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GC Rich Sequence (1):
Recent article
GC Rich Sequence
Abstract
We report here on the existence of a high-level compositional organization of isochores in the human genome. By using a segmentation algorithm incorporating the long-range correlations existing in human DNA, we find that every chromosome is composed of a few huge segments (~ 10^{7} bp) of relatively...
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PMID: 21517526
PDF is available here.
PDF is available here.
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Journal of Virology (84)13 2010
Abstract
We performed in vitro binding assays with N-terminal proteins encoding amino acids 1 to 160 of wild-type ICP27 or arginine-to-lysine substitution mutants. The R138,148,150K triple mutant bound weakly to sequences that were bound by the wild-type protein and single and double mutants. Furthermore, du...
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PMID: 20410270
PDF is available here.
PDF is available here.
Abstract
We describe the development of novel overlap sequences that can be used for the construction of fusion DNA fragments, including the one-step fusion of three fragments in a single PCR and also for in-frame fusions. Novel poly G or C stretches showed strong and also specific annealing to the complemen...
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PMID: 19159667
PDF is available here.
PDF is available here.
Abstract
We also used nucleotide sequences encoding for active centers of bacterial adenylate cyclases. Inverse correlation between the GC-content (G+C) and the total level of preterminal codons usage (PCU) was observed (R = - 0.97). For nucleotide sequences encoding for active centers from adenylate cyclase...
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PMID: 19280988
PDF is available here.
PDF is available here.
BMC Genomics (10)1 2009
Abstract
The present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels...
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PMID: 19344507
PDF is available here.
PDF is available here.
DNA and Cell Biology (27)12 2008
Abstract
Saffron (Crocus sativus L.) shows different biological properties, some of which relate to its special components including safranal (deglycosylated picrocrocin). In our previous study on the mechanism of saffron functions, interaction of saffron carotenoids with DNA and oligonucleotides was reporte...
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PMID: 19040376
PDF is available here.
PDF is available here.
Endocrinology (149)11 2008
Abstract
We describe transgenic animals overexpressing a transgene containing three tandem GC-rich sites linked to a minimal TATA or thymidine kinase promoter and a luciferase gene. Several mouse lines expressing the transgenes were characterized and, in line 15, E2 induced a 9-fold increase in luciferase ac...
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PMID: 18635651
PDF is available here.
PDF is available here.
Genome Research (18)11 2008
Reduced purifying selection prevails over positive selection in human copy number variant evolution.
Abstract
We question our previous proposition that copy number variants (CNVs) are often retained in the human population because of their adaptive benefit. We show that genic biases of CNVs are best explained, not by positive selection, but by reduced efficiency of selection in eliminating deleterious chang...
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PMID: 18687881
PDF is available here.
PDF is available here.
Abstract
The ISCR elements ISCR3, ISCR4, ISCR5, ISCR14, and ISCR16 all share a percent G+C of 68 to 69%. They also share between 75% and 97% identity in their transposase open reading frames. Furthermore, with the exception of ISCR5, they are all found adjacent to sections of groEL that display the highest i...
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PMID: 18663029
PDF is available here.
PDF is available here.
Journal of Lipid Research (49)10 2008
Abstract
Change in phosphoethanolamine pool size in tumor tissues is an important indicator of tumor prognosis and drug therapy efficacy. Phosphoethanolamine is the substrate of the regulatory enzyme CTP:phosphoethanolamine cytidylyltransferase (ECT) in the de novo biosynthesis of phosphatidylethanolamine (P...
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PMID: 18583706
PDF is available here.
PDF is available here.
Genome Research (18)10 2008
Abstract
We describe a statistical approach, compositionally orthogonalized co-occurrence analysis (coCOA) that detects pairs of oligonucleotides that preferentially co-occur in pairs of sequence regions, controlling for correlations between the compositions of the analyzed regions. coCOA identified three cl...
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PMID: 18799692
PDF is available here.
PDF is available here.
