Genomes and Genes
at rich sequence
Summary: A nucleic acid sequence that contains an above average number of ADENINE and THYMINE bases.
- Fenn J, Cameron S, Whiting M. The complete mitochondrial genome sequence of the Mormon cricket (Anabrus simplex: Tettigoniidae: Orthoptera) and an analysis of control region variability. Insect Mol Biol. 2007;16:239-52 pubmed publisher..simplex individuals from 12 different populations. Variance studies between these individuals show that the A + T-rich region contains significant phylogenetic signal to be used in population studies...
- Kato T, Inagaki H, Yamada K, Kogo H, Ohye T, Kowa H, et al. Genetic variation affects de novo translocation frequency. Science. 2006;311:971 pubmed..Alleles with an asymmetric center do not form the t(11;22). Our data show the importance of genome sequence on chromosomal rearrangements, a class of human mutation that is thought to be random. ..
- Saito S, Tamura K, Aotsuka T. Replication origin of mitochondrial DNA in insects. Genetics. 2005;171:1695-705 pubmed
- Tolstorukov M, Virnik K, Adhya S, Zhurkin V. A-tract clusters may facilitate DNA packaging in bacterial nucleoid. Nucleic Acids Res. 2005;33:3907-18 pubmed
- Jordan I, Kondrashov F, Adzhubei I, Wolf Y, Koonin E, Kondrashov A, et al. A universal trend of amino acid gain and loss in protein evolution. Nature. 2005;433:633-8 pubmed..Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day. ..
- Edelmann L, Spiteri E, Koren K, Pulijaal V, Bialer M, Shanske A, et al. AT-rich palindromes mediate the constitutional t(11;22) translocation. Am J Hum Genet. 2001;68:1-13 pubmed
- Janssen S, Cuvier O, Muller M, Laemmli U. Specific gain- and loss-of-function phenotypes induced by satellite-specific DNA-binding drugs fed to Drosophila melanogaster. Mol Cell. 2000;6:1013-24 pubmed..Chromatin opening of satellite III by P9 is proposed to suppress PEV of white-mottled flies, whereas chromatin opening of satellite V by P31 is proposed to create an inopportune "sink" for the GAGA factor (GAF). ..
- Rocha E, Danchin A. Base composition bias might result from competition for metabolic resources. Trends Genet. 2002;18:291-4 pubmed..We suggest that the higher energy cost and limited availability of G and C over A and T/U could be a basis for the understanding of these differences. ..
- Kurahashi H, Emanuel B. Long AT-rich palindromes and the constitutional t(11;22) breakpoint. Hum Mol Genet. 2001;10:2605-17 pubmed..Our data lend support to the hypothesis that palindrome-mediated double-strand breaks in meiosis cause illegitimate recombination between 11q23 and 22q11 resulting in this recurrent translocation. ..
- Wang G, Qian R, Li Q, Niu T, Chen C, Xu X. The association between PPP1R3 gene polymorphisms and type 2 diabetes mellitus. Chin Med J (Engl). 2001;114:1258-62 pubmed..15; 95% CI: 0.62-2.14, P = 0.65). A joint effect between the Asp905 and BMI increases the risk of type 2 diabetes, and Asp905Tyr and ARE polymorphism of PPP1R3 gene are not the major diabetogenic gene variants in Chinese population. ..
- Kube D, Laser H, von Knethen A, Tesch H. The AT-rich region between -54 to -66 is important for the promoter activity of interleukin-10 in Epstein-Barr virus positive Burkitt's lymphoma cells. Genes Immun. 1999;1:105-14 pubmed..This underlines the importance of the AT-rich region for EBV-associated IL-10 promoter regulation. Our results further the understanding of how the IL-10 gene could be regulated in B cell lymphomas. ..
- Kurahashi H, Inagaki H, Ohye T, Kogo H, Kato T, Emanuel B. Palindrome-mediated chromosomal translocations in humans. DNA Repair (Amst). 2006;5:1136-45 pubmed..We propose that the PATRR adopts a cruciform structure in male meiotic cells, creating genomic instability that leads to the recurrent translocation...
- Inagaki H, Ohye T, Kogo H, Yamada K, Kowa H, Shaikh T, et al. Palindromic AT-rich repeat in the NF1 gene is hypervariable in humans and evolutionarily conserved in primates. Hum Mutat. 2005;26:332-42 pubmed..Although such palindromic regions are usually unstable and disappear rapidly due to deletion, the 17PATRR in the NF1 gene was stably conserved during evolution for reasons that are still unknown. ..
