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PubMed2026

Signals of Natural Selection Across Regions of Low Recombination in Wild Populations of the Purple Sea Urchin, Strongylocentrotus purpuratus.

Structural variants (SVs) are increasingly recognized as important components of genetic architecture. Yet our understanding of the evolutionary forces maintaining SVs in natural populations is limited. Chromosomal inversions in particular can facilitate local adaptation in populations with high gene flow, including many marine species. The purple sea urchin (Strongylocentrotus purpuratus) is a powerful system to study these dynamics due to its high gene flow, lack of population structure, and broad latitudinal range. We analyzed whole genome sequence data from 137 individuals sampled across seven populations to identify regions of low recombination using scans for elevated linkage disequilibrium and genetic differentiation. Such regions may arise from structural variants, including chromosomal inversions. We identified nine regions showing signatures of reduced recombination, including three way genotype clustering, long range linkage, and hanging bridge patterns frequently associated with inversion polymorphisms. The regions were polymorphic within locations and along the species range with three loci showing concordant signatures of balancing and spatially heterogeneous selection based on enrichment of outliers and distinct patterns of allelic age. Additionally, these loci showed enrichment for genes associated with biomineralization and development. Our results provide the first evidence for regions of low recombination in the purple sea urchin genome, several of which display genomic signatures consistent with structural variants such as chromosomal inversions. These findings add to growing evidence that regions of reduced recombination constitute an important component of standing genetic variation in natural populations and may play a key role in adaptation to heterogeneous environments.

Strongylocentrotus purpuratus↗
PubMed2000

Colonization of America by Drosophila subobscura: spatial and temporal lethal-gene allelism.

About twenty years ago Drosophila subobscura, a western Palearctic species, colonized both North and South America. Lethal genes in the O chromosome has been subject to much research. Lethal gene allelisms between American populations far away have been studied. These allelisms were not negligible, but all cases were due to the lethal gene completely associated to the O5 chromosomal inversion. Here we analyze the lethal genes in a new American population of D. subobscura (Centralia, Washington), located fairly close to a previously studied population (Bellingham, Washington) and separated in space and time with other American populations (Gilroy I and II in California and Santiago de Chile). The frequencies of lethal and semilethal genes of Centralia were 16.9+/-4.6 and 6.2+/-3.0, respectively. The intrapopulational allelism of Centralia was 0.122+/-0.036. Interpopulational allelisms were studied using the lethal genes from the populations separated in space and time from Centralia. The interpopulational allelisms between Centralia and Gilroy I (California) and between Centralia and Bellingham (Washington) were higher than the intrapopulational allelism (0.155+/-0.032 and 0.153+/-0.024, respectively). In all these cases allelism was due to a complete association between a lethal gene and the O5 chromosomal inversion. Accordingly, no other lethal genes are shared in these populations.

Alleles↗
PubMed1989

Organization and orientation of a human T cell receptor delta chain V gene segment that suggests an inversion mechanism is utilized in its rearrangement.

A human T cell receptor (TcR) delta chain variable region segment, V delta 3, has been mapped 2 kilobases 3' to the constant (C delta) gene. The V delta 3 gene segment is in an inverted transcriptional orientation to the diversity regions (D delta), joining regions (J delta) and C delta gene segments. Analyses of TcR delta cDNA clone, KT041, showed that V delta 3 is linked to D delta 1, D delta 2, J delta 3 and C delta and that this message encodes a potentially functional TcR delta chain. These findings indicate that a functional TcR delta gene can be constructed through a chromosomal inversion, suggesting that in human, chromosomal inversion is one of the important rearrangement mechanisms.

Base Sequence↗
PubMed2005

A new recurrent inversion, inv(7)(p15q34), leads to transcriptional activation of HOXA10 and HOXA11 in a subset of T-cell acute lymphoblastic leukemias.

Chromosomal translocations with breakpoints in T-cell receptor (TCR) genes are recurrent in T-cell malignancies. These translocations involve the TCRalphadelta gene (14q11), the TCRbeta gene (7q34) and to a lesser extent the TCRgamma gene at chromosomal band 7p14 and juxtapose T-cell oncogenes next to TCR regulatory sequences leading to deregulated expression of those oncogenes. Here, we describe a new recurrent chromosomal inversion of chromosome 7, inv(7)(p15q34), in a subset of patients with T-cell acute lymphoblastic leukemia characterized by CD2 negative and CD4 positive, CD8 negative blasts. This rearrangement juxtaposes the distal part of the HOXA gene cluster on 7p15 to the TCRbeta locus on 7q34. Real time quantitative PCR analysis for all HOXA genes revealed high levels of HOXA10 and HOXA11 expression in all inv(7) positive cases. This is the first report of a recurrent chromosome rearrangement targeting the HOXA gene cluster in T-cell malignancies resulting in deregulated HOXA gene expression (particularly HOXA10 and HOXA11) and is in keeping with a previous report suggesting HOXA deregulation in MLL-rearranged T- and B cell lymphoblastic leukemia as the key factor in leukaemic transformation. Finally, our observation also supports the previous suggested role of HOXA10 and HOXA11 in normal thymocyte development.

