Search PubMed⌕ Search

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.

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

At least 829 records · Page 46Linked to original sources
PubMed2001

Historical population size change of bowhead whales inferred from DNA sequence polymorphism data.

Nucleotide sequence data from the mitochondrial control region were used from a phylogenetic context to investigate the long-term history of a population of bowhead whales (Balaena mysticetus). In addition, the coalescence time of these sequences was used to estimate the age of the inferred patterns of population size change. The results indicate that mitochondrial genetic polymorphism was not affected by a recent bottleneck that occurred near the turn of the 20th century, thereby preserving the signature of historical population size change in the mitochondrial genome. Further analysis showed that this population underwent an expansion initiated in the Middle to Late Pleistocene. As such, early Holocene changes in Arctic sea ice distribution appear to have had little influence on patterns of genetic variability in this population.

Animals↗
PubMed2006

Comparative analysis of complete mitochondrial DNA control region of four species of Strigiformes.

The sequence of the whole mitochondrial (mt) DNA control region (CR) of four species of Strigiformes was obtained. Length of the CR was 3,290 bp, 2,848 bp, 2,444 bp, and 1,771 bp for Asio flammeus, Asio otus, Athene noctua, and Strix aluco, respectively. Interestingly, the length of the control region was maximum in Asio flammeus among all the avian mtDNA control regions sequenced thus far. In addition, the base composition and organization of mtDNA CR of Asio flammeus were identical to those reported for other birds. On the basis of the differential frequencies of base substitutions, the CR may be divided two variable domains, I and III, and a central conserved domain, II. The 3' end of the CR contained many tandem repeats of varying lengths and repeat numbers. In Asio flammeus, the repeated sequences consisted of a 126 bp sequence that was repeated seven times and a 78 bp sequence that was repeated 14 times. In Asio otus, there were also two repeated sequences, namely a 127 bp sequence that was repeated eight times and a 78 bp sequence that was repeated six times. The control region of Athene noctua contained three sets of repeats: a 89 bp sequence that was repeated three times, a 77 bp sequence that was repeated four times, and a 71 bp sequence that was repeated six times. Strix aluco, however, had only one repeated sequence, a 78 bp sequence that was repeated five times. The results of this study seem to indicate that these tandem repeats may have resulted from slipped-strand mispairing during mtDNA replication. Moreover, there are many conserved motifs within the repeated units. These sequences could form stable stem-loop secondary structures, which suggests that these repeated sequences play an important role in regulating transcription and replication of the mitochondrial genome.

Animals↗
PubMed2006

Geographic distribution of an extinct equid (Equus hydruntinus: Mammalia, Equidae) revealed by morphological and genetical analyses of fossils.

Equus hydruntinus inhabited Europe and the Middle East for more than 300 000 years. For a long time, palaeontological data failed to place E. hydruntinus into the equid phylogenetic tree, confronted with the fact that it shares primitive Equus characters with both zebras and asses, and derived characters with asses and hemiones. However, the study of a recently discovered skull points to a relationship with hemiones. Extraction of DNA from ancient samples from Crimea (E. hydruntinus) and Iran (E. cf. hydruntinus) yielded 134-288 bp of the mtDNA control region and 143 bp of the cytochrome b gene. This DNA analysis supports the proximity of E. hydruntinus and Equus hemionus suggested by skull and limb bone analyses, and rejects proximity to either Equus burchelli or the asses suggested by tooth morphology. Dental morphology may thus be of poor taxonomical value if used alone for establishing equid phylogenetic relationships. Furthermore, the small genetic distance between E. cf. hydruntinus of Iran and the classical E. hydruntinus of Crimea suggests that both samples belong to the same species. Accordingly, the geographic range of E. hydruntinus -- until now believed to be restricted to Europe, Israel, and Turkey -- can be extended towards East as far as Iran.

Animals↗
PubMed2002

Tandem repeats and length variation in the mitochondrial DNA control region of Epirrita autumnata (Lepidoptera: Geometridae).

