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Locus Control Region (0):
Recent article
Locus Control Region
Abstract
We show that Ldb1 controls gene expression at multiple levels. Ldb1 stabilizes its erythroid complex partners on β-globin chromatin, even though it is not one of the DNA-binding components. In addition, Ldb1 is necessary for enrichment of key transcriptional components in the locus, including P-TEF...
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PMID: 20570862
PDF is available here.
PDF is available here.
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Abstract
The complete nucleotide sequence of mitochondrial genome of the Great bustard (Otis tarda) was determined by using polymerase chain reaction (PCR) method. The genome is 16,849 bp in size, containing 13 protein-coding, 2 ribosomal and 22 transfer RNA genes. Sequences of the tRNA genes can be folded i...
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PMID: 19823949
PDF is available here.
PDF is available here.
Abstract
We generated CD4-specific Th2 LCR-deficient (cLCR KO) mice using Cre-LoxP recombination. The number of CD4 T cells in the cLCR KO mouse was comparable to that in wild-type mice. The expression of Th2 cytokines was dramatically reduced in in vitro-stimulated naïve CD4 T cells. Deletion of the LCR le...
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PMID: 20483988
PDF is available here.
PDF is available here.
Abstract
Abstract
In IGHD patients, promoter SNPs 6, 8 and 9 were associated with height and IGF-1 levels. In controls, SNPs 6 and 11 were associated with height. Homozygosity for the minor allele of SNP 9, associated with lower IGF-I levels in patients, was significantly more frequent among patients than among contr...
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PMID: 20190537
PDF is available here.
PDF is available here.
Veterinary Pathology (46)4 2009
Abstract
Papillomas and fibropapillomas may occur in the skin and in different organs in animals. Ten different genotypes of bovine papillomavirus (BPV) have been identified. BPV-1 through BPV-10 are all strictly species-specific, but BPV-1/2 may also infect other species such as equids, inducing fibroblasti...
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PMID: 19276046
PDF is available here.
PDF is available here.
Human Mutation (30)2 2009
Abstract
We have constructed an updated comprehensive phylogeny of global human mtDNA variation, based on both coding- and control region mutations. This complete mtDNA tree includes previously published as well as newly identified haplogroups, is easily navigable, will be continuously and regularly updated...
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PMID: 18853457
PDF is available here.
PDF is available here.
Animal Genetics (40)1 2009
Abstract
We investigated the genetic diversity and population structure of forest musk deer by analysing a 582-bp fragment of the mitochondrial DNA (mtDNA) control region (CR) in three captive breeding populations in Sichuan Province, China. Ninety-four variable sites and 27 haplotypes were observed in 109 i...
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PMID: 19076935
PDF is available here.
PDF is available here.
Abstract
We explored the activity of human beta-globin HS5, the orthologue of the CTCF-dependent chicken HS4 insulator. An extra copy of HS5 placed between the beta-globin locus control region (LCR) and downstream genes on a transgene fulfills the classic predictions for an enhancer-blocker. Ectopic HS5 does...
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PMID: 19074263
PDF is available here.
PDF is available here.
Iubmb Life (60)12 2008
Abstract
We discuss the significance of ACH formation, provide an overview of the proteins implicated in chromatin looping at the beta-globin locus, and evaluate the relationship between nuclear organization and beta-globin gene expression.
(c) 2008 IUBMB....
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PMID: 18767169
PDF is available here.
PDF is available here.
Human Mutation (29)12 2008
Abstract
We have identified a novel large control region deletion spanning positions 16154 to 16307 (m.16154_16307del154). The population prevalence of this deletion is low, since it was only observed in 1 out of over 120,000 mtDNA genomes studied. The deletion is present in a nonheteroplasmic state, and was...
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PMID: 18629826
PDF is available here.
PDF is available here.
EMBO Reports (9)9 2008
Abstract
We show that hGH-N activation is accompanied by positioning of the hGH-N promoter to this LCR transcriptional domain. Selectively blocking LCR transcription inhibits the formation of this active 'looped' conformation. Thus, HSI is crucial for establishing a domain of noncoding PolII transcription, a...
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PMID: 18636089
PDF is available here.
PDF is available here.
