Genomes and Genes
gc rich sequence
Summary: A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.
- Kendrick S, Akiyama Y, Hecht S, Hurley L. The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern. J Am Chem Soc. 2009;131:17667-76 pubmed publisher..Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition. ..
- Kudla G, Helwak A, Lipinski L. Gene conversion and GC-content evolution in mammalian Hsp70. Mol Biol Evol. 2004;21:1438-44 pubmed..We failed to detect any effect of GC content on the translation efficiency at high temperatures. Taken together, our data strongly support the biased gene conversion hypothesis of GC-content evolution. ..
- Versteeg R, van Schaik B, van Batenburg M, Roos M, Monajemi R, Caron H, et al. The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res. 2003;13:1998-2004 pubmed..Ridges are therefore an integral part of a higher order structure in the genome related to transcriptional regulation. ..
- Aerts S, Thijs G, Dabrowski M, Moreau Y, De Moor B. Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics. 2004;5:34 pubmed
- Marais G. Biased gene conversion: implications for genome and sex evolution. Trends Genet. 2003;19:330-8 pubmed..Most BGC(GC) events probably occur during meiosis, which has implications for our understanding of the evolution of sex and recombination. ..
- Semon M, Mouchiroud D, Duret L. Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum Mol Genet. 2005;14:421-7 pubmed..We show here that using gene windows artificially enhances the correlation. The assertion that the expression of a given gene depends on the GC-content of the region where it is located is therefore not supported by the data. ..
- Vinogradov A. DNA helix: the importance of being GC-rich. Nucleic Acids Res. 2003;31:1838-44 pubmed
- Louie E, Ott J, Majewski J. Nucleotide frequency variation across human genes. Genome Res. 2003;13:2594-601 pubmed
- Galtier N, Duret L. Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution. Trends Genet. 2007;23:273-7 pubmed..We argue that these regions, far from contributing to human adaptation, might represent the Achilles' heel of our genome. ..
- Ponger L, Duret L, Mouchiroud D. Determinants of CpG islands: expression in early embryo and isochore structure. Genome Res. 2001;11:1854-60 pubmed..These observations are consistent with the hypothesis that the occurrence of these CGIs is the consequence of gene expression at this stage, when the methylation pattern is installed. ..
- Yi S, Li W. Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids. Mol Biol Evol. 2005;22:1223-30 pubmed..We hypothesize that sudden changes in recombination rate have caused the changes in substitution rate at this locus. ..
- Tang G, Bandwar R, Patel S. Extended upstream A-T sequence increases T7 promoter strength. J Biol Chem. 2005;280:40707-13 pubmed
- Chakrabarti R, Schutt C. Novel sulfoxides facilitate GC-rich template amplification. Biotechniques. 2002;32:866, 868, 870-2, 874 pubmed..We introduce them as novel PCR enhancers. We identify tetramethylene sulfoxide as the most potent sulfur-oxygen compound in the enhancement of PCR amplification and as one of the most potent PCR enhancers currently known. ..
- Pavlicek A, Clay O, Jabbari K, Paces J, Bernardi G. Isochore conservation between MHC regions on human chromosome 6 and mouse chromosome 17. FEBS Lett. 2002;511:175-7 pubmed
- Galtier N, Bazin E, Bierne N. GC-biased segregation of noncoding polymorphisms in Drosophila. Genetics. 2006;172:221-8 pubmed..These results, together with previous reports, suggest that GC-biased gene conversion has influenced base composition evolution in Drosophila and explain the correlation between intron and exon GC content. ..
- Wan X, Xu D, Kleinhofs A, Zhou J. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol. 2004;4:19 pubmed..The synonymous codon usage bias could be simply expressed as 1+ (p/2)log2(p/2) + ((1-p)/2)log2((l-p)/2), where p = GC3. The software we developed for measuring SCUO (codonO) is available at http://digbio.missouri.edu/~wanx/cu/codonO. ..
- Duret L, Eyre Walker A, Galtier N. A new perspective on isochore evolution. Gene. 2006;385:71-4 pubmed..In this article we review the existing support for these two hypotheses, and discuss how they can be combined to provide a new perspective on isochore evolution. ..
- Kudla G, Lipinski L, Caffin F, Helwak A, Zylicz M. High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol. 2006;4:e180 pubmed..We conclude that silent-site GC content correlates with gene expression efficiency in mammalian cells. ..
- Hube F, Reverdiau P, Iochmann S, Gruel Y. Improved PCR method for amplification of GC-rich DNA sequences. Mol Biotechnol. 2005;31:81-4 pubmed..Therefore, this method can be recommended to amplify other GC-rich genomic templates. ..
- Fleming J, Spencer T, Safe S, Bazer F. Estrogen regulates transcription of the ovine oxytocin receptor gene through GC-rich SP1 promoter elements. Endocrinology. 2006;147:899-911 pubmed publisher..These results support the hypothesis that the antiluteolytic effects of IFNT are mediated by direct inhibition or silencing of ESR1 gene transcription, thereby precluding ESR1/SP1 from stimulating OXTR gene transcription...
