Down syndrome (DS) is caused by trisomy of chromosome 21 (Hsa21) and presents a complex phenotype that arises from abnormal dosage of genes on this chromosome. However, the individual ...dosage-sensitive genes underlying each phenotype remain largely unknown. To help dissect genotype--phenotype correlations in this complex syndrome, the first fully transchromosomic mouse model, the Tc1 mouse, which carries a copy of human chromosome 21 was produced in 2005. The Tc1 strain is trisomic for the majority of genes that cause phenotypes associated with DS, and this freely available mouse strain has become used widely to study DS, the effects of gene dosage abnormalities, and the effect on the basic biology of cells when a mouse carries a freely segregating human chromosome. Tc1 mice were created by a process that included irradiation microcell-mediated chromosome transfer of Hsa21 into recipient mouse embryonic stem cells. Here, the combination of next generation sequencing, array-CGH and fluorescence in situ hybridization technologies has enabled us to identify unsuspected rearrangements of Hsa21 in this mouse model; revealing one deletion, six duplications and more than 25 de novo structural rearrangements. Our study is not only essential for informing functional studies of the Tc1 mouse but also (1) presents for the first time a detailed sequence analysis of the effects of gamma radiation on an entire human chromosome, which gives some mechanistic insight into the effects of radiation damage on DNA, and (2) overcomes specific technical difficulties of assaying a human chromosome on a mouse background where highly conserved sequences may confound the analysis. Sequence data generated in this study is deposited in the ENA database, Study Accession number: ERP000439.
We report the analyses of breakpoints in 31 phenotypically normal and 14 abnormal carriers of balanced translocations. Our study assesses the differences between balanced translocations in normal ...carriers and those in abnormal carriers, focusing on the presence of genomic imbalances at the breakpoints or elsewhere in the genome, presence of cryptic chromosome rearrangements, and gene disruption. Our hypothesis is that all four features will be associated with phenotypic abnormalities and absent or much less frequent in a normal population. In the normal cohort, we identified neither genomic imbalances at the breakpoints or elsewhere in the genome nor cryptic chromosome rearrangements. In contrast, we identified candidate disease-causing imbalances in 4/14 abnormal patients. These were three breakpoint associated deletions and three deletions unrelated to the breakpoints. All six de novo deletions originated on the paternally inherited chromosome. Additional complexity was also present in one of these cases. Gene disruption by the breakpoints was present in 16/31 phenotypically normal individuals and in 5/14 phenotypically abnormal patients. Our results show that translocations in phenotypically abnormal patients are molecularly distinct from those in normal individuals: the former are more likely to be associated with genomic imbalances at the breakpoints or elsewhere and with chromosomal complexity, whereas the frequency of gene disruption is similar in both normal and abnormal translocation carriers.
Down syndrome is one of the most common congenital disorders leading to a wide range of health problems in humans, including frequent otitis media. The Tc1 mouse carries a significant part of human ...chromosome 21 (Hsa21) in addition to the full set of mouse chromosomes and shares many phenotypes observed in humans affected by Down syndrome with trisomy of chromosome 21. However, it is unknown whether Tc1 mice exhibit a hearing phenotype and might thus represent a good model for understanding the hearing loss that is common in Down syndrome. In this study we carried out a structural and functional assessment of hearing in Tc1 mice. Auditory brainstem response (ABR) measurements in Tc1 mice showed normal thresholds compared to littermate controls and ABR waveform latencies and amplitudes were equivalent to controls. The gross anatomy of the middle and inner ears was also similar between Tc1 and control mice. The physiological properties of cochlear sensory receptors (inner and outer hair cells: IHCs and OHCs) were investigated using single-cell patch clamp recordings from the acutely dissected cochleae. Adult Tc1 IHCs exhibited normal resting membrane potentials and expressed all K(+) currents characteristic of control hair cells. However, the size of the large conductance (BK) Ca(2+) activated K(+) current (I(K,f)), which enables rapid voltage responses essential for accurate sound encoding, was increased in Tc1 IHCs. All physiological properties investigated in OHCs were indistinguishable between the two genotypes. The normal functional hearing and the gross structural anatomy of the middle and inner ears in the Tc1 mouse contrast to that observed in the Ts65Dn model of Down syndrome which shows otitis media. Genes that are trisomic in Ts65Dn but disomic in Tc1 may predispose to otitis media when an additional copy is active.