Abstract
We propose that erythroid specific factors together with ubiquitous proteins mediate a change in chromatin configuration that juxtaposes the globin genes and the LCR. The proximity then facilitates the transfer of activities from the LCR to the globin genes. In this article we will discuss recent ob...
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PMID: 18500726
PDF is available here.
PDF is available here.
Abstract
In this study, the mitochondrial DNA (mtDNA) control region and the mitochondrial cytochrome b gene of stranded Indo-Pacific humpback dolphin (Sousa chinensis) samples from the Pearl River Estuary and Xiamen waters were sequenced and analyzed. The result of mtDNA control region revealed 34 variable...
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PMID: 18721786
PDF is available here.
PDF is available here.
Abstract
We analyzed expression and H3 K79 modification levels of wild-type (WT) and transcriptionally impaired beta-globin mutant genes during erythroid differentiation. Analysis of fractionated erythroid cells derived from WT/Delta locus control region (LCR) heterozygous mice reveals no significant H3 K79...
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PMID: 18441235
PDF is available here.
PDF is available here.
Animal Genetics (39)3 2008
Abstract
We investigated the genetic diversity of P. monodon (n = 355) from eight geographical regions by genotyping at 10 microsatellite loci. The average observed heterozygosity at various loci ranged from 0.638 to 0.743, indicating a high level of genetic variability in this region. Significant departures...
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PMID: 18454804
PDF is available here.
PDF is available here.
Abstract
We systematically regenerate functional beta-globin intron 2 elements that rescue LCR activity directed by 5'HS3. Evaluation in transgenic mice demonstrates that an Oct-1 binding site and an enhancer in the intron cooperate to increase expression levels from LCR globin transgenes. Replacement of the...
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PMID: 18404216
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)7 2008
Abstract
We have addressed the influence of transgene copy number (CN) on expression of hCD2 transgenes. CN reduction resulted in a decrease, increase or no effect on variegation depending upon the site of integration. This finding argues that repeat-induced gene silencing is not the principle cause of hCD2...
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PMID: 18296483
PDF is available here.
PDF is available here.
Abstract
We have employed a boundary trap assay, an enhancer activity assay, chromatin immunoprecipitations, and chromosome conformation capture analyses to demonstrate that the two HMR silencer elements are in close proximity and functionally communicate with one another in vivo. We further show that silenc...
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PMID: 18195043
PDF is available here.
PDF is available here.
Abstract
We sequenced the Ggamma- and Agamma-globin gene promoters and the DNase I-2 hypersensitive sites in the locus control regions (HS2-LCR) of patients with HbF level disparities as compared to their betaS haplotypes. Sixty-four (51.2%) patients had CAR/Ben genotype; 36 (28.8%) Ben/Ben; 18 (14.4%) CAR/C...
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PMID: 18235968
PDF is available here.
PDF is available here.
Human Gene Therapy (19)2 2008
Abstract
We constructed helper-dependent, fiber-chimeric adenoviral vectors that efficiently transduce human hematopoietic stem cells. We found that vectors carrying a 23-kb fragment of the beta-globin locus control region (LCR) flanked by adeno-associated virus inverted terminal repeats (Ad.LCR) preferentia...
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PMID: 18177253
PDF is available here.
PDF is available here.
Advances in Genetics (61) 2008
Abstract
We will review the beta-globin locus as a model system to study long-range activation, briefly describe the different models for long-range activation, and summarize the recent findings that the LCR of the beta-globin locus is in close proximity to the active promoters. Although it is now firmly est...
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PMID: 18282504
PDF is available here.
PDF is available here.
Experimental Cell Research (314)1 2008
Abstract
We explored the similarities and differences in the regulatory effects between alpha-upstream regulatory element (alpha-URE) and beta-locus control region (beta-LCR). The results showed that, after exchange, the developmental switching modes of human alpha- and beta-like globin genes had changed, wi...
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PMID: 17996867
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
About 100 variable positions were identified within the four specimens in each halibut species, with the control regions as the most variable parts of the genomes (10 times that of the mitochondrial ribosomal DNA). Due to tandem repeat arrays, the control regions have unusually large sizes compared...
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PMID: 18186947
PDF is available here.
PDF is available here.
Abstract
Evidences indicate that locus control region (LCR) of beta-globin spatially closes to the downstream active gene promoter to mediate the transcriptional activation by looping. DNA binding proteins may play an important role in the looping formation. NF-E2 is one of the key transcription factors in b...