- Dorman C. H-NS, the genome sentinel. Nat Rev Microbiol. 2007;5:157-61 pubmed..Broadly similar conclusions have emerged from a study of H-NS binding to DNA in Escherichia coli. How do these findings affect our view of H-NS and its ability to influence bacterial evolution? ..
- 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
- Louie E, Ott J, Majewski J. Nucleotide frequency variation across human genes. Genome Res. 2003;13:2594-601 pubmed
- Segurado M, de Luis A, Antequera F. Genome-wide distribution of DNA replication origins at A+T-rich islands in Schizosaccharomyces pombe. EMBO Rep. 2003;4:1048-53 pubmed..The absence of consensus elements in A+T-rich islands implies that different sequences can target the ORC to different ORIs. ..
- Nimmakayalu M, Gotter A, Shaikh T, Emanuel B. A novel sequence-based approach to localize translocation breakpoints identifies the molecular basis of a t(4;22). Hum Mol Genet. 2003;12:2817-25 pubmed..The sequence of this breakpoint further suggests that a stem-loop secondary structure mechanism is responsible for the formation of other, non-recurrent translocations involving LCR-B of 22q11.2. ..
- Zhang H, Freudenreich C. An AT-rich sequence in human common fragile site FRA16D causes fork stalling and chromosome breakage in S. cerevisiae. Mol Cell. 2007;27:367-79 pubmed..Our data suggest that the FRA16D Flex1 sequence causes increased chromosome breakage by forming secondary structures that stall replication fork progression...
- Lang B, Blot N, Bouffartigues E, Buckle M, Geertz M, Gualerzi C, et al. High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes. Nucleic Acids Res. 2007;35:6330-7 pubmed
- Chen J, Ren H, Shaw J, Wang Y, Li M, Leung A, et al. Lsr2 of Mycobacterium tuberculosis is a DNA-bridging protein. Nucleic Acids Res. 2008;36:2123-35 pubmed publisher..DNA bridging by Lsr2 also provides a mechanism of transcriptional regulation by Lsr2. ..
- Afek A, Lukatsky D. Genome-wide organization of eukaryotic preinitiation complex is influenced by nonconsensus protein-DNA binding. Biophys J. 2013;104:1107-15 pubmed publisher..We also show that nonconsensus binding has genome-wide influence on transcriptional frequency. ..
- Qian W, Tan G, He S, Zhang X, Zhang X, Gao Y, et al. Identification of a new AT-rich-element binding factor PsATF1 and its combined effect with PsGBF on the activation of PsCHS1 promoter. Front Biosci. 2007;12:1670-9 pubmed..These results provide theoretical basis to the plant defense gene expression mechanism regulated by multiple activators. ..
- Shimosato T, Kitazawa H, Katoh S, Tohno M, Iliev I, Nagasawa C, et al. Augmentation of T(H)-1 type response by immunoactive AT oligonucleotide from lactic acid bacteria via Toll-like receptor 9 signaling. Biochem Biophys Res Commun. 2005;326:782-7 pubmed..Moreover, the swine TLR9 transfectant demonstrated its usefulness for evaluation of immunostimulation by bacterial DNA through the detection of T(H)-1, T(H)-2 type cytokine induction via TLR9 signaling. ..
- Bai D, Yang M, Chen Y. PiggyBac transposon-mediated gene transfer in Cashmere goat fetal fibroblast cells. Biosci Biotechnol Biochem. 2012;76:933-7 pubmed..The results showed that PB had a preference for AT rich regions of the goat genome. Thus this study confirms the function of PB transposon in GFFs and provides a potential genetic tool for producing transgenic goats. ..
- Tirosh I, Sigal N, Barkai N. Divergence of nucleosome positioning between two closely related yeast species: genetic basis and functional consequences. Mol Syst Biol. 2010;6:365 pubmed publisher..Our results provide evolutionary insights to the genetic determinants and regulatory function of nucleosome positioning...
- Zaitlin D, Pierce A. Nuclear DNA content in Sinningia (Gesneriaceae); intraspecific genome size variation and genome characterization in S. speciosa. Genome. 2010;53:1066-82 pubmed publisher..Veronicaceae, Lamiales). Multiple measurements on three accessions indicated that the genome size of A. majus is ~633 × 10? base pairs, which is approximately 40% of the previously published estimate. ..