Adolescent↗
PubMed1996

A new method for detecting pericentric inversions using COD-FISH.

A new approach for detecting chromosomal inversions, based on the recently developed technique of chromosome orientation and direction fluorescence in situ hybridization (COD-FISH), is presented. COD-FISH is a strand-specific modification of standard FISH technology which allows the hybridization of single-stranded probes to one, and only one, chromatid of a metaphase chromosome. It can be used to determine the absolute 5'-to-3' direction of DNA target sequences with respect to the short-to-long arm direction of a given chromosome. Since an inversion reverses the orientation of DNA sequences within the inverted region, an inversion becomes detectable as a "switch" in probe signal from one chromatid to the other, when compared to a reference probe outside of the inverted region. Pericentric inversions in chromosomes 1, 8, 10, and X, which had previously been identified by chromosome banding, were analyzed by the COD-FISH technique. The results presented here demonstrate that COD-FISH can be used for the detection of pericentric inversions and that, in some instances, it provides additional information not obtainable by more conventional methods of cytogenetic analysis. Practical limitations of the COD-FISH technique are also discussed.

Centromere↗
PubMed1992

Pericentric inversion of chromosome 7 (inv(7) (p22q11.2)) and ring chromosome 8 (r(8) (p23q24.3)) in a girl with minor anomalies.

A 13 year old girl was referred with congenital microcephaly, developmental delay, a prominent nose, highly arched palate, and an apparently low set left ear. She was found to have a pericentric inversion of one chromosome 7 and a ring chromosome 8, 46,XX,inv(7) (pter----p22::q11.23----p22::q11.23----qter), r(8) (p23q24.3). The concurrence of these two abnormalities is a rare event and has not been reported previously.

Abnormalities, Multiple↗
PubMed2005

The effect of an inversion system and the time interval between matings on postcopulatory sexual selection in the seaweed fly, Coelopa frigida.

The seaweed fly, Coelopa frigida, exhibits LMSP. A large chromosomal inversion system affects many traits including egg-to-adult viability via heterosis. Consequently, there is also considerable potential for cryptic female mate choice to operate on the basis of sperm karyotype. Here, we investigated the effect of time interval and chromosomal inversion karyotype on postcopulatory sexual selection. Homokaryotypic females were mated with a male of the same and a male of the opposite homokaryotype. The order of the matings was varied so cryptic female mate choice could operate either in concert or antagonistically with LMSP. LMSP was found when there was a 24 h time interval between matings, irrespective of the order in which the males were mated. However, when the males were mated in quick succession the order of mating was important. When LMSP and cryptic female mate choice work in concert a high level of LMSP was found. However, when the male of opposite homokaryotype mated first, then first male sperm precedence was observed. This suggests that polyandrous females might be able to bias paternity but only when matings occur in quick succession. Consequently, population density is likely to affect the operation of postcopulatory sexual selection.

Animals↗
PubMed2005

Gene flow between chromosomal forms of the malaria vector Anopheles funestus in Cameroon, Central Africa, and its relevance in malaria fighting.

Knowledge of population structure in a major vector species is fundamental to an understanding of malaria epidemiology and becomes crucial in the context of genetic control strategies that are being developed. Despite its epidemiological importance, the major African malaria vector Anopheles funestus has received far less attention than members of the Anopheles gambiae complex. Previous chromosomal data have shown a high degree of structuring within populations from West Africa and have led to the characterization of two chromosomal forms, "Kiribina" and "Folonzo." In Central Africa, few data were available. We thus undertook assessment of genetic structure of An. funestus populations from Cameroon using chromosomal inversions and microsatellite markers. Microsatellite markers revealed no particular departure from panmixia within each local population and a genetic structure consistent with isolation by distance. However, cytogenetic studies demonstrated high levels of chromosomal heterogeneity, both within and between populations. Distribution of chromosomal inversions was not random and a cline of frequency was observed, according to ecotypic conditions. Strong deficiency of heterokaryotypes was found in certain localities in the transition area, indicating a subdivision of An. funestus in chromosomal forms. An. funestus microsatellite genetic markers located within the breakpoints of inversions are not differentiated in populations, whereas in An. gambiae inversions can affect gene flow at marker loci. These results are relevant to strategies for control of malaria by introduction of transgenes into populations of vectors.

Africa, Central↗
PubMed2005

Roles for replichores and macrodomains in segregation of the Escherichia coli chromosome.