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PMID: 18308612
PDF is available here.
PDF is available here.
Molecular Ecology (17)1 2008
Abstract
We report rapid change of morphology and mitochondrial genes in white-footed mice (Peromyscus leucopus) in the Chicago (Illinois, USA) region. We sequenced mitochondrial DNA COX2 from 55 museum skins of white-footed mice caught in the Chicago area since 1855 and from 44 mice recently trapped in the...
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PMID: 17892465
PDF is available here.
PDF is available here.
Abstract
We show here the major roles played by 2 lesser-known locus control region elements, termed HS1 and HS4. Partial deletions within HS4 markedly reduce in vivo globin expression requiring multiple VC per cell to correct the anemia. Most strikingly, addition of HS1 to HS2-3-4 increases globin expressio...
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PMID: 17921347
PDF is available here.
PDF is available here.
Molecular Cell (28)5 2007
Abstract
We show that NLI/Ldb1 and erythroid-binding partners GATA-1/SCL/LMO2 bind in vivo to the beta-globin locus control region (LCR). The C-terminal LIM interaction domain of NLI is required for formation of the complex on chromatin. Loss of the LIM domain converts NLI into a dominant-negative inhibitor...
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PMID: 18082606
PDF is available here.
PDF is available here.
Abstract
We have previously reported that a 2.1-kb homology (H) sequence, conserved between mouse and human, regulates the odorant receptor (OR) gene MOR28 in transgenic mice. Here, we narrowed down the essential sequences of the H to a core of 124 bp by using a transient expression system in zebrafish embry...
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PMID: 18077433
PDF is available here.
PDF is available here.
Clinical Genetics (72)6 2007
Abstract
We evaluated the contribution of 67 single nucleotide polymorphisms (SNPs) within the beta-globin gene cluster to disease severity in groups of 207 mild- and 305 severe unrelated patients from Thailand with Hemoglobin E (HbE)/beta(0)-thalassemia and normal alpha-globin genes. Our analysis showed tha...
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PMID: 17894837
PDF is available here.
PDF is available here.
Abstract
Mitochondrial DNA sequences of the entire control region were analyzed in 200 unrelated individuals from Macedonia. A total of 163 different haplotypes were found as determined by 177 polymorphic sites. The probability of a random match was calculated as 1:121 (0.83%). The basic phylogenetic structu...
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PMID: 19083765
PDF is available here.
PDF is available here.
Abstract
We compared the pattern of histone acetylation and pol II binding across the beta-globin locus at fetal and adult stages of human development. To make this comparison possible, we introduced an external control into experimental samples in chromatin immunoprecipitation (ChIP) assays. Using this comm...
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PMID: 17881636
PDF is available here.
PDF is available here.
Abstract
We sequenced three complete mitochondrial genomes (one from each of three California populations) and compared them to two published mtDNA genomes from an Asian congener, Tigriopus japonicus. Several features of the mtDNA genome appear to be conserved within the genus: 1) the unique order of the pro...
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PMID: 17855023
PDF is available here.
PDF is available here.
Abstract
We report a novel set of genetic markers in the DNaseI hypersensitive sites comprising the human beta-globin locus chromatin hub (CH), namely HS-111 and 3'HS1. The HS-111 (-21 G>A) and 3'HS1 (+179 C>T) transitions form CH haplotypes, which occur at different frequencies in beta-thalassemia intermedi...
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PMID: 17654503
PDF is available here.
PDF is available here.
Abstract
We intend to briefly describe the progress made in the field and discuss future directions.
(c) 2007 Wiley-Liss, Inc....
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PMID: 17910027
PDF is available here.
PDF is available here.
Abstract
We evaluate these HSs for function. Deletion of HSI, located 5' to the promoter (kb -2.1) had no significant effect on hDBP expression. In contrast, deletion of HSIV and HSV from intron 1 repressed hDBP expression and eliminated copy number dependency without a loss of liver specificity. Chromatin i...
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PMID: 17785430
PDF is available here.
PDF is available here.
Journal of Cell Biology (179)2 2007
Abstract
We provide evidence that mRNA release from the transcription site requires the heptad repeat structure of the C-terminal domain (CTD) of RNA polymerase II. The mammalian CTD, which is essential for normal co-transcriptional maturation of mRNA precursors, comprises 52 heptad repeats. We show that a t...