- Shewchuk B, Cooke N, Liebhaber S. The human growth hormone locus control region mediates long-distance transcriptional activation independent of nuclear matrix attachment regions. Nucleic Acids Res. 2001;29:3356-61 pubmed..These data point out discordance between sequence-based MAR predictions and in vivo MAR function and predict a novel MAR-independent mechanism for long-distance activation of hGH-N gene expression. ..
- Hong M, Lee E, Jo Y, Park H, Kim S, Hwang J, et al. Complete nucleotide sequence and organization of the mitogenome of the silk moth Caligula boisduvalii (Lepidoptera: Saturniidae) and comparison with other lepidopteran insects. Gene. 2008;413:49-57 pubmed publisher..As previously suggested, Bombycidae (Bombyx mori and B. mandarina) and Saturniidae (Antheraea pernyi and C. boisduvalii) formed a reciprocal monophyletic group...
- Ishizuka T, Yoshida J, Yamamoto Y, Sumaoka J, Tedeschi T, Corradini R, et al. Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences. Nucleic Acids Res. 2008;36:1464-71 pubmed publisher..The promotion of double-duplex invasion by the chiral (d) PNA monomer units was ascribed to both destabilization of PNA/PNA duplex and stabilization of PNA/DNA duplexes. ..
- Otaka H, Ishikawa H, Morita T, Aiba H. PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action. Proc Natl Acad Sci U S A. 2011;108:13059-64 pubmed publisher..We conclude that the polyU tail of sRNAs is essential for Hfq action in general. The data also indicate that the terminator polyU tail plays a role in Hfq-dependent stabilization of sRNAs. ..
- Shaffer C, Stephens G, Thompson B, Funches L, Bernat J, Craig C, et al. Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin. Proc Natl Acad Sci U S A. 2002;99:14332-7 pubmed..Mutations recovered in HP2 act as dominant suppressors of position effect variegation, confirming a role in heterochromatin spreading and gene silencing. ..
- Mack D, Chiu T, Dickerson R. Intrinsic bending and deformability at the T-A step of CCTTTAAAGG: a comparative analysis of T-A and A-T steps within A-tracts. J Mol Biol. 2001;312:1037-49 pubmed..The difference in helical parameters between A-T steps lying within A-tracts, versus A-T steps within alternating AT sequences, demonstrates the importance of neighboring steps on the conformation of a given dinucleotide step. ..
- Valls N, Richter M, Subirana J. Structure of a DNA duplex with all-AT base pairs. Acta Crystallogr D Biol Crystallogr. 2005;61:1587-93 pubmed..Such interactions are similar to those found in DNA fibres. The structural parameters of the individual base steps coincide with those found in other structures which contain CG terminal base pairs. ..
- Cuvier O, Hart C, Käs E, Laemmli U. Identification of a multicopy chromatin boundary element at the borders of silenced chromosomal domains. Chromosoma. 2002;110:519-31 pubmed..We propose that the BE28 repeat clusters could fulfill a similar function, acting as a local boundary between hetero- and euchromatin in a process involving interactions between the BEAF and D1 proteins. ..
- Morton B, Bi I, McMullen M, Gaut B. Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition. Genetics. 2006;172:569-77 pubmed..The data indicate multiple context effects on mutations, resulting in significant variation in mutation dynamics across the genome. ..
- Lerat E, Capy P, Biémont C. The relative abundance of dinucleotides in transposable elements in five species. Mol Biol Evol. 2002;19:964-7 pubmed
- Merino E, Fernandez Becerra C, Madeira A, Machado A, Durham A, Gruber A, et al. Pilot survey of expressed sequence tags (ESTs) from the asexual blood stages of Plasmodium vivax in human patients. Malar J. 2003;2:21 pubmed..Moreover, since the GC-content of the P. vivax genome is strikingly different from that of P. falciparum, these ESTs will help in the validation of gene predictions for P. vivax and to create a gene index of this malaria parasite. ..
- Schmid M, Steinlein C. Chromosome Banding in Amphibia. XXXIII. Demonstration of 5-Methylcytosine-Rich Heterochromatin in Anura. Cytogenet Genome Res. 2016;148:35-43 pubmed publisher..5-MeC-rich DNA sequences can be embedded both in AT- and GC-rich repetitive DNA. The experimental parameters that have major influence on the reproducibility and quality of the anti-5-MeC antibody labeling are discussed. ..
