SEARCH · Search PubMed

Results for “Locus Control Region”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 847 records · Page 47Linked to original sources

PubMed2006

Genetic signatures of intermediate divergence: population history of Old and New World Holarctic ravens (Corvus corax).

Many studies of phylogeography, speciation, and species limits restrict their focus to a narrow issue: gene tree monophyly. However, reciprocal monophyly does not provide an ideal touchstone criterion of any aspect of evolutionary divergence. There is a continuum of divergence stages as isolated populations go from initial allele frequency differences to well-differentiated species. Studying intermediate stages of divergence will increase our understanding of geographical speciation, species limits, and conservation priorities. We develop a conceptual framework and terminology for thinking about the stages of 'intermediate polyphyly'. The Holarctic clade of common ravens (Corvus corax), found throughout much of Eurasia and North America, provides a case study of these stages of intermediate divergence. We used coalescent, phylogenetic, and population genetic methods to investigate the history and current status of this Old World-New World distribution using 107 mitochondrial control region sequences. Phylogenetically, New World and Old World samples are intermixed. However, most samples are grouped into small subclades that are restricted to either the New World or the Old World, and only one haplotype is shared between the hemispheres. Analysis of moleculalr variance (amova) results reflect this low haplotype sharing between hemispheres (Phi(ST) = 0.13, P < 0.01). Isolation with Migration (im) coalescent results suggest a sustained period of divergence between the hemispheres and low levels of maternal gene flow. Although there has not been sufficient time to evolve reciprocal monophyly and some gene flow may occur, New World and Old World ravens are genetically quite distinct. We use this example to demonstrate these early stages of divergence as populations go from sharing only internal haplotypes, to sharing no haplotypes, to having population specific subclades. Studies of phylogeography, speciation and systematics will benefit from increased attention to these stages of intermediate polyphyly.

Animals↗

PubMed2000

Genetic diversity and gene flow among southeastern Queensland koalas (Phascolarctos cinereus).

Habitat fragmentation and destruction associated with the rapid urban and rural development of southeast Queensland presents an immediate threat to the survival of koala populations within this region. A sensitive method combining heteroduplex analysis (HDA) with temperature gradient gel electrophoresis (TGGE) was optimized to detect within-species variation in a mitochondrial DNA (mtDNA) control-region fragment, approximately 670 bp in length, from the koala. Eight different haplotypes were characterized in koalas, of which four were novel. Analysis of mtDNA diversity in 96 koalas from five populations in southeast Queensland revealed that the number of haplotypes in a single population ranged from one to five, with an average within-population haplotype diversity of 0.379 +/- 0.016, and nucleotide diversity of 0.22 +/- 0.001%. Nucleotide divergence between populations averaged 0.09 +/- 0.001% and ranged from 0.00 to 0.14%. Significant genetic heterogeneity was observed among most populations, suggesting that koala populations may be spatially structured along matrilines, although this may not be universal. The limited distribution of the central phylogenetic haplotype suggested the possibility of historical population bottlenecks north of the Gold Coast, while the presence of two highly divergent haplotypes at the Moreton site may indicate the occurrence of one or more undocumented translocation events into this area.

Animals↗

PubMed2004

Population structure and genetic variability of six bar wrasse (Thallasoma hardwicki) in northern South China Sea revealed by mitochondrial control region sequences.

The genetic relationships among northern South China Sea populations of the six bar wrasse (Thallasoma hardwicki) were investigated. Fish collected from the Solomon Islands were used for geographic comparison. In 1998 and 1999, a total of 100 fish were sampled from 6 localities of the northern South China Sea and 3 localities of the Solomon Islands. Genetic variations in DNA sequences were examined from the first hypervariable region (HVR-1) of the mitochondrial control region, as amplified by polymerase chain reaction. High levels of haplotypic diversity (h = 0.944 +/- 0.0016, pi = 0.0224 +/- 0.01171) in the HVR-1 region of the mitochondrial control region of T. hardwicki were detected. This yielded 94 haplotypes that exhibited a minimum spanning tree with a starburst structure, suggestive of a very recent origin for most haplotypes. Neutrality tests indicated that the pattern of genetic variability in T. hardwicki is consistent either with genetic hitchhiking by an advantageous mutation or with population expansion. Partitioning populations into coherent geographic groups divided the northern South China Sea samples (Phi(CT) = 0.0313, P < 0.001) into 3 major groups: a north-central group composed of northwestern Taiwan and northern Vietnam; a southwestern group containing southern Vietnam; and a southern group including the central Philippines. These results are in concordance with mesoscale boundaries proposed by allozyme markers, thus highlighting the importance of identifying transboundary units for the conservation and management of fisheries in the South China Sea.