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PMID: 17938247
PDF is available here.
PDF is available here.
Abstract
We characterize demethylation events of the Th2 cytokine locus control region (LCR). rad50 hypersensitive site 7 (RHS7), a hypersensitive site within this LCR, becomes demethylated in a STAT6-dependent manner and only in cells stimulated under type 2 conditions. Robust demethylation appears to requi...
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PMID: 17940027
PDF is available here.
PDF is available here.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics (24)5 2007
Abstract
One hundred and twenty-six mutations in D-loop region were found in twenty-three patients with familial breast cancer, and four mutations were new. In all of twenty-three patients, thirty-seven mutations were found in D310 which was hot spot of D-loop region in mitochondrial DNA. In these mutations,...
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PMID: 17922420
PDF is available here.
PDF is available here.
Abstract
Genes from the Hox family are involved in the common task of providing nascent embryonic tissues with their positional identity. They are organised in clusters in most species. Mouse Hox genes are regulated in part by gene-proximal regulatory elements, but owe several of their essential properties t...
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PMID: 17870464
PDF is available here.
PDF is available here.
Abstract
BPV-1 DNA is the predominant viral type detected in equine sarcoids and represents the only reported natural cross species infection of papillomaviruses. In this study, nucleotide variations in the LCR and the E2 regions of equine sarcoid-associated BPV-1 were characterised by sequence analysis. Var...
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PMID: 17412385
PDF is available here.
PDF is available here.
Abstract
Duplication of opsin genes has a crucial role in the evolution of visual system. Zebrafish have four green-sensitive (RH2) opsin genes (RH2-1, RH2-2, RH2-3, and RH2-4) arrayed in tandem. They are expressed in the short member of the double cones (SDC) but differ in expression areas in the retina and...
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PMID: 17646658
PDF is available here.
PDF is available here.
Abstract
We extended the distance between the LCR and genes by 2.3 kbp within the context of a yeast artificial chromosome, followed by the generation of transgenic mice (TgM). In these TgM lines, epsilon-globin gene expression decreased by 90%, while the more distantly located gamma- or beta-globin genes we...
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PMID: 17548470
PDF is available here.
PDF is available here.
Abstract
We show that the LCR interacts with multiple liver-specific transcription factors, including hepatocyte nuclear factor 3beta (HNF-3beta), HNF-6alpha, CCAAT/enhancer binding protein alpha (C/EBPalpha), and C/EBPbeta. RNA polymerase II is also recruited to the locus through the LCR. Nongenic transcrip...
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PMID: 17526725
PDF is available here.
PDF is available here.
Journal of Immunology (179)2 2007
Abstract
We find that the CTCF region plays a very minor role in LCR function. In contrast, we report the in vivo function of two additional downstream elements located in the region of the LCR that supports CTCF-independent enhancer-blocking activity in cell culture. Internal deletion of either of these ele...
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PMID: 17617601
PDF is available here.
PDF is available here.
Abstract
We have analyzed the methylation status of regions in the murine beta-like globin locus in uncultured primitive and definitive erythroblasts and other cultured primary and transformed cell types. A large ( approximately 20-kb) domain is hypomethylated only in primitive erythroid cells; it extends fr...
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PMID: 17452448
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)22 2007
Abstract
We used recently established I/11 cells as a model system that faithfully recapitulates the in vivo erythroid differentiation program to study the molecular events that accompany and underlie ACH formation. Upon I/11 cell induction, histone modifications changed, the ACH was formed, and the beta-glo...
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PMID: 17428799
PDF is available here.
PDF is available here.
DNA Sequence (18)3 2007
Abstract
The complete nucleotide sequence of the mitochondrial genome for the Senegal sole Solea senegalensis Kaup was determined. The mitochondrial DNA was 16,659 base pairs (bp) in length. Sequence features of the 13 protein-coding genes, two ribosomal RNAs and 22 transfer RNAs are described. The non-codin...
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PMID: 17454000
PDF is available here.
PDF is available here.
Abstract
We dissected the pathway from GATA-1 binding to cofactor recruitment, chromatin loop formation, and transcriptional activation. Analysis of GATA-1-mediated activation of the beta-globin locus, in which GATA-1 assembles dispersed complexes at the promoters and the distal locus control region (LCR), r...