Hereditas (Beijing) (30)9 2008
Abstract
These results suggest that the third codon positions, introns, 3'-untranslated regions and 3' flanking sequences may evolve similarly while first and second codon positions, 5' flanking sequences and 5' untranslated region were expected to bear more selective stress for holding their functions....
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PMID: 18779175
PDF is available here.
PDF is available here.
Chromosoma (117)4 2008
Abstract
We localised chromosome 7 DNA regions, endowed with different gene densities, in the nuclei of human lymphocytes. Our results showed that this chromosome in cell nuclei is arranged radially with the gene-dense/GC-richest regions exposed towards the nuclear interior and the gene-poorest/GC-poorest on...
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PMID: 18418623
PDF is available here.
PDF is available here.
Abstract
We show that HS: (i) are characterized by a much higher GC level (approximately 56%) than the average GC level of the human genome (approximately 41%); (ii) are overwhelmingly located in the GC-richest compartment of the genome, which is predominantly associated with an open chromatin structure; (ii...
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PMID: 18436395
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)12 2008
Abstract
I interferon induction indicating a novel link mRNA metabolism and innate immunity....
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PMID: 18515351
PDF is available here.
PDF is available here.
DNA Sequence (19)3 2008
Abstract
Simple sequence repeats (SSRs) are omnipresent in prokaryotes and eukaryotes, and are found anywhere in the genome in both protein encoding and noncoding regions. In present study the whole genome sequences of seven chromosomes (Shigella flexneri 2a str301 and 2457T, Shigella sonnei<...
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PMID: 18464038
PDF is available here.
PDF is available here.
Abstract
We identified the proximal promoter for the human LAT gene and found that it contains binding sites for members of the Ets and Runx transcription factor families. In the present study, we show that the promoter also contains 5 GC-rich elements that contribute to promoter activity and that are capabl...
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PMID: 18343609
PDF is available here.
PDF is available here.
Abstract
We showed that Sp1 and Sp3 over-expression activates CD97 promoter activity in HEK293 cells. Our data characterize for the first time the activity of the human CD97 promoter which is controlled by Sp1/Sp3 transcription factors in SMCs....
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PMID: 18329191
PDF is available here.
PDF is available here.
Abstract
We discovered a unique chromatin structure within the Bmal1 promoter. The RORE region, which is a critical cis element for the circadian regulation of the Bmal1 gene, is comprised of GC-rich open chromatin. The 3'-flanking region of the promoter inhibited rhythmic transcription in the reporter gene...
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PMID: 18332112
PDF is available here.
PDF is available here.
Genome Research (18)4 2008
Abstract
We investigated the association between human recombination rates and adaptation in primates, by considering rates of protein evolution (measured by d(N)/d(S)) between human, chimpanzee, and rhesus macaque. We found no correlation between either broad- or fine-scale rates of recombination and rates...
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PMID: 18199888
PDF is available here.
PDF is available here.
Abstract
We show that, while the protocols used eliminated the original genomic context, they replaced it with the plasmid contexts whose compositional properties affected the results....
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PMID: 18177737
PDF is available here.
PDF is available here.
Abstract
We report that -213/-24 fragment (region B) has higher E2-responsiveness than that of region A in MCF-7 cells, but not in HeLa cells. Deletion and mutation analyses of region B showed that multiple GC-sites are involved in the E2-stimulated response and one 30-bp fragment (-213 to -184 bp) is essent...
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PMID: 18206366
PDF is available here.
PDF is available here.
Abstract
Electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding of 13 alkaloids to two GC-rich DNA duplexes which are critical sequences in human survivin promoter. Negative ion ESI-MS was first applied to screen the binding of the alkaloids to the duplexes. Six alkaloids (inc...
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PMID: 17968851
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)5 2008
Abstract
Invasion of two PNA strands to double-stranded DNA is one of the most promising methods to recognize a predetermined site in double-stranded DNA (PNA = peptide nucleic acid). In order to facilitate this 'double-duplex invasion', a new type of PNA was prepared by using chiral PNA monomers in which a...
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PMID: 18203747
PDF is available here.
PDF is available here.