Recent work has highlighted two main levels of global organization of the Escherichia coli chromosome. Macrodomains are large domains inferred from structural data consisting of loci showing the same intracellular positioning. Replichores, defined by base composition skews, coincide with the replication arms in normal cells. We used chromosome inversions to show that the dif site, which resolves chromosome dimers, only functions when located at the junction of the replichores, whatever their size. This is the first evidence that replichore polarization has a role in chromosome segregation. We also show that disruption of the Ter macrodomain provokes a cell-cycle defect independent from dimer resolution. This confirms the existence of the Ter macrodomain and suggests a role in chromosome dynamics.

Cell Division↗
PubMed2003

Evolutionary pace of chromosomal polymorphism in colonizing populations of Drosophila subobscura: an evolutionary time series.

Biologists have long debated the speed, uniformity, and predictability of evolutionary change. However, evaluating such patterns on a geographic scale requires time-series data on replicate sets of natural populations. Drosophila subobscura has proven an ideal model system for such studies. This fly is broadly distributed in the Old World, but was introduced into both North and South America just over two decades ago and then spread rapidly. Rapid, uniform, and predictable evolution would be demonstrated if the invading flies evolved latitudinal clines that progressively converged on those of the native populations. Evolutionary geneticists quickly capitalized on this opportunity to monitor evolutionary dynamics. Just a few years after the introduction, they surveyed chromosomal inversion frequencies in both North and South America. On both continents they detected incipient latitudinal clines in chromosome inversion frequencies that almost always had the same sign with latitude as in the Old World. Thus the initial evolution of chromosomal polymorphisms on a continental scale was remarkably rapid and consistent. Here we report newer samples of inversion frequencies for the colonizing populations: the time series now spans almost one decade for North America and almost two decades for South America. Almost all inversions in the New World continue to show the same sign of frequency with latitude as in the Old World. Nevertheless, inversion clines have not consistently increased in steepness over time; nor have they consistently continued to converge on the Old World baseline. However, five arrangements in South America show directional, continentwide shifts in frequency. Overall, the initial consistency of clinal evolutionary trajectories seen in the first surveys seems not to have been maintained.

Animals↗
PubMed1999

[Isolating the ends of yeast artificial chromosome by inverse polymerase chain reaction].

OBJECTIVE: To establish a highly efficient method for isolating yeast artificial chromosome(YAC) ends. METHODS: Based on the sequence of TAC vector, the frequent cutting enzymes were used to cleave within the vector and the genomic insert to generate relatively small fragments,which were ligated and subsequently amplified using vector primers that are in inverse orientation. The PCR products were purified and sequenced. RESULTS 8 YAC termini were isolated from YAC 776E2,964C5,11D8 and 8D1. CONCLUSION: The results suggest that inverse PCR be an efficient method for isolating YAC termini.

Chromosomes, Artificial, Yeast↗
PubMed2004

Population structure of the malaria vector Anopheles funestus in Senegal based on microsatellite and cytogenetic data.

The study of chromosomal inversions distribution within natural Anopheles funestus populations from West Africa revealed high levels of genetic structuring. In Burkina Faso, this was interpreted as evidence for incipient speciation, and two chromosomal forms were described, namely 'Folonzo' and 'Kiribina'. Assignation of field collected specimens to one chromosomal form depends upon application of an algorithm based on chromosomal inversions. We assessed relevance and applicability of this algorithm on An. funestus populations from Senegal, where both forms occur. Furthermore, we estimated the level of genetic differentiation between populations using microsatellite loci spread over the whole genome. Significant genetic differentiation was revealed between geographical populations of An. funestus, and the pattern observed suggested isolation by distance. Chromosomal heterogeneity was not detected by microsatellite markers. Thus, although incipient speciation could not be ruled out by our data, our results suggest that differential environmental selection pressure acting on inversions should be considered a major factor in shaping their distribution in wild An. funestus populations.

Animals↗
PubMed1997

The EVI1 gene in myeloid leukemia.

Leukemia is an acquired genetic disease caused by the accumulation of chromosomal abnormalities which modify either the biochemical property or the level of expression of proteins. Frequent genetic abnormalities identified in human leukemia are chromosomal rearrangements such as chromosomal translocations and inversions. Chromosome band 3q26 is the site of the breakpoint of recurring translocations and inversions observed in patients with myeloid leukemias. Two genes located at 3q26 have been implicated in development or progression of myeloid leukemia. They are MDS1 and EVI1. MDS1, first identified as part of a fusion transcript resulting from the t(3;21)(q26;q22), encodes a small protein of unknown function. EVI1 encodes a zinc finger protein inappropriately overexpressed by chromosomal rearrangements (in man) or by retroviral insertion (in the mouse). Both genes are rearranged by the t(3;21)(q26;q22) and by the t(3;12)(p13;q22). As a result of the translocation, they are expressed as fusion genes either with AML1 or with TEL. EVI1 and MDS1 are unusual in that they can either encode separate proteins, or they can be expressed as one protein which we named MDS1/EVI1. EVI1 and MDS1/EVI1 have opposite functions as transcription factors. In this report, we review the current information on the two genes, and on their involvement in myeloid leukemia.