- Cordaux R, Lee J, Dinoso L, Batzer M. Recently integrated Alu retrotransposons are essentially neutral residents of the human genome. Gene. 2006;373:138-44 pubmed..These results also imply that selective processes specifically targeting Alu elements can be ruled out as explanations for the accumulation of Alu elements in GC-rich regions of the human genome. ..
- Albertini V, Jain A, Vignati S, Napoli S, Rinaldi A, Kwee I, et al. Novel GC-rich DNA-binding compound produced by a genetically engineered mutant of the mithramycin producer Streptomyces argillaceus exhibits improved transcriptional repressor activity: implications for cancer therapy. Nucleic Acids Res. 2006;34:1721-34 pubmed..The new MTM derivative SDK could be an effective agent for treatment of cancer and other diseases with abnormal expression or activity of GC-rich DNA-binding transcription factors. ..
- Duan J, Antezana M. Mammalian mutation pressure, synonymous codon choice, and mRNA degradation. J Mol Evol. 2003;57:694-701 pubmed..This may explain why nucleotide motif preferences are very similar in transcribed and nontranscribed mammalian DNA even though the preferences appear to be adaptive only in transcribed DNA. ..
- Arezi B, Xing W, Sorge J, Hogrefe H. Amplification efficiency of thermostable DNA polymerases. Anal Biochem. 2003;321:226-35 pubmed..However, when amplicon length or GC content was increased, Pfu formulations with dUTPase exhibited significantly higher efficiencies than Taq, Pfu, and other archaeal DNA polymerases. We discuss the implications of these results. ..
- Saccone S, Federico C, Bernardi G. Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds. Gene. 2002;300:169-78 pubmed..This finding has interesting implications for the formation of GC-rich isochores of warm-blooded vertebrates. ..
- Lobry J, Sueoka N. Asymmetric directional mutation pressures in bacteria. Genome Biol. 2002;3:RESEARCH0058 pubmed..However, the variation in G+C content between species is influenced by factors other than asymmetric mutation pressure. ..
- Medstrand P, van de Lagemaat L, Mager D. Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res. 2002;12:1483-95 pubmed..Such a process may provide an explanation for the shifting distributions of retroelements with time. ..
- Wobus M, Wandel E, Prohaska S, Findeiss S, Tschop K, Aust G. Transcriptional regulation of the human CD97 promoter by Sp1/Sp3 in smooth muscle cells. Gene. 2008;413:67-75 pubmed publisher..Our data characterize for the first time the activity of the human CD97 promoter which is controlled by Sp1/Sp3 transcription factors in SMCs. ..
- Whitten C, Swygert S, Butler S, Finco T. Transcription of the LAT gene is regulated by multiple binding sites for Sp1 and Sp3. Gene. 2008;413:58-66 pubmed publisher..Collectively, these results provide compelling data that implicates Sp1 and Sp3 in the transcriptional regulation of the human LAT gene. ..
- Shinoda N, Yoshida T, Kusama T, Takagi M, Hayakawa T, Onodera T, et al. High GC contents of primer 5'-end increases reaction efficiency in polymerase chain reaction. Nucleosides Nucleotides Nucleic Acids. 2009;28:324-30 pubmed publisher..As a result, there were significant correlations between the amplification signals and the GC contents in the first 1 approximately 3 bps of primer 5'-end. ..
- Suzuki A, Sanda N, Miyawaki Y, Fujimori Y, Yamada T, Takagi A, et al. Down-regulation of PROS1 gene expression by 17beta-estradiol via estrogen receptor alpha (ERalpha)-Sp1 interaction recruiting receptor-interacting protein 140 and the corepressor-HDAC3 complex. J Biol Chem. 2010;285:13444-53 pubmed publisher
- Sahdev S, Saini S, Tiwari P, Saxena S, Singh Saini K. Amplification of GC-rich genes by following a combination strategy of primer design, enhancers and modified PCR cycle conditions. Mol Cell Probes. 2007;21:303-7 pubmed..The reported approach can be utilized to improve the amplification of templates with high GC content, which are otherwise relatively difficult to resolve. ..
- Washietl S, Pedersen J, Korbel J, Stocsits C, Gruber A, Hackermüller J, et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007;17:852-64 pubmed..One hundred seventy-five selected candidates were tested by RT-PCR in six tissues, and expression could be verified in 43 cases (24.6%). ..
- Costantini M, Auletta F, Bernardi G. Isochore patterns and gene distributions in fish genomes. Genomics. 2007;90:364-71 pubmed..Moreover, in each genome the GC-poorest isochore families comprised a group of "long isochores" (2-20 Mb in size), which were the lowest in GC and varied in size distribution and relative amount from one genome to the other. ..