Abstract
We analysed complete or almost complete nucleotide sequences of the human, chimp, mouse, rat, chicken, dog, and other genomes to find that they contain extremely long (A+T) a (G+C) blocks that do not occur at all in the corresponding randomized sequences. The longest is an (A+T) block containing 104...
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PMID: 18092828
PDF is available here.
PDF is available here.
Abstract
We re-determined all 79 boundaries of previously identified human isochores at single-nucleotide resolution, and then compared the boundary coordinates with other genome features. We found that 55.7% of isochore boundaries coincide with termini of repeat elements; 45.6% of isochore boundaries coinci...
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PMID: 18092827
PDF is available here.
PDF is available here.
Abstract
We compared SSRs in housekeeping and tissue-specific genes in human and mouse, in terms of SSR types and distributions in different regions including 5'-UTRs, introns, coding exons, 3'-UTRs, and upstream regions. Among all these regions, SSRs in the 5'-UTR show the most distinction between housekeep...
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PMID: 17964742
PDF is available here.
PDF is available here.
Nature Protocols (3)8 2008
Abstract
We present a novel method termed 'Slowdown PCR', which allows the successful PCR-amplification of extremely GC-rich (>83%) DNA targets. The protocol relies on the addition of 7-deaza-2'-deoxyguanosine, a dGTP analog to the PCR mixture and a novel standardized cycling protocol with varying temperatur...
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PMID: 18714299
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1779)1 2008
Abstract
Soluble epoxide hydrolase (sEH) is a multifunctional protein encoded by the EPHX2 gene. The biological functions and enzyme kinetics of sEH have been extensively investigated, however, little is known about its transcriptional regulation and mechanisms of tissue specific expression. Here, a lucifera...
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PMID: 18078836
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
To shed light on the function of these microRNAs and possible crosstalk between microRNA-based gene regulation and genomic imprinting, we performed extensive in silico analyses of the microRNAs in this imprinted region and their predicted target genes.Bioinformatic analysis reveals that these microR...
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PMID: 18651963
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
We found that the evolutionary variability and intrinsic secondary structure stability of these sequences share an inverse relationship. Simulations of most likely single nucleotide evolution in Psilotum nudum and Nephroselmis olivacea mRNAs, indicate that helix-forming propensities of mutated mRNAs...
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PMID: 18226235
PDF is available here.
PDF is available here.
BMC Bioinformatics (9)1 2008
Abstract
We describe a new algorithm and software for the computation of absent words. It is more efficient than previous algorithms and easier to use. It directly computes unwords without the need to specify a length estimate. Moreover, it avoids the space requirements of index structures such as suffix tre...
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PMID: 18366790
PDF is available here.
PDF is available here.
Abstract
Here we analyze SNP allele frequencies, retrotransposon insertion polymorphisms (RIPs), as well as fixed substitutions accumulated in the human lineage since its divergence from chimpanzee to indicate that biased gene conversion (BGC) has been playing a role in within-genome GC content variation. Ye...
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PMID: 18371205
PDF is available here.
PDF is available here.
BMC Genomics (9)1 2008
Abstract
Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophob...
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PMID: 18460197
PDF is available here.
PDF is available here.
Bioconjugate Chemistry (19)1 2008
Abstract
We previously complexed ODN with galactosylated poly( l-lysine) (Gal-PLL) to enhance its site-specific delivery to hepatocytes. To avoid the use of polycations, in this study we conjugated galactosylated poly(ethylene glycol) (Gal-PEG (MW of PEG: 3486 +/- 500 Da)) to ODN via an acid-labile ester lin...
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PMID: 17850109
PDF is available here.
PDF is available here.
Nucleic Acids Research (36)1 2008
Abstract
We found that PMA induced the mRNA level and protein expression of cPLA2alpha. In addition, two Sp1-binding sites of cPLA2alpha promoter were required for response to PMA and c-Jun overexpression. Small interfering RNA (siRNA) of c-Jun and nucleolin inhibited PMA induced the promoter activity and pr...
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PMID: 18025046
PDF is available here.
PDF is available here.