The organization of the mitochondrial DNA (mtDNA) control region (CR) of the autumnal moth, Epirrita autumnata, is described. The E. autumnata CR presents a distinct type of lepidopteran CR with domains of non-repetitive and repetitive sequences. The CRs show considerable length variation owing to a variable number of short approximately 29-bp sequence blocks that are repeated between 6 and 14 times in tandem. The organization of such a tandem array is unique among the insect CRs examined so far. Furthermore, the E. autumnata CR, which may reach 1075 bp in length, is considerably longer than previously reported lepidopteran CRs, which reach 311-499 bp in length. Like other lepidopteran CRs, the E. autumnata CR contains two long homopolymer runs that may be involved in mtDNA replication and (or) transcription.

Animals↗
PubMed2001

Histone acetylation beyond promoters: long-range acetylation patterns in the chromatin world.

Histone acetylation is an important regulatory mechanism that controls transcription and diverse nuclear processes. While great progress has been made in understanding how localized acetylation and deacetylation control promoter activity, virtually nothing is known about the consequences of acetylation throughout entire chromosomal regions. An increasing number of genes have been found to reside in large chromatin domains that are controlled by regulatory elements many kilobases away. Recent studies have shown that broad histone acetylation patterns are hallmarks of chromatin domains. The purpose of this review is to discuss how such patterns are established and their implications for regulating gene expression.

Acetylation↗
PubMed2006

Concerted evolution of duplicated control regions within an ostracod mitochondrial genome.

The luminescent marine ostracod Vargula hilgendorfii comprises distinct populations around the Japanese islands. Its mitochondrial DNA is unusual, with duplicated control regions (CRs; CR#1 and CR#2). We determined the sequences of ostracod CRs in 7 different populations. The sequences of CR#1 and CR#2 within any population were extremely similar, above 99.7%; moreover, their derived evolutionary tree indicates that the pairs of CRs have evolved in concert within each mitochondrial genome. These results suggest that an exact replication mechanism controls the concerted evolution of CRs.

Animals↗
PubMed2001

Targeted histone acetylation and altered nuclease accessibility over short regions of the pea plastocyanin gene.

The chromatin structure of the pea plastocyanin gene (PetE) was examined at three different transcriptional states by investigating the acetylation states of histones H3 and H4 and the nuclease accessibility of the gene in pea roots, etiolated shoots, and green shoots. The acetylation states of histones associated with different regions of PetE were analyzed by chromatin immunoprecipitation with antibodies specific for acetylated or nonacetylated histone H3 or H4 tails, followed by polymerase chain reaction quantification. Comparison of pea tissues indicated that histone hyperacetylation was associated with increased PetE transcription in green shoots. Moreover, hyperacetylation of both histones H3 and H4 was targeted to the enhancer/promoter region in green shoots, suggesting that only specific nucleosomes along the gene were modified. Time-course digestions of nuclei with micrococcal nuclease and DNaseI indicated that the enhancer/promoter region was more resistant to digestion in the inactive gene in pea roots than was the same region in the active gene in shoots, whereas the transcribed region of PetE was digested similarly among the tissues. This finding indicates that transcription is accompanied by changes in the nuclease accessibility of the enhancer/promoter region only. Moreover, these results indicate that the changes in nuclease accessibility are organ specific, whereas histone hyperacetylation is light dependent, and they suggest that changes in nuclease accessibility precede histone hyperacetylation during PetE activation.

Acetylation↗
PubMed2006

Phylogeography and Pleistocene refugia of the adder (Vipera berus) as inferred from mitochondrial DNA sequence data.

In order to contribute to the debate about southern glacial refugia used by temperate species and more northern refugia used by boreal or cold-temperate species, we examined the phylogeography of a widespread snake species (Vipera berus) inhabiting Europe up to the Arctic Circle. The analysis of the mitochondrial DNA (mtDNA) sequence variation in 1043 bp of the cytochrome b gene and in 918 bp of the noncoding control region was performed with phylogenetic approaches. Our results suggest that both the duplicated control region and cytochrome b evolve at a similar rate in this species. Phylogenetic analysis showed that V. berus is divided into three major mitochondrial lineages, probably resulting from an Italian, a Balkan and a Northern (from France to Russia) refugial area in Eastern Europe, near the Carpathian Mountains. In addition, the Northern clade presents an important substructure, suggesting two sequential colonization events in Europe. First, the continent was colonized from the three main refugial areas mentioned above during the Lower-Mid Pleistocene. Second, recolonization of most of Europe most likely originated from several refugia located outside of the Mediterranean peninsulas (Carpathian region, east of the Carpathians, France and possibly Hungary) during the Mid-Late Pleistocene, while populations within the Italian and Balkan Peninsulas fluctuated only slightly in distribution range, with larger lowland populations during glacial times and with refugial mountain populations during interglacials, as in the present time. The phylogeographical structure revealed in our study suggests complex recolonization dynamics of the European continent by V. berus, characterized by latitudinal as well as altitudinal range shifts, driven by both climatic changes and competition with related species.