Amino Acid Sequence↗
PubMed1989

[Pericentric inversion of the human Y chromosome].

Pericentric inversion of the human Y chromosome has an estimated frequency of the one per thousand. This inversion is always inherited but also is possible a de novo presentation. Sometimes this inverted chromosome is associated with the Down, Klinefelter and other chromosomal syndromes. For the carriers of pericentric inversion the risk of the mental retardation or multiple abortion is not apparently increase and there is not relation with abnormal phenotypic features. For some authors the pericentric inversion of the human Y chromosome is only a rare chromosomal heteromorphism.

Adolescent↗
PubMed2000

Fusion of the nucleoporin gene, NUP98, and the putative RNA helicase gene, DDX10, by inversion 11 (p15q22) chromosome translocation in a patient with etoposide-related myelodysplastic syndrome.

We report a 50-year-old man who developed therapy-related myelodysplastic syndrome after treatment with etoposide-including chemotherapy for extratesticular germ cell tumor. Chromosomal analysis showed inversion 11 (p15q22) translocation. Reverse transcriptase-polymerase chain reaction amplification of patient RNA showed a fusion transcript of nucleoporin gene NUP98, and putative DEAD-box RNA helicase gene DDX10. NUP98 is implicated in the transformation through aberrant nucleocytoplasmic transport. DDX10 is suggested to be involved in ribosome assembly. The NUP98-DDX10 fusion transcript may promote the development of secondary hematological malignancies caused by DNA-topoisomerase II inhibitors through aberrant nucleocytoplasmic transport and/or alteration in ribosome assembly.

Antineoplastic Agents, Phytogenic↗
PubMed2003

Replicated anterior zeugopod (raz): a polydactylous mouse mutant with lowered Shh signaling in the limb bud.

A unique limb phenotype is described in a radiation-induced mutant mouse resulting from an inversion of a proximal segment of chromosome 5. The limb phenotype in the homozygous mutant presents with two anterior skeletal elements in the zeugopod but no posterior bone, hence the name replicated anterior zeugopod, raz. The zeugopod phenotype is accompanied by symmetrical central polydactyly of hand and foot. The chromosomal inversion includes the Shh gene and the regulatory locus, located approximately 1 Mb away, within the Lmbr1 gene. In homozygous mutants, the expression of Shh mRNA and Shh protein is severely downregulated to about 20% of wild-type limb buds, but Shh expression appears normal throughout the remainder of the embryo. Correspondingly, Gli3 expression is upregulated and posteriorly expanded in the raz/raz limb bud. We propose that the double anterior zeugopod and symmetrical central polydactyly are due to an increased and uniform concentration of the Gli3 repressor form because of lowered Shh signaling.

Animals↗
PubMed1999

Population structure, speciation, and introgression in the Anopheles gambiae complex.

We review here what is known about the population structure and evolutionary dynamics of members of the Anopheles gambiae complex with emphasis on the situation in West Africa. First, the importance of the 2nd chromosome inversion polymorphism is demonstrated especially in adaptation to levels of aridity, a major environmental variable in Africa. This affects the distribution of karyotypes on both a macro- and micro-geographic scale as well as temporally. Such differentiation leads to karyotypes being differentially effective transmitters of malaria and differentially susceptible to indoor residual spraying of insecticides. Second, we review the evidence that cryptic taxa, especially in An. gambiae s.s., exist. This observation stems from both karyotype studies and molecular studies. It is abundantly clear that West African populations of An. gambiae s.s. are often not panmictic units, with premating factors evidently acting to maintain distinct genetic forms. Third, we review phylogenetic studies that have revealed the presence of introgression between the two most important vectors, An. gambiae and An. arabiensis. This is most evident for the 2nd chromosome inversions. This interpretation of phylogenetic data is consistent with a direct laboratory study indicating inversions in this chromosome are stably maintained in back-crossed populations. All of this information has led to the view that members of the An. gambiae complex are highly variable with an abundance of adaptive genetic variation. This presents a significant challenge to vector control programs designed to reduce malaria in sub-Saharan Africa.

Africa, Western↗
PubMed1986

Paracentric inversions in human chromosome 7.

A paracentric inversion (7)(q11q22) and mosaicism 46,XX/45,X was detected in a female with minor malformations. The same inversion was observed in the mother of the patient. The analysis of high resolution banded chromosomes revealed no visible imbalance in the inverted long arm of the chromosome 7. All published cases of paracentric inversions in the human chromosome 7 are reviewed and the relationship between this inversion and the occurrence of an aneuploidy of the sex chromosomes is discussed.

Adolescent↗