Short Arm Sequences Research Articles

Massive expansion of sex-specific SNPs, transposon-related elements, and neocentromere formation shape the young W-chromosome from the mosquitofish Gambusia affinis

BackgroundThe Western mosquitofish, Gambusia affinis, is a model for sex chromosome organization and evolution of female heterogamety. We previously identified a G. affinis female-specific marker, orthologous to the aminomethyl transferase (amt) gene of the related platyfish (Xiphophorus maculatus). Here, we have analyzed the structure and differentiation of the G. affinis W-chromosome, using a cytogenomics and bioinformatics approach.ResultsThe long arm of the G. affinis W-chromosome (Wq) is highly enriched in dispersed repetitive sequences, but neither heterochromatic nor epigenetically silenced by hypermethylation. In line with this, Wq sequences are highly transcribed, including an active nucleolus organizing region (NOR). Female-specific SNPs and evolutionary young transposable elements were highly enriched and dispersed along the W-chromosome long arm, suggesting constrained recombination. Wq copy number expanded elements also include female-specific transcribed sequences from the amt locus with homology to TE. Collectively, the G. affinis W-chromosome is actively differentiating by sex-specific copy number expansion of transcribed TE-related elements, but not (yet) by extensive sequence divergence or gene decay.ConclusionsThe G. affinis W-chromosome exhibits characteristic genomic properties of an evolutionary young sex chromosome. Strikingly, the observed sex-specific changes in the genomic landscape are confined to the W long arm, which is separated from the rest of the W-chromosome by a neocentromere acquired during sex chromosome evolution and may thus have become functionally insulated. In contrast, W short arm sequences were apparently shielded from repeat-driven differentiation, retained Z-chromosome like genomic features, and may have preserved pseudo-autosomal properties.

Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time.

(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.

Congenital Heart Defects in Neonates: Determining the Incidence of Genetic Testing and Follow-up Consultation at UCLA

Congenital Heart Defects in Neonates: Determining the Incidence of Genetic Testing and Follow-up Consultation at UCLA

WHIM Syndrome Cured by Chromothripsis

WHIM Syndrome Cured by Chromothripsis

Development of a highly sensitive semi-quantitative real-time PCR and molecular beacon probe assay for the detection of respiratory syncytial virus

Molecular beacons are a novel class of oligonucleotide probe capable of reporting the accumulation of target amplicon during real-time PCR by the emission of a fluorescent signal. A novel assay for the detection and estimation of respiratory syncytial virus (RSV) nucleic acid in clinical specimens based on real-time PCR utilising such a probe was developed. The probe consisted of two short arm sequences and a central loop sequence complementary to a region of the N gene (the target amplicon). The probe was characterised and a semi-quantitative nested real-time PCR using a LightCycler instrument was optimised. Standard curves were generated using cycle threshold ( C t) values calculated from several assays over a range of logarithmic RSV titres. Linear coefficient correlations were close to one ( r 2=0.998) and the detection limit of the optimised assay was reproducibly shown to be 1×10 −4 pfu/ml. The intra-assay coefficient of variation (CV) of C t values of the optimal assay was 0.8% and the CV of quantification data was 6.6%. The interassay CV of C t values was 2.0% and the quantification CV was 6.7%. The validity of the assay for the detection of RSV in clinical specimens was assessed by analysing ten specimens previously assayed in a different laboratory. Real-time PCR analysis was completely consistent with the results of prior analysis. The rapidity, sensitivity and specificity of the assay should greatly facilitate epidemiological studies, particularly in adults as existing methods perform better on clinical specimens from children.

Molecular Characterization of Tiny Ring X Chromosomes from Females with Functional X Chromosome Disomy and Lack of cis X Inactivation

Small ring X chromosomes were first described in mosaic karyotypes of females with the relatively benign phenotype of Turner syndrome. The presence of these rings in association with more severe phenotypes including mental retardation has raised the possibility that they lack sequences necessary for X chromosome inactivation, specifically genes within the X inactivation center (XIC) essential for cis X-inactivation. We recently showed that ring X chromosomes ascertained because of the severe phenotype do not express XIST, a candidate for the relevant gene, and that they are in fact active chromosomes. We now report studies of the genetic content of 11 of these ring X chromosomes (9 associated with severe phenotypes). Our results indicate that these chromosomes contain contiguous segments of DNA and have variable proximal and distal breakpoints and some include mainly long arm or mainly short arm sequences. As expected for ring chromosomes, they lack telomeric sequences. Many of the ring chromosomes lack the XIST locus, consistent with XIST being necessary for cis inactivation. However, the breakpoints in four ring chromosomes that have XIST sequences but do not express XIST suggest that other sequences within the XIC distal to XIST as it is now defined are also needed.