Animals↗
PubMed2006

Late Pleistocene divergence and subsequent population expansion of two closely related fish species, Japanese anchovy (Engraulis japonicus) and Australian anchovy (Engraulis australis).

Climatic oscillations during the Pleistocene ice ages produced great changes in species' geographical distribution and abundance, which could be expected to have genetic consequences. Living in the temperate upwelling zones of the northwestern Pacific, Japanese anchovy (Engraulis japonicus) might have been affected by these severe climatic oscillations. To investigate the effects of Pleistocene climatic changes on the evolution in Japanese anchovy, fragments of 522 bp at the 5' end of mitochondrial DNA control region were sequenced for 241 individuals from 13 localities and 37 individuals of Australian anchovy. Japanese anchovy and Australian anchovy are reciprocally monophyletic and a late Pleistocene transequatorial divergence between the two species was indicated. High levels of haplotype diversity (>0.99) were found for all samples, indicating a high level of genetic diversity. Analyses of molecular variance and the conventional population statistic F(ST) revealed no significant genetic structure throughout the range of Japanese anchovy. Both mismatch distribution analyses and neutrality tests suggested a late Pleistocene population expansion for both Japanese anchovy (79,000-317,000 years ago) and Australian anchovy (45,000-178,000 years ago).

Animals↗
PubMed2006

Population structure and gene flow among wild populations of the black muntjac (Muntiacus crinifrons) based on mitochondrial DNA control region sequences.

The black muntjac (Muntiacus crinifrons) is a rare species endemic to China and its current distribution is confined to partial mountain ranges in eastern China. To assess the population structure and gene flow among the extant populations, we sequenced a portion of the mitochondrial control region (424 bp) for 47 samples collected from its current three large populations (Huangshan, Tiammushan and Suichang). A total of 18 unique haplotypes were defined based on 22 polymorphic sites. Of these haplotypes, 15 ones were population-specific and only one haplotype was shared among the three populations. Significant genetic differentiation was detected between Suichang and Huangshan populations (ø(ST)=0.1677, P<0.001) or between Suichang and Tianmushan populations (ø(ST)=0.2002, P<0.001), indicating that the Suichang population may be spatially structured from other two populations along matriline. The Mantel test revealed that this significant differentiation was not driven by geographic distance (P=0.14), implying that genetic divergence of Suichang population might result from recent human disturbances. Phylogenetic analyses suggested the mitochondrial control region haplotypes were split into two well divergent clades (Clade I and Clade II). Interestingly, the two distinct haplotype clades were found to coexist in Suichang area. The nested clade analysis revealed a significant phylogeographic structure among the black muntjac populations (total cladogram: chi2=18.68; P<0.001), which was inferred to result from past fragmentation followed by range expansion. The population expansion was supported by the analysis of mismatch distribution and the tests of neutrality. Therefore, we suggest that the coexistence of distinct haplotypes in Suichang population was induced by historical population expansion after fragmentation and that the current genetic differentiation should be attributed to the reduction of female-mediated gene flow due to recent habitat fragmentation and subsequent loss.

Animals↗
PubMed1995

Evolutionary duplication of a hepatic control region in the human apolipoprotein E gene locus. Identification of a second region that confers high level and liver-specific expression of the human apolipoprotein E gene in transgenic mice.

We have identified a second hepatic control region (HCR-2) in the human apolipoprotein (apo) E gene locus that confers liver expression of the human apoE gene in transgenic mice. This HCR-2 sequence is located 27 kilobases downstream of the apoE gene and 10 kilobases downstream of the previously described liver-specific enhancer (HCR-1). Nucleotide sequence analysis of the HCR-2 region revealed a sequence that shares 85% identity to the functional 319-base pair domain of HCR-1. To test its activity, transgenic mice were prepared with a fusion construct containing a human apoE gene fragment, which is not normally expressed in the liver, ligated to a 632-base pair region containing the HCR-2 sequence. This construct resulted in high levels of liver-specific apoE transgene expression, indicating that HCR-2 can function as a hepatic enhancer and has an activity similar to that of HCR-1. Hence, these findings suggest that there are at least two hepatic control regions, HCR-1 and HCR-2, capable of controlling the liver expression of this human apolipoprotein gene locus.

