rearrangements that accompany amplicon formation. © 2005 Wiley-Liss, Inc. [source] Detection of unidentified chromosome abnormalities in human neuroblastoma by spectral karyotyping (SKY)GENES, CHROMOSOMES AND CANCER, Issue 3 2001Ninette Cohen Spectral karyotyping (SKY) is a novel technique based on the simultaneous hybridization of 24 fluorescently labeled chromosome painting probes. It provides a valuable addition to the investigation of many tumors that can be difficult to define by conventional banding techniques. One such tumor is neuroblastoma, which is often characterized by poor chromosome morphology and complex karyotypes. Ten primary neuroblastoma tumor samples initially analyzed by G-banding were analyzed by SKY. In 8/10 tumors, we were able to obtain additional cytogenetic information. This included the identification of complex rearrangements and material of previously unknown origin. Structurally rearranged chromosomes can be identified even in highly condensed metaphase chromosomes. Following the SKY results, the G-banding findings were reevaluated, and the combination of the two techniques resulted in a more accurate karyotype. This combination allows identification not only of material gained and lost, but also of breakpoints and chromosomal associations. The use of SKY is therefore a powerful tool in the genetic characterization of neuroblastoma and can contribute to a better understanding of the molecular events associated with this tumor. © 2001 Wiley-Liss, Inc. [source] Array-MLPA: comprehensive detection of deletions and duplications and its application to DMD patients,HUMAN MUTATION, Issue 1 2008Fanyi Zeng Abstract Multiplex ligation-dependent probe amplification (MLPA) is widely used to screen genes of interest for deletions and duplications. Since MLPA is usually based on size-separation of the amplification products, the maximum number of target sequences that can be screened in parallel is usually limited to ,40. We report the design of a robust array-based MLPA format that uses amplification products of essentially uniform size (100,120,bp) and distinguishes between them by virtue of incorporated tag sequences. We were thus able to increase probe complexity to 124, with very uniform product yields and signals that have a low coefficient of variance. The assay designed was used to screen the largest set studied so far (249 patients) of unrelated Duchenne muscular dystrophy (DMD) cases from the Chinese population. In a blind study we correctly assigned 98% of the genotypes and detected rearrangements in 181 cases (73%); i.e., 163 deletions (65%), 13 duplications (5%), and five complex rearrangements (2%). Although this value is significantly higher for Chinese patients than previously reported, it is similar to that found for other populations. The location of the rearrangements (76% in the major deletion hotspot) is also in agreement with other findings. The 96-well flow-through microarray system used in this research provides high-throughput and speed; hybridization can be completed in 5 to 30,minutes. Since array processing and data analysis are fully automated, array-MLPA should be easy to implement in a standard diagnostic laboratory. The universal array can be used to analyze any tag-modified MLPA probe set. Hum Mutat 29(1), 190,197, 2008. © 2007 Wiley-Liss, Inc. [source] Enzyme-Triggered and Self-Cleaving Fragrant Alcohol PrecursorsCHEMISTRY & BIODIVERSITY, Issue 6 2008Felix Flachsmann Abstract The high volatility and water solubility of many natural perfumery alcohols leads to their rapid loss in fabric-care and personal-care applications. A dramatically enhanced substantivity is achieved by the use of fragrance precursors as controlled-release systems. In the first part of this article, we present multi-odorant precursors, in which the enzymatic cleavage of esters or carbonates of fragrant alcohols triggers subsequent steps leading to the release of fragrant ketones, lactones, and additional fragrant alcohols. In the second part, a study on oligocarbonates of fragrant alcohols is presented. Therein, the outstanding enzyme-independent performance of gluconolactone oligocarbonate 27 for the long-lasting release of (Z)-hex-3-en-1-ol is highlighted. We show that these polyfunctional compounds undergo complex rearrangements and intramolecular substitution reactions which lead to the observed release kinetics. [source] | ||||||||||||||||