The prevalence and distribution of gonococcal and chlamydial infections in the general population are poorly understood. Development of nucleic acid amplification tests, such as the ligase chain ...reaction assay, provides new opportunities to estimate the prevalence of untreated infections in the population.
To estimate the overall prevalence of untreated gonococcal and chlamydial infections and to describe patterns of infection within specific demographic subgroups of the young adult population in Baltimore, Md.
Cross-sectional behavioral survey based on a probability sample of Baltimore households with collection of urine specimens between January 1997 and September 1998.
A total of 728 adults aged 18 to 35 years completed the interview portion of the study, and 579 of these respondents also provided a urine specimen adequate for testing.
Prevalence of untreated infection, as measured by the percentage of specimens testing positive for gonococcal and chlamydial infection by ligase chain reaction, weighted to reflect variations in probabilities of sample selection from the population. Alternate estimates of the prevalence of recent treated infection were derived from clinically diagnosed cases reported to the Baltimore City Health Department and by diagnoses reported by participants in the survey.
An estimated 5.3% (SE, 1.4%) of the population aged 18 to 35 years has an untreated gonococcal infection, and 3.0% (SE, 0.8%) is estimated to have an untreated chlamydial infection. While 7.9% (SE, 1.6%) of the population is estimated to have either an untreated gonococcal or chlamydial infection, estimated prevalence is substantially higher among black women (15.0%; SE, 3.7%). Few participants with untreated infections reported dysuria or discharge during the 6 months preceding testing. The estimated number of untreated gonococcal infections in the population (9241; SE, 2441) substantially exceeds both the number of such infections diagnosed among Baltimore adults aged 18 to 35 years and reported to the Baltimore City Health Department during 1998 (4566), and the estimated number of diagnoses derived using participants' reports for the 12 months prior to the survey (4708 SE, 1918 to 5231 SE, 2092). The estimated number of untreated chlamydial infections (5231; SE, 1395) is also greater than the number of cases reported to the health department in 1998 (3664) but is slightly less than the estimated number of diagnoses derived using participants' reports of chlamydial infections diagnosed during the 12 months prior to the survey (5580 SE, 1918 to 6975 SE, 2441).
In 1997-1998, the estimated number of undiagnosed gonococcal and chlamydial infections prevalent in the population of Baltimore adults aged 18 to 35 years approached or exceeded the number of infections that were diagnosed and treated annually.
Array painting is a technique that uses microarray technology to rapidly map chromosome translocation breakpoints. Previous methods to map translocation breakpoints have used fluorescence in situ ...hybridization (FISH) and have consequently been labor-intensive, time-consuming and restricted to the low breakpoint resolution imposed by the use of metaphase chromosomes. Array painting combines the isolation of derivative chromosomes (chromosomes with translocations) and high-resolution microarray analysis to refine the genomic location of translocation breakpoints in a single experiment. In this protocol, we describe array painting by isolation of derivative chromosomes using a MoFlo flow sorter, amplification of these derivatives using whole-genome amplification and hybridization onto commercially available oligonucleotide microarrays. Although the sorting of derivative chromosomes is a specialized procedure requiring sophisticated equipment, the amplification, labeling and hybridization of DNA is straightforward, robust and can be completed within 1 week. The protocol described produces good quality data; however, array painting is equally achievable using any combination of the available alternative methodologies for chromosome isolation, amplification and hybridization.
We describe genomic structures of 59 X-chromosome segmental duplications that include the proteolipid protein 1 gene (
PLP1) in patients with Pelizaeus-Merzbacher disease. We provide the first report ...of 13 junction sequences, which gives insight into underlying mechanisms. Although proximal breakpoints were highly variable, distal breakpoints tended to cluster around low-copy repeats (LCRs) (50% of distal breakpoints), and each duplication event appeared to be unique (100 kb to 4.6 Mb in size). Sequence analysis of the junctions revealed no large homologous regions between proximal and distal breakpoints. Most junctions had microhomology of 1–6 bases, and one had a 2-base insertion. Boundaries between single-copy and duplicated DNA were identical to the reference genomic sequence in all patients investigated. Taken together, these data suggest that the tandem duplications are formed by a coupled homologous and nonhomologous recombination mechanism. We suggest repair of a double-stranded break (DSB) by one-sided homologous strand invasion of a sister chromatid, followed by DNA synthesis and nonhomologous end joining with the other end of the break. This is in contrast to other genomic disorders that have recurrent rearrangements formed by nonallelic homologous recombination between LCRs. Interspersed repetitive elements (
Alu elements, long interspersed nuclear elements, and long terminal repeats) were found at 18 of the 26 breakpoint sequences studied. No specific motif that may predispose to DSBs was revealed, but single or alternating tracts of purines and pyrimidines that may cause secondary structures were common. Analysis of the 2-Mb region susceptible to duplications identified proximal-specific repeats and distal LCRs in addition to the previously reported ones, suggesting that the unique genomic architecture may have a role in nonrecurrent rearrangements by promoting instability.