Abstract
We investigated the molecular mechanisms of transcriptional regulation of the human AhRR by cloning its regulatory DNA region located in intron I of the AhRR. By means of reporter gene analyses and generation of deletion variants, we identified a functional, 3-methylcholanthrene-sensitive xenobiotic...
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PMID: 17890447
PDF is available here.
PDF is available here.
Human Molecular Genetics (16)22 2007
Abstract
We examined genomic DNA isolated from 355 normal subjects for genetic variants in transcription factor binding motifs. Of seven variants identified, the most common was a GC to TT dinucleotide substitution at -694/-695 (allele frequency of 0.467 in Caucasians and 0.329 in African Americans) within a...
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PMID: 17720980
PDF is available here.
PDF is available here.
Abstract
We have applied a comparative phylogenomic analysis to study the evolutionary relationships between GC content, CpG-dinucleotide content (CpGs), potential nuclear factor I (NFI) binding sites, and potential Z-DNA forming regions (ZDRs) as representative structural and functional GC-rich genomic elem...
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PMID: 17925442
PDF is available here.
PDF is available here.
FEBS Letters (581)24 2007
Abstract
We evaluated the association of specific sequences (i.e. CpG/CpNpG motifs, homonucleotides, short repeats) and mutations within the genes. We classified 1337 published mutations in BRCA1 (1765 BRCA2 mutations) for each specific sequence, and employed computer simulation combined with mathematical ca...
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PMID: 17826769
PDF is available here.
PDF is available here.
Molecular Endocrinology (21)10 2007
Abstract
We show a direct interaction between FOXO3a and STAT5 in these cells, which may provide a link between STAT5 and the AP1 transcription factors on the SOCS3 promoter. We conclude that regulation of SOCS3 expression by GH in a pro-B cell involves not only the pSRE, but also a transcriptionally active...
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PMID: 17609438
PDF is available here.
PDF is available here.
Molecular Endocrinology (21)10 2007
Abstract
We and others have shown that prostaglandins can also up-regulate SOCS3 expression. Here we used T47D breast cancer cells treated with prostaglandin E2 (PGE2) to examine this pathway. T47D cells responded to PGE2 stimulation with a significant increase in SOCS3 mRNA that was independent of de novo p...
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PMID: 17636039
PDF is available here.
PDF is available here.
Abstract
We examined all Alu elements over 200 nucleotides and all B1 elements over 100 nucleotides in the human and mouse genomes, and analyzed the number of copies of each element at various stringencies from 22 nucleotides to full length. Over 98% of 923,277 Alus and 365,377 B1s examined were unique when...
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PMID: 17407136
PDF is available here.
PDF is available here.
Abstract
We mapped isochores on fish chromosomes and assessed gene densities in isochore families. Because of the availability of sequence data, we have concentrated our investigations on four species, zebrafish (Brachydanio rerio), medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus), and pufferfi...
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PMID: 17590311
PDF is available here.
PDF is available here.
Abstract
We show that HMMs can be used to analyse complex gene structures with bell-shaped length distribution by using convolution of geometric distributions. Thus, we have introduced macros-states to model the distributions of the lengths of the regions. Our study shows that simple HMM could be used to mod...
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PMID: 17486342
PDF is available here.
PDF is available here.
Abstract
We have examined two highly GC-rich human genes namely insulin receptor (IR) and cSRC kinase. In silico analysis of these genes revealed that their -5' and -3' sequences have > 80% GC content. Primers designed through these GC-rich regions had high self-dimer free energy values (DeltaG). Null mutati...
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PMID: 17490855
PDF is available here.
PDF is available here.
DNA Sequence (18)4 2007
Abstract
We examined GC nucleotide composition, relative synonymous codon usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI) and gene length for 308 prokaryotic mechanosensitive ion channel (MSC) genes from six evolutionary groups: Euryarchaeota, Actinobacteria, Alphaproteobacteria,...
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PMID: 17541832
PDF is available here.
PDF is available here.
Abstract
The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was used to assess the significance of deviation of the observed and expected freq...
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PMID: 17914237
PDF is available here.