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PMID: 17438135
PDF is available here.
PDF is available here.
Journal of Neuroscience (27)19 2007
Abstract
We have characterized the activity of three cis-regulatory sequences involved in forebrain expression of vertebrate Dlx genes: upstream regulatory element 2 (URE2), I12b, and I56i. The three regulatory elements display regional and temporal differences in their activities within the lateral ganglion...
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PMID: 17494687
PDF is available here.
PDF is available here.
Abstract
The structure and evolution of the mtDNA control region (CR) and its flanking genes in economically important dipterans from the family Muscidae (Brachycera: Calyptratae), Haematobia irritans, Musca domestica, Atherigona orientalis, and Stomoxys calcitrans are presented in this paper, along with the...
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PMID: 17460806
PDF is available here.
PDF is available here.
Pediatric Research (61)5 Pt 2 2007
Abstract
DNA segments that are separated from the promoter region of a gene by many thousands of bases may nonetheless regulate the transcriptional activity of that gene. This finding has led to the investigation of mechanisms underlying long-range chromatin interactions. In intermitotic cells, chromosomes d...
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PMID: 17413850
PDF is available here.
PDF is available here.
Abstract
We analyzed sequences of mitochondrial DNA control region to provide genetic evidence for the evolution and dispersal scenario of the three species proposed by Fooden and Albrecht [Fooden, J., Albrecht, G.H. 1999. Tail-length evolution in fascicularis-group macaques (Cercopithecidae: Macaca). Int. J...
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PMID: 17321761
PDF is available here.
PDF is available here.
Abstract
We investigated the potential impact of Pleistocene range shifts on phylogeographic patterns using 458 nucleotides of mitochondrial control-region from 102 individuals sampled from 10 populations across the current range. We found 31 haplotypes defined by 33 polymorphic positions. Phylogenetic analy...
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PMID: 17428688
PDF is available here.
PDF is available here.
Trends in Genetics (23)3 2007
Abstract
The formation of genomic loops by proteins bound at sites scattered along a chromosome has a central role in many cellular processes, such as transcription, recombination and replication. Until recently, few such loops had been analyzed in any detail, and there was little agreement about the nature...
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PMID: 17280735
PDF is available here.
PDF is available here.
Journal of Molecular Biology (366)3 2007
Abstract
We expressed GATA-1 in the non-hematopoietic HeLa cell line that does not express other hematopoietic transcription factors but does express GATA-2, GATA-3, and GATA-6. We found that production of the GATA-1 protein resulted in the formation of LCR DNase I HSs 1-4 in their normal locations, and that...
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PMID: 17196618
PDF is available here.
PDF is available here.
EMBO Journal (26)3 2007
Abstract
We find that in somatic cells and tissues, DNA methylation at these ICRs is associated with histone H4-lysine-20 and H3-lysine-9 trimethylation. The unmethylated allele, in contrast, has H3-lysine-4 dimethylation and H3 acetylation. These differential modifications are also detected at maternally me...
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PMID: 17255950
PDF is available here.
PDF is available here.
Molecular Ecology (16)3 2007
Abstract
We assessed the effects of hybridization on the Spanish white-headed ducks, which constitute 25% of the global population of this species, using a panel of eight nuclear intron markers, 10 microsatellite loci, and mtDNA control region sequences. These data allowed parental individuals, F(1) hybrids,...
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PMID: 17257118
PDF is available here.
PDF is available here.
Molecular Ecology (16)3 2007
Abstract
We examined morphometric and genetic differentiation among males of four sympatric putative species within the deep-water genus Diplotaxodon. These taxa live in a narrow-light spectrum environment where only blue light is present, and males differ primarily in 'monochromatic' black, white and silver...
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PMID: 17257120
PDF is available here.
PDF is available here.
Molecular Ecology (16)3 2007
Abstract
We sampled individuals of three endemic rodent species, Hylomyscus denniae, Hybomys lunaris and Lophuromys woosnami from four localities in the Albertine Rift. We analysed mitochondrial DNA sequence variation from fragments of the cytochrome b and control region genes and found significant phylogeog...
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PMID: 17257121
PDF is available here.
PDF is available here.