Analysis of Variance↗

PubMed2001

Self-incompatibility in the genus Arabidopsis: characterization of the S locus in the outcrossing A. lyrata and its autogamous relative A. thaliana.

As a starting point for a phylogenetic study of self-incompatibility (SI) in crucifers and to elucidate the genetic basis of transitions between outcrossing and self-fertilizing mating systems in this family, we investigated the SI system of Arabidopsis lyrata. A. lyrata is an outcrossing close relative of the self-fertile A. thaliana and is thought to have diverged from A. thaliana approximately 5 million years ago and from Brassica spp 15 to 20 million years ago. Analysis of two S (sterility) locus haplotypes demonstrates that the A. lyrata S locus contains tightly linked orthologs of the S locus receptor kinase (SRK) gene and the S locus cysteine-rich protein (SCR) gene, which are the determinants of SI specificity in stigma and pollen, respectively, but lacks an S locus glycoprotein gene. As described previously in Brassica, the S haplotypes of A. lyrata differ by the rearranged order of their genes and by their variable physical sizes. Comparative mapping of the A. lyrata and Brassica S loci indicates that the S locus of crucifers is a dynamic locus that has undergone several duplication events since the Arabidopsis--Brassica split and was translocated as a unit between two distant chromosomal locations during diversification of the two taxa. Furthermore, comparative analysis of the S locus region of A. lyrata and its homeolog in self-fertile A. thaliana identified orthologs of the SRK and SCR genes and demonstrated that self-compatibility in this species is associated with inactivation of SI specificity genes.

Amino Acid Sequence↗

PubMed1997

Intergenic transcription and transinduction of the human beta-globin locus.

We have identified novel nuclear transcripts in the human beta-globin locus using nuclear run-on analysis in erythroid cell lines and in situ hybridization analysis of erythroid tissue. These transcripts extend across the LCR and intergenic regions but are undetectable in nonerythroid cells. Surprisingly, transient transfection of a beta-globin gene (epsilon, gamma, or beta) induces transcription of the LCR and intergenic regions from the chromosomal beta-globin locus in nonerythroid cell lines. The beta-globin genes themselves, however, remain transcriptionally silent. Induction is dependent on transcription of the globin gene in the transfected plasmid but does not require protein expression. Using in situ hybridization analysis, we show that the plasmid colocalizes with the endogenous beta-globin locus providing insight into the mechanism of transinduction.

Animals↗

PubMed2005

Prediction of beta-barrel membrane proteins by searching for restricted domains.

BACKGROUND: The identification of beta-barrel membrane proteins out of a genomic/proteomic background is one of the rapidly developing fields in bioinformatics. Our main goal is the prediction of such proteins in genome/proteome wide analyses. RESULTS: For the prediction of beta-barrel membrane proteins within prokaryotic proteomes a set of parameters was developed. We have focused on a procedure with a low false positive rate beside a procedure with lowest false prediction rate to obtain a high certainty for the predicted sequences. We demonstrate that the discrimination between beta-barrel membrane proteins and other proteins is improved by analyzing a length limited region. The developed set of parameters is applied to the proteome of E. coli and the results are compared to four other described procedures. CONCLUSION: Analyzing the beta-barrel membrane proteins revealed the presence of a defined membrane inserted beta-barrel region. This information can now be used to refine other prediction programs as well. So far, all tested programs fail to predict outer membrane proteins in the proteome of the prokaryote E. coli with high reliability. However, the reliability of the prediction is improved significantly by a combinatory approach of several programs. The consequences and usability of the developed scores are discussed.

Algorithms↗

PubMed2006

Genetic isolation and divergence in sexual traits: evidence for the northern rockhopper penguin Eudyptes moseleyi being a sibling species.

The taxonomic status of populations of rockhopper penguins (Eudyptes chrysocome) is still enigmatic. Northern populations differ from southern ones in breeding phenology, song characteristics and head ornaments used as mating signals. We conducted a molecular analysis using mitochondrial DNA sequencing to test if there is a gene flow barrier between northern (subtropical) populations and southern (subantarctic) populations in relation to the Subtropical Convergence, a major ecological boundary for marine organisms. Sequences of the control region and the ND2 gene were analysed in rockhopper penguins and in the macaroni penguin (Eudyptes chrysolophus), a closely related species. Genetic distances and phylogenetic analyses showed a clear split into three clades, two rockhopper clades and the macaroni penguin. Moreover, Theta(ST) and gene flow estimates also suggested genetic structuring within the northern rockhoppers. Our results add further support to the notion that the two rockhopper penguin taxa, often considered as two subspecies, can be recognized as two species E. chrysocome and E. moseleyi. The divergence in mating signals found between these two taxa seems to have occurred recently and relatively rapidly. Thus, the behavioural changes may have been enough to isolate these taxa without the need for morphological differentiation. The findings have important conservational implications, since E. moseleyi is far less abundant than E. chrysocome, but more populations may warrant an uplisting to endangered status if full species status should be recognized for more subpopulations.