- Boettner M, Steffens C, von Mering C, Bork P, Stahl U, Lang C. Sequence-based factors influencing the expression of heterologous genes in the yeast Pichia pastoris--A comparative view on 79 human genes. J Biotechnol. 2007;130:1-10 pubmed..These results could provide a basis for a knowledge-oriented optimisation of gene sequences both to increase protein yields and to help target selection and the design of high-throughput expression approaches. ..
- Ouyang Z, Zhou J. BadR (BB0693) controls growth phase-dependent induction of rpoS and bosR in Borrelia burgdorferi via recognizing TAAAATAT motifs. Mol Microbiol. 2015;98:1147-67 pubmed publisher..This newly recognized role for BadR to fine-tune the activation of the RpoN-RpoS pathway at strategic times in Bb's life cycle potentially represents another layer of gene control over Ïƒ(54)-dependent gene regulation. ..
- Bharadwaj R, Trainor C, Pasceri P, Ellis J. LCR-regulated transgene expression levels depend on the Oct-1 site in the AT-rich region of beta -globin intron-2. Blood. 2003;101:1603-10 pubmed..In addition, the Oct-1 site in the ATR is required for high-level 5'HS3 beta/gamma-globin transgene expression and should be retained in LCRbeta-globin expression cassettes designed for gene therapy. ..
- Ernstsson S, Bjornsdottir S, J nsson Z, Thorbjarnardottir S, Eggertsson G, Palsdottir A. Identification and nucleotide sequence analysis of a cryptic plasmid, pRM21, from Rhodothermus marinus. Plasmid. 2003;49:188-91 pubmed..Of 40 additional R. marinus strains screened for plasmids, six (15%) were found to harbour plasmids with the same size and restriction pattern as pRM21...
- Inukai T, Sano Y. Sequence rearrangement in the AT-rich minisatellite of the novel rice transposable element Basho. Genome. 2002;45:493-502 pubmed..Because the AT-rich minisatellite contained in Basho possessed several motifs of the matrix attachment region (MAR) in its repeat unit, the functional role as MAR in the rice genome was discussed. ..
- Smits W, Grossman A. The transcriptional regulator Rok binds A+T-rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis. PLoS Genet. 2010;6:e1001207 pubmed publisher..In these ways, Rok appears to be functionally analogous to H-NS, a nucleoid associated protein found in Gram negative bacteria and Lsr2 of high G+C Mycobacteria...
- Chavda S, Mulder K, Brown T, Mackay H, Babu B, Westrate L, et al. DNA recognition: design, synthesis and biophysical characteristics of pyrrole(H) based polyamides. Med Chem. 2010;6:150-8 pubmed
- Soller M, White K. ELAV multimerizes on conserved AU4-6 motifs important for ewg splicing regulation. Mol Cell Biol. 2005;25:7580-91 pubmed publisher..Collectively, our results suggest that ELAV multimerization and binding to multiple AU(4-6) motifs contribute to target RNA recognition and processing in a complex cellular environment...
- Cheng Y, Dylla S, Turnbough C. A long T. A tract in the upp initially transcribed region is required for regulation of upp expression by UTP-dependent reiterative transcription in Escherichia coli. J Bacteriol. 2001;183:221-8 pubmed..A tract on upp expression and regulation are due to increases in the fraction of both G6- and A7-initiated transcripts that avoid reiterative transcription and are elongated normally. ..
- Breusegem S, Sadat Ebrahimi S, Douglas K, Clegg R, Loontiens F. Increased stability and lifetime of the complex formed between DNA and meta-phenyl-substituted Hoechst dyes as studied by fluorescence titrations and stopped-flow kinetics. J Mol Biol. 2001;308:649-63 pubmed..With poly(dA).poly(dT), poly[d(A-T)] and poly[d(A-5BrU)], k(on) (between 6.1 x 10(7) M(-1) x s(-1) and 5.2 x 10(8) M(-1) x s(-1)) depends on the DNA. ..
- Kurahashi H, Inagaki H, Hosoba E, Kato T, Ohye T, Kogo H, et al. Molecular cloning of a translocation breakpoint hotspot in 22q11. Genome Res. 2007;17:461-9 pubmed..All of these results support a previously proposed paradigm that unusual DNA secondary structure plays a role in the mechanism by which palindrome-mediated translocations occur. ..
- Dias E, Carareto C. msechBari, a new MITE-like element in Drosophila sechellia related to the Bari transposon. Genet Res (Camb). 2011;93:381-5 pubmed publisher..The estimated recent origin of the element and the homogeneity observed between copies found in the genome suggests that msechBari could be active in D. sechellia. ..