ABSTRACT
Investigation of rare familial forms of renal cell carcinoma (RCC) has led to the identification of genes such as VHL and MET that are also implicated in the pathogenesis of sporadic RCC. In ...order to identify a novel candidate renal tumor suppressor gene, we characterized the breakpoints of a constitutional balanced translocation, t(5;19)(p15.3;q12), associated with familial RCC and found that a previously uncharacterized gene UBE2QL1 was disrupted by the chromosome 5 breakpoint. UBE2QL1 mRNA expression was downregulated in 78.6% of sporadic RCC and, although no intragenic mutations were detected, gene deletions and promoter region hypermethylation were detected in 17.3% and 20.3%, respectively, of sporadic RCC. Reexpression of UBE2QL1 in a deficient RCC cell line suppressed anchorage‐independent growth. UBE2QL1 shows homology to the E2 class of ubiquitin conjugating enzymes and we found that (1) UBE2QL1 possesses an active‐site cysteine (C88) that is monoubiquitinated in vivo, and (2) UBE2QL1 interacts with FBXW7 (an F box protein providing substrate recognition to the SCF E3 ubiquitin ligase) and facilitates the degradation of the known FBXW7 targets, CCNE1 and mTOR. These findings suggest UBE2QL1 as a novel candidate renal tumor suppressor gene.
(A) Sanger sequencing of der(5) and der(19) breakpoints of a renal tumour associated constitutional translocation shows the chromosome 5 breakpoint to disrupt a previously uncharacterised gene, UBE2QL1. (B) UBE2QL1 shows homology to the ubiquitin conjugating enzyme family and an in silico search revealed a possible FBXW7 binding domain. We show that UBE2QL1 does bind both ubiquitin and FBXW7. (C) UBE2QL1 shows growth suppression (left) and inhibition of anchorage independent growth (middle), which is dependent upon the active‐site cysteine residue (right).
Studies of sexual and other sensitive behaviors are often fraught with a variety of reporting biases. When IAQs are used to collect data, respondents may underreport certain sensitive behaviors and ...overreport normative behaviors. SAQs can also pose problems: requiring that respondents be literate and be able to follow skip patterns. In recent years, the development of computerized technologies-audio-CASI and T-ACASI-have begun to overcome some of the limitations of IAQs and SAQs. By providing a more private mode for data collection and standardized delivery of all questions, as well as automated skip patterns and range checks, audio-CASI and T-ACASI have been tested in a number of studies and found to be an effective way of reducing response bias, and thus, contributing to a better understanding of the prevalence and patterns of sexual and other sensitive behaviors.
A study examined the relationship between assessed levels of medical literacy, respondent characteristics and the quality of measurements made in the 1997/98 Baltimore Sexually Transmitted Disease ...(STD) and Behavior Survey. Data suggest that, although persons with low medical literacy will provide answers on paper self-administered forms, they may respond to questions they don't completely understand.
Although the human genome sequence was declared complete in 2004, the sequence was interrupted by 341 gaps of which 308 lay in an estimated approximately 28 Mb of euchromatin. While these gaps ...constitute only approximately 1% of the sequence, knowledge of the full complement of human genes and regulatory elements is incomplete without their sequences.
We have used a combination of conventional chromosome walking (aided by the availability of end sequences) in fosmid and bacterial artificial chromosome (BAC) libraries, whole chromosome shotgun sequencing, comparative genome analysis and long PCR to finish 8 of the 11 gaps in the initial chromosome 22 sequence. In addition, we have patched four regions of the initial sequence where the original clones were found to be deleted, or contained a deletion allele of a known gene, with a further 126 kb of new sequence. Over 1.018 Mb of new sequence has been generated to extend into and close the gaps, and we have annotated 16 new or extended gene structures and one pseudogene.
Thus, we have made significant progress to completing the sequence of the euchromatic regions of human chromosome 22 using a combination of detailed approaches. Our experience suggests that substantial work remains to close the outstanding gaps in the human genome sequence.
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