Animals↗

PubMed2006

Contrasting patterns of genetic structure in two species of the coral trout Plectropomus (Serranidae) from east and west Australia: introgressive hybridisation or ancestral polymorphisms.

Inter-specific genetic relationships among regional populations of two species of grouper (Plectropomus maculatus and Plectropomus leopardus) were examined using mitochondrial and nuclear markers. mtDNA revealed contrasting regional inter-specific patterns whilst nuclear markers revealed contrasting patterns among markers, irrespective of region. In eastern Australia (EA) the species form a single mtDNA lineage, but the two species are reciprocally monophyletic in Western Australia (WA). This supports previous evidence for hybridisation between these species on the east coast. WA P. leopardus forms a sister relationship with the EA P. leopardus-maculatus clade while WA P. maculatus is more basal and sister to the P. leopardus lineages, indicating mtDNA does not suffer from incomplete lineage sorting for these species. In contrast, one of three nuclear markers (locus 7-90TG) differentiated the species into two reciprocally monophyletic clades, with no evidence of hybridisation or ancestral polymorphism. The remaining two nuclear markers (2-22 and ETS-2) did not separate these two species, while distinguishing other plectropomid species, suggesting incomplete lineage sorting at these nuclear loci. These results together with coalescence analyses suggest that P. leopardus females have hybridised historically with P. maculatus males and that P. maculatus mitochondria were displaced through introgressive hybridisation and fixation in the P. maculatus founder population on the Great Barrier Reef. The contrasting regional patterns of mtDNA structure may be attributed to Quaternary sea-level changes and shelf width differences driving different reef configurations on each coast. These reef configurations have provided opportunities for local scale interaction and reproduction among species on the narrower EA continental shelves, but not on the broader WA continental shelves.

Animals↗

PubMed1998

MARs mission update.

Genes are organized as chromatin domains and positioned in the nucleus through regions of nuclear matrix association, termed MARs. Although well-studied, the mechanisms regulating expression of the beta-globin locus remain an enigma. Here, we show that certain MAR sequences of the beta-globin locus are conserved and reiterated throughout the genome in association with other genes of the hematopoietic lineage. Further, the density of the MARs within the beta-globin locus and the sharing of these sequences by the various members of this gene cluster suggest that they may provide critical gene regulatory components.

Base Sequence↗

PubMed2006

Multiple promoters control expression of the Yersinia enterocolitica phage-shock-protein A (pspA) operon.

The widely conserved phage-shock-protein A (pspA) operon encodes an extracytoplasmic stress response system that is essential for virulence in Yersinia enterocolitica, and has been linked to other important phenotypes in Escherichia coli, Salmonella enterica and Shigella flexneri. Regulation of pspA operon expression is mediated through a promoter upstream of pspA that depends on sigma factor RpoN (sigma(54)) and the enhancer binding protein PspF. PspA, PspB and PspC, encoded within the pspA operon, also regulate expression by participating in a putative signal transduction pathway that probably serves to modulate PspF activity. All of this suggests that appropriate expression of the pspA operon is critical. Previous genetic analysis of the Y. enterocolitica pspA operon suggested that an additional level of complexity might be mediated by PspF/RpoN-independent expression of some psp genes. Here, an rpoN null mutation and interposon analysis were used to confirm that PspF/RpoN-independent gene expression does originate within the psp locus. Molecular genetic approaches were used to systematically analyse the two large non-coding regions within the psp locus. Primer extension, control region deletion and site-directed mutagenesis experiments led to the identification of RpoN-independent promoters both upstream and downstream of pspA. The precise location of the PspF/RpoN-dependent promoter upstream of pspA was also determined. The discovery of these RpoN-independent promoters reveals yet another level of transcriptional complexity for the Y. enterocolitica pspA operon that may function to allow low-level constitutive expression of psp genes and/or additional regulation under some conditions.

Bacterial Proteins↗

PubMed2003

Rearrangement patterns of JC virus noncoding control region from different biological samples.