Animals↗
PubMed1998

Identification of upstream regulatory elements that repress expression of adult beta-like globin genes in a primitive erythroid environment.

Our investigations have focused on localizing cis-elements responsible for the down regulation of the adult beta-like globin genes (delta and beta) in immature, or primitive erythroid tissues. We studied their activity after transfection into K562 cells, an erythroleukemia cell line with an embryonic-fetal phenotype. Analyzed DNA sequences included delta and beta 5' flanking regions extending from approximately -500 to +50bp (promoter regions), truncated delta and beta 5' flanking regions extending from approximately -250 to +50 bp, and chimeric promoter constructions, which consisted of a distal delta or beta fragment fused to a proximal beta or delta sequence. In CAT reporter constructions no appreciable level of CAT activity was supported by the beta globin promoter, and only low level activity by the delta promoter. Truncation of the beta globin promoter led to a 2-3 fold increase in promoter activity. In contrast, deletion of the upstream portion of the delta promoter led to a 10 fold decrease in expression. Coupling of the upstream beta globin sequence from approximately -500 to -250 bp to the truncated delta promoter fragment led to complete extinction of transcription activity, consistent with a negative regulatory effect of the beta globin gene upstream element(s). Fusion of the upstream portion of the delta promoter to the truncated beta globin promoter yielded a modest increase in promoter strength relative to the truncated beta gene promoter, indicating the presence of a positive transcriptional element(s) in the upstream delta globin regulatory region. Site-directed mutagenesis of binding sites for the repressor proteins BP1 and BP2 in the upstream portion of the beta globin gene flanking region led to a 4-6 fold increase in promoter activity. DNase I footprinting of the upstream delta-globin region revealed protected sequences corresponding to consensus binding sites for GATA-1 and BP2. These results confirm that sequences in the upstream promoter region of the adult beta globin gene contribute to its factor-mediated suppression early in development and then may modulate its expression at a later stage.

Binding Sites↗
PubMed2005

Genome-wide linkage in three Dutch families maps a locus for abdominal aortic aneurysms to chromosome 19q13.3.

OBJECTIVES: Elucidation of the genetic background of familial abdominal aortic aneurysm (AAA) suggests a genetic etiology. METHODS AND RESULTS: We carried out a genome-wide scan in three Dutch families with four or five affected siblings. Suggestive loci were further studied by subsequent fine mapping of the locus performed in 101 affected sib-pairs. The genome-wide scan was performed with 400 DNA markers and results were given as non-parametric, multipoint linkage scores (NPL). We observed a suggestive linkage for AAA (NPL score 3.25 at D19S902, 72.72 cM) on chromosome 19q in the three families. After fine mapping on chromosome 19, the NPL score became nominal in the 101 affected sib-pairs. A separate analysis of the three families with fine mapping revealed a peak with significant evidence for linkage (NPL score 3.95 at D19S904, 78.08 cM) on chromosome 19q. This peak was situated to the right compared to the region found in a previously published article for familial AAA on chromosome 19q. CONCLUSIONS: Our results identified a candidate locus in three Dutch families with AAA at chromosome 19q13.3. Separate analysis of these three families provides evidence for genetic heterogeneity.

Aged↗
PubMed2004

The complete mitochondrial genomes sequences of Asio flammeus and Asio otus and comparative analysis.

The complete mitochondrial genomes of Asio flammeus and Asio otus were sequenced and found to span 18858 bp and 18493 bp, respectively. It is surprising to find the former to be the largest among all avian mitochondrial genomes sequenced so far. The two genomes have very similar gene order with that of Gallus gallus, neither contains the pseudo control region, but both have a single extra base, namely Cytidine, at position 174 in ND3 gene. The control regions of Asio flammeus and Asio otus' mitochondrial genomes span 3288 bp and 2926 bp respectively, which are the longest among vertebrates except for Myxine glutinosa and contribute to the large size of two genomes. The 3' end of the control region of Asio flammeus and Asio otus contains many tandemly repeated sequences, which are highly similar to a putative control element, i.e. Mt5, and may form stable stem-loop secondary structures. Such repeated sequences probably play an important role in regulating transcription and replication of mitochondrial genome. Our results may provide important clues for uncovering the origin and evolution mechanisms of mitochondrion genome.