PDF is available here.
Abstract
Our data also demonstrate that the ORF2 translation initiation is not directed by internal initiation, either. It is very inefficient and presumably based on a reinitiation event....
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PMID: 17470553
PDF is available here.
PDF is available here.
Molecular and Cellular Biochemistry (301)1-2 2007
Abstract
We demonstrate that the histone H3 at the GC-rich region in the minimal promoter of p16(INK4a) is hypermethylated, with a concurrent reduction of both the activity of p16(INK4a) promoter and the level of endogenous p16(INK4a) mRNA. Moreover, we show that the specific mutation of the GC-rich region o...
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PMID: 17333389
PDF is available here.
PDF is available here.
Nucleic Acids Research (35)Web Server issue 2007
Abstract
We present a CodonO webserver service as a user-friendly tool for codon usage bias analyses across and within genomes in real time. The webserver is available at http//www.sysbiology.org/CodonO. Contact: wanhenry@yahoo.com....
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PMID: 17537810
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)26 2007
Abstract
We applied directed evolution to E. coli ribosomal protein S1. Two selected mutants enabled 12- and 8-fold higher expression levels from GC-rich DNA targets. General improvements in translation efficiency over a range of genes from Rhodopseudomonas palustris and E. coli was achieved using an S1 muta...
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PMID: 17412688
PDF is available here.
PDF is available here.
Chromosoma (116)3 2007
Abstract
The chromosomal location of centromere-specific histone H3 (CENH3) is the assembly site for the kinetochore complex of active centromeres. Chromatin immunoprecipitation data indicated that CENH3 interacts in barley with cereba, a centromeric retroelement (CR)-like element conserved among cereal cent...
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PMID: 17483978
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (282)22 2007
Abstract
We demonstrated that a Sp1-based promoter is essential for constitutive transcription and a NF-kappaB-based intronic enhancer is responsible for cytokine-mediated induction. Here we show that nucleophosmin (NPM), a RNA-binding protein, binds to an 11G single-stranded loop in the promoter region and...
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PMID: 17426024
PDF is available here.
PDF is available here.
Abstract
We chose to investigate the regulatory effect of gastrin on TFF2 expression. The expression of mRNA and protein of TFF2 was determined by RT-PCR and immunohistochemical staining, respectively. A series of truncated and mutant murine TFF2 promoter constructs was generated. Promoter activity was asses...
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PMID: 17332476
PDF is available here.
PDF is available here.
Trends in Genetics (23)6 2007
Abstract
We argue that these regions, far from contributing to human adaptation, might represent the Achilles' heel of our genome....
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PMID: 17418442
PDF is available here.
PDF is available here.
Journal of Biotechnology (130)1 2007
Abstract
We have applied a comparative analysis to 79 different human cDNAs expressed in Pichia pastoris. The cDNAs were cloned in an expression vector for intracellular expression and recombinant protein expression was monitored in a standardized procedure and classified with respect to the expression level...
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PMID: 17389146
PDF is available here.
PDF is available here.
Abstract
We have identified novel over-represented and conserved motifs in the upstream regions of human and mouse miRNA stem-loop sequences by means of a new bioinformatic processing regimen. We observed sequence conservation -500 bp upstream in 189 human and mouse miRNAs declining with increasing distance...
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PMID: 17499549
PDF is available here.
PDF is available here.
Cancer Science (98)6 2007
Abstract
We report that both DNA topoisomerase I and II inhibitors such as SN-38 and etoposide, but not cisplatin, 5-fluorouracil or actinomycin D, can induce phosphorylation of the transcription factor Sp1. Furthermore, DNA topoisomerase inhibitors were shown to transactivate GC-box-dependent promoters such...
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PMID: 17441964
PDF is available here.
PDF is available here.
Abstract
We apply a well-known least-squares optimal segmentation algorithm to isochore discovery. The algorithm finds the best division of the sequence into k pieces, such that the segments are internally as homogeneous as possible. We show how this simple segmentation method can be applied to isochore disc...
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PMID: 17389148
PDF is available here.
PDF is available here.