The JC virus (JCV) is generally considered the etiological agent of progressive multifocal leukoencephalopathy (PML), a demyelinating brain illness, often associated with immunosuppression and significantly frequent in acquired immunodeficiency syndrome (AIDS) patients. The primary infection by JCV is usually asymptomatic and the virus can remain in a latent status in the kidney. As a consequence of immunological alterations of the host, the virus can show a genetic variability in the noncoding control region (NCCR) due to deletions, duplications, and insertions as compared with the archetype. The NCCR of the archetype strain can be divided into six regions, named boxes A to F. In this study, the authors evaluated the presence of the JCV genome in different biological samples, such as urine, peripheral blood mononuclear cells (PBMCs) and cerebral spinal fluid (CSF) by means of polymerase chain reaction (PCR). After sequencing of the PCR fragments, the NCCR structure of isolated JCV strains was analyzed in order to verify the presence of different viral variants. An analysis of the homology and of the multiple alignment of the obtained sequences in comparison with the archetype strain has been carried out. The results indicated the presence of different rearrangements among the analyzed samples. Whereas in the urine, the NCCR structure always appeared very similar to that of the archetype, in the PBMCs and CSF, the NCCR sequences showed specific and characteristic rearrangements as compared to the archetype. These different rearrangements could be correlated with the emerging of an NCCR organization more suitable for the development of PML.

AIDS-Related Opportunistic Infections↗

PubMed2003

Negative feedback regulation ensures the one receptor-one olfactory neuron rule in mouse.

In the mouse olfactory system, each olfactory sensory neuron (OSN) expresses only one odorant receptor (OR) gene in a monoallelic and mutually exclusive manner. Such expression forms the genetic basis for OR-instructed axonal projection of OSNs to the olfactory bulb of the brain during development. Here, we identify an upstream cis-acting DNA region that activates the OR gene cluster in mouse and allows the expression of only one OR gene within the cluster. Deletion of the coding region of the expressed OR gene or a naturally occurring frame-shift mutation allows a second OR gene to be expressed. We propose that stochastic activation of only one OR gene within the cluster and negative feedback regulation by that OR gene product are necessary to ensure the one receptor-one neuron rule.

Alleles↗

PubMed1998

Retroviral vectors aimed at the gene therapy of human beta-globin gene disorders.

We are focusing on the development of complex retroviral vectors containing human beta-globin gene and beta-LCR for the gene therapy of sickle cell disease and beta-thalassemias. First generation vectors containing mutated splice-sites to insure stability of proviral transfer enabled long-term reconstitution in 10/12 transplanted mice for a least 8 months with high expression levels in 2 out of 3 mice analyzed (5% and 20% murine beta). Transfer and expression were also achieved in secondary recipients (range: 3-11% murine beta). Position independent expression was not observed. In an effort to increase the efficiency of gene transfer and obtain complete reconstitution of recipient mice with exclusively transduced cells while enriching for proviral integration into active chromatin regions, we have incorporated a cassette expressing CD24 or the green fluorescent protein (GFP). Stable transfer to murine bone marrow cells allowed efficient FACS-sorting of pure populations of transduced cells. A family of vectors based on these principles and containing segments of gamma- or delta-globin genes were also designed for systematic analysis of their anti-sickling properties.

Anemia, Sickle Cell↗

PubMed1998

mtDNA haplogroup X: An ancient link between Europe/Western Asia and North America?

On the basis of comprehensive RFLP analysis, it has been inferred that approximately 97% of Native American mtDNAs belong to one of four major founding mtDNA lineages, designated haplogroups "A"-"D." It has been proposed that a fifth mtDNA haplogroup (haplogroup X) represents a minor founding lineage in Native Americans. Unlike haplogroups A-D, haplogroup X is also found at low frequencies in modern European populations. To investigate the origins, diversity, and continental relationships of this haplogroup, we performed mtDNA high-resolution RFLP and complete control region (CR) sequence analysis on 22 putative Native American haplogroup X and 14 putative European haplogroup X mtDNAs. The results identified a consensus haplogroup X motif that characterizes our European and Native American samples. Among Native Americans, haplogroup X appears to be essentially restricted to northern Amerindian groups, including the Ojibwa, the Nuu-Chah-Nulth, the Sioux, and the Yakima, although we also observed this haplogroup in the Na-Dene-speaking Navajo. Median network analysis indicated that European and Native American haplogroup X mtDNAs, although distinct, nevertheless are distantly related to each other. Time estimates for the arrival of X in North America are 12,000-36,000 years ago, depending on the number of assumed founders, thus supporting the conclusion that the peoples harboring haplogroup X were among the original founders of Native American populations. To date, haplogroup X has not been unambiguously identified in Asia, raising the possibility that some Native American founders were of Caucasian ancestry.