Overrepresentation of chromosome 12p sequences and karyotypic evolution in i(12p)-negative testicular germ-cell tumors revealed by fluorescence in situ hybridization

Human testicular germ-cell tumors (TGCTs) comprise a heterogeneous group of solid neoplasms. These tumors are characterized by the presence of a highly specific chromosomal abnormality, i.e., an isochromosome of the short arm of chromosome 12. At present, this i(12p) chromosome is found in more than 80% of TGCTs. Isochromosome 12p has also been observed in some ovarian and extragonadal germ cell tumors. In the remaining so-called i(12p)-negative TGCTs other abnormalities involving chromosome 12, mainly 12p, can be found. In order to establish whether 12p abnormalities other than i(12p) are a common phenomenon in TGCTs, a panel of 11 i(12p)-negative tumors was investigated using multicolor fluorescence in situ hybridization. All TGCTs examined appeared to contain chromosomal abnormalities involving 12p, resulting in a distinct overrepresentation of short arm sequences. In addition, indications were obtained for a clonal evolution in one of the tumors. Our data suggest that the occurrence of 12p abnormalities is a common phenomenon in i(12p)-negative TGCTs and that these abnormalities, analogous to i(12p), may contribute to the process of tumor development.

Molecular Cytogenetics of Human Germ Cell Tumours: i(12p) and Related Chromosomal Anomalies

Human testicular germ cell tumours (TGCTs) comprise a heterogeneous group of solid neoplasms. These tumours are characterized by a highly specific chromosomal anomaly, i.e. an isochromosome of the short arm of chromosome 12. At present, this i(12p) chromosome has been observed in about 80% of TGCTs. Also in dysgerminomas of the ovary and in some extragonadal germ cell tumours i(12p) has been observed. In the remaining so-called i(12p)-negative tumours other cytogenetic abnormalities can be found. In addition, TGCTs are usually highly aneuploid. The exact nature and role of these different anomalies in tumour development are as yet undefined. Here we present a molecular cytogenetic analysis of a diverse group of gonadal and extragonadal germ cell tumours. Our results indicate that all tumours examined exhibit anomalies involving 12p [i(12p) and/or others], resulting in a distinct overrepresentation of short arm sequences. Thus, we argue that the occurrence of 12p abnormalities may be a characteristic of both i(12p)-positive and -negative TGCTs and that these abnormalities may, through similar mechanisms, contribute to the process of TGCT development. This notion is substantiated by our finding that in all cases the supernumerary 12p sequences are of uniparental origin.

Frequent occurrence of translocations of the short arm of chromosome 15 to other D-group chromosomes

The presence of DA/DAPI (distamycin A/4,6-diamino-2-phenyl-indole) heteromorphism on the short arm of human acrocentric chromosomes was investigated in 127 individuals. In 7 cases, a DA/DAPI signal was observed on an acrocentric chromosome other than 15. Subsequently, in situ hybridization (ISH) with a pericentromeric probe specific for chromosome 15 was carried out. In all 7 cases, three ISH signals were present in every metaphase, i.e., on both chromosomes 15 and on the third DA/DAPI-fluorescence-positive acrocentric chromosome (a chromosome 13 or 14), indicating that a chromosome 15 short arm was also present on these chromosomes. Therefore, we conclude that translocations of short arm sequences from chromosome 15 onto other D-group chromosomes occur frequently. Moreover, it appears that DA/DAPI staining remains specific for the short arm of chromosome 15, despite a number of recent papers suggesting otherwise.

Analysis of two 47,XXX males reveals X-Y interchange and maternal or paternal nondisjunction.

Two cases of 47,XXX males were studied, one of which has been published previously (Bigozzi et al. 1980). Analysis of X-linked restriction fragment length polymorphisms revealed that in this case, one X chromosome was of paternal and two were of maternal origin, whereas in the other case, two X chromosomes were of paternal and one of maternal origin. Southern blot analysis with Y-specific DNA probes demonstrated the presence of Y short arm sequences in both XXX males. In one case, the results obtained pointed to a paracentric inversion on Yp of the patient's father. In situ hybridization indicated that the Y-specific DNA sequences were localized on Xp22.3 in one of the three X chromosomes in both cases. The presence of Y DNA had no effect on random X inactivation. It is concluded that both XXX males originate from aberrant X-Y interchange during paternal meiosis, with coincident nondisjunction of the X chromosome during maternal meiosis in case 1, and during paternal meiosis II in case 2.