Animals↗
PubMed1999

Analysis of control elements for position-independent expression of human alpha-lactalbumin YAC.

A major problem in the production of transgenic animal bioreactors using microinjections is the low production rate of high-expressing transgenic animals due to the position effect. We previously reported that transgenic rats carrying the 210 kb yeast artificial chromosome (YAC) including the human alpha-lactalbumin gene express the transgene in a position-independent manner. The 210 kb YAC was thought to have all the elements necessary for position-independent expression. In this paper, we constructed fragmented YAC clones and a cosmid clone, and produced transgenic rats to analyze these elements. Transgenic rats with both the 50 kb upstream and downstream regions of the alpha-lactalbumin gene had position-independent expression. Transgenic rats with the 20 kb upstream and downstream regions, however, had position-dependent expression. Therefore, all the elements necessary for position-independent expression are thought to be located in the 50 kb upstream to 50 kb downstream region of the alpha-lactalbumin gene. Furthermore, we replaced the human alpha-lactalbumin promoter with the bovine alphaS1-casein promoter in the 210 kb YAC and produced transgenic rats. Position-dependent expression was observed. The elements required for position-independent expression of the bovine alphaS1-casein gene are different from those required for the human alpha-lactalbumin gene, despite the fact that the two genes have the same tissue and developmental specificity.

Animals↗
PubMed2003

Hierarchical interactions control CD4 gene expression during thymocyte development.

CD4 gene regulation provides an ideal model for understanding the molecular events that drive T cell development. In this paper we use a transgenic approach to identify a CD4 LCR containing a stage-specific thymocyte enhancer (TE) and a region that protects against position effect variegation. Surprisingly, the TE acts indirectly through the previously defined proximal enhancer and is strongly induced upon commitment to the T cell lineage. We also describe a complex series of hierarchical control element interactions that orchestrate CD4 expression throughout thymopoiesis. These data provide a framework for understanding how CD4 gene expression is regulated in response to lineage commitment decisions.

Animals↗
PubMed2006

The complete mitochondrial genome sequence and characterization of single-nucleotide polymorphisms in the control region of the Asian seabass (Lates calcarifer).

We determined the complete mtDNA nucleotide sequence of Lates calcarifer using the shotgun sequencing method. The mitochondrial DNA (mtDNA) was 16,535 base pairs (bp) in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major noncoding control region (CR). The CR was unusually short at only 768 bp. A striking feature of the mitochondrial genome was the high G+C content (46.1%), which is among the highest in fish. The gene order was identical to that of a typical vertebrate. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 30 fish species representing 14 suborders clearly showed Lates calcarifer was located in the cluster of fish species from the order Perciformes, supporting the traditional systematic classification. We characterized single-nucleotide polymorphisms (SNPs) in the CR by sequencing the complete CR of 25 individuals obtained from Australia and Singapore. A total of 68 SNPs were detected. Eighteen SNPs were fixed with alternative nucleotides in Australian and Singapore seabass, and these SNPs could be used for differentiating fish from the two countries.

Animals↗
PubMed2005

Molecular phylogeny of avian genus Syrmaticus based on the mitochondrial cytochrome B gene and control region.

Mitochondrial DNA cytochrome b (cyt b) and control region (CR) nucleotide sequences were used to study the molecular phylogeny of the genus Syrmaticus. We found that the substitution rates among the three codon positions of cyt b were heterogeneous and the transition-transversion ratio was highly biased. As to CR sequences of the genus, most variable sites were in the peripheral domains. All molecular phylogenetic trees based on the two genes showed that: 1) the Syrmaticus was monophyletic and included five species with the following cladistic relationship: (S. reevesii, (S. soemmerringii, (S. mikado, (S. humiae and S. ellioti)))). Using the TN genetic distance of cyt b, we inferred the divergence time of the five species according to putative molecular clock and found that values were largely in agreement with the geological scenarios. The origin and speciation processes of the studied group were inferred by combining molecular and biogeographical evidences.

Animals↗