Asia, Western↗

PubMed2004

Mitochondrial gene diversity in the common vole Microtus arvalis shaped by historical divergence and local adaptations.

The phylogeography of the common vole (Microtus arvalis) was examined by analysing mitochondrial DNA (mtDNA) sequence variation in 1044 base pairs (bp) of the cytochrome b (cytb) gene and in 322 bp of the control region (ctr) among 106 individuals from 58 locations. The geographical distribution of four previously recognized cytb evolutionary lineages in Europe was refined and a new lineage was found in southern Germany. All lineages were distributed allopatrically, except in one sample that was probably located in a contact zone. The occurrence of several lineages in the Alps is in keeping with their recent recolonization from distinct sources. The translation of 84 cytb DNA sequences produced 33 distinct proteins with relationships that differed from those of the DNA haplotypes, suggesting that the mtDNA lineages did not diverge in response to selection. In comparison with M. agrestis, a neutrality test detected no overall evidence for selection in the cytb gene, but a closer examination of a structural model showed that evolutionarily conserved and functionally important positions were often affected. A new phylogeographical test of random accumulation of nonsynonymous mutations generated significant results in three lineages. We therefore conclude that the molecular diversity of cytb in M. arvalis is overall the result of the demographic history of the populations, but that there have been several episodes of local adaptation to peculiar environments.

Adaptation, Biological↗

PubMed2001

Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus.

Methylation of histones at specific residues plays an important role in transcriptional regulation. Chromatin immunoprecipitation of dimethylated lysine 9 on histone H3 across 53 kilobases of the chicken beta-globin locus during erythropoiesis shows an almost complete anticorrelation between regions of elevated lysine 9 methylation and acetylation. Lysine 9 is methylated most over constitutive condensed chromatin and developmentally inactive globin genes. In contrast, lysine 4 methylation of histone H3 correlates with H3 acetylation. These results lead us to propose a mechanism by which the insulator in the beta-globin locus can protect the globin genes from being silenced by adjacent condensed chromatin.

Acetylation↗

PubMed1998

Trading genes along the silk road: mtDNA sequences and the origin of central Asian populations.

Central Asia is a vast region at the crossroads of different habitats, cultures, and trade routes. Little is known about the genetics and the history of the population of this region. We present the analysis of mtDNA control-region sequences in samples of the Kazakh, the Uighurs, the lowland Kirghiz, and the highland Kirghiz, which we have used to address both the population history of the region and the possible selective pressures that high altitude has on mtDNA genes. Central Asian mtDNA sequences present features intermediate between European and eastern Asian sequences, in several parameters-such as the frequencies of certain nucleotides, the levels of nucleotide diversity, mean pairwise differences, and genetic distances. Several hypotheses could explain the intermediate position of central Asia between Europe and eastern Asia, but the most plausible would involve extensive levels of admixture between Europeans and eastern Asians in central Asia, possibly enhanced during the Silk Road trade and clearly after the eastern and western Eurasian human groups had diverged. Lowland and highland Kirghiz mtDNA sequences are very similar, and the analysis of molecular variance has revealed that the fraction of mitochondrial genetic variance due to altitude is not significantly different from zero. Thus, it seems unlikely that altitude has exerted a major selective pressure on mitochondrial genes in central Asian populations.

Africa↗

PubMed2004

The utility of the neglected mitochondrial control region for evolutionary studies in lepidoptera (insecta).

The insect mitochondrial control region (=AT-rich-region) is a rarely used genetic marker in phylogeographic studies and population genetic surveys. Reasons for this are that the high AT content and the presence of tandem repeats and indels pose technical and analytical problems. We provide a new pair of primers and the first taxonomically wide-scale description of control region (CR) structure in an insect order after sequencing it in 31 lepidopteran species. We assessed levels of variation occurring in the CR and cytochrome oxidase I (COI) by sequencing and comparison. Intrapopulation analyses in five species of butterflies showed that CR was more variable than COI. Interpopulation variation from three populations of Erebia triaria and E. palarica was slightly lower in the CR than COI with regard to single-nucleotide polymorphisms, but the results were concordant between both markers and highly congruent with regard to population differentiation. Using 15 species of Satyrinae we found that the CR has the same, or stronger, phylogenetic resolution as COI. Our results indicate that the CR can be of importance in addition to COI in population genetic studies. Alignments for the whole CR are direct and unambiguous at the intraspecific level. Indels show phylogenetic signal, but make this marker more complex to use than COI for higher phylogenetic analyses. Nevertheless, alignments at the generic level are straightforward over one part of the CR. The combination CR+COI appears to be a very promising phylogenetic tool to resolve fast-evolving species-level phylogenies.

Animals↗