- Yuan Y, Compton S, Sobczak K, Stenberg M, Thornton C, Griffith J, et al. Muscleblind-like 1 interacts with RNA hairpins in splicing target and pathogenic RNAs. Nucleic Acids Res. 2007;35:5474-86 pubmed..Our results provide a mechanistic basis for dsCUG-induced MBNL1 sequestration and highlight a striking similarity in the binding sites for MBNL proteins on splicing precursor and pathogenic RNAs. ..
- Li L, Li Q, Yu Y, Zhong M, Yang L, Wu Q, et al. A primer design strategy for PCR amplification of GC-rich DNA sequences. Clin Biochem. 2011;44:692-8 pubmed publisher..It proves that the secondary structures cannot be formed at higher annealing temperature conditions (>65°C), and we can overcome this difficulty easily by designing primers and using higher annealing temperature. ..
- Kuryavyi V, Cahoon L, Seifert H, Patel D. RecA-binding pilE G4 sequence essential for pilin antigenic variation forms monomeric and 5' end-stacked dimeric parallel G-quadruplexes. Structure. 2012;20:2090-102 pubmed publisher..coli RecA-mediated strand exchange in vitro. We discuss how interactions between RecA and monomeric pilE G-quadruplex could facilitate the specialized recombination reactions leading to pilin diversification. ..
- Sharp P, Bailes E, Grocock R, Peden J, Sockett R. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 2005;33:1141-53 pubmed..For example, Clostridium perfringens, the species with the highest value of S, can have a generation time as short as 7 min. ..
- Vinogradov A. Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic Acids Res. 2005;33:559-63 pubmed
- Li W, Bernaola Galván P, Carpena P, Oliver J. Isochores merit the prefix 'iso'. Comput Biol Chem. 2003;27:5-10 pubmed..It can be shown that DNA sequences that are rejected by the binomial test may not be rejected by the ANOVA test. ..
- Galtier N. Gene conversion drives GC content evolution in mammalian histones. Trends Genet. 2003;19:65-8 pubmed..Thus, it seems that gene conversion is a biased process that tends to increase the DNA GC content, a conclusion that has implications for the evolution of isochores in vertebrates. ..
- Birdsell J. Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution. Mol Biol Evol. 2002;19:1181-97 pubmed..These findings have a number of important implications for the way we view genome evolution and suggest a new model for the evolution of sex. ..
- Konu O, Li M. Correlations between mRNA expression levels and GC contents of coding and untranslated regions of genes in rodents. J Mol Evol. 2002;54:35-41 pubmed..norvegicus), suggesting that conflicting demands posed by different aspects of transcriptional and translational machineries (e.g., efficiency versus fidelity) may set an upper limit for GC3. ..
- Kanaya S, Kinouchi M, Abe T, Kudo Y, Yamada Y, Nishi T, et al. Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome. Gene. 2001;276:89-99 pubmed..We used SOM to examine codon usage heterogeneity in the E. coli O157 genome, which contains 'O157-unique segments' (O-islands), and showed that SOM is a powerful tool for characterization of horizontally transferred genes. ..
- Pavlicek A, Jabbari K, Paces J, Paces V, Hejnar J, Bernardi G. Similar integration but different stability of Alus and LINEs in the human genome. Gene. 2001;276:39-45 pubmed
- Eyre Walker A, Hurst L. The evolution of isochores. Nat Rev Genet. 2001;2:549-55 pubmed..However, although we have known about isochores for over 25 years, we still have a poor understanding of why they exist. In this article, we review the current evidence for the three main hypotheses. ..
- Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860-921 pubmed..We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence. ..
- Bernardi G. Misunderstandings about isochores. Part 1. Gene. 2001;276:3-13 pubmed..Rev. Genet. 2 (2001) 549) will also be addressed. The present paper is a complement to two review articles which were published last year (Bernardi, Gene 241 (2000) 3; Gene 259(1) (2000) 31). ..
- Smith N, Eyre Walker A. Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans. Mol Biol Evol. 2001;18:982-6 pubmed..Similar patterns of polymorphism were also observed in noncoding DNA, suggesting that natural selection or biased gene conversion may affect large tracts of the human genome. ..
- Lio P, Vannucci M. Finding pathogenicity islands and gene transfer events in genome data. Bioinformatics. 2000;16:932-40 pubmed..Software and numerical results (profiles, scalograms, high and low frequency components) for all the genome sequences analyzed are available upon request from the authors. ..
- Rodr guez Trelles F, Tarr o R, Ayala F. Fluctuating mutation bias and the evolution of base composition in Drosophila. J Mol Evol. 2000;50:1-10 pubmed..The shift in mutation bias has affected the extent of the rate variation among sites in Xdh...
- Boissinot S, Entezam A, Young L, Munson P, Furano A. The insertional history of an active family of L1 retrotransposons in humans. Genome Res. 2004;14:1221-31 pubmed..Also, the intra-chromosomal distribution of Ta-1 elements is not uniform. Ta-1 elements tend to cluster, and the maximal gaps between Ta-1 inserts are larger than would be expected from a model of uniform random insertion. ..