The orientation bias of Chi sequences is a general tendency of G-rich oligomers

Gene

Volumn 259, Issue 1-2, 2000, Pages 207-215

  Uno, Reina ^a   Nakayama, Yoichi ^a   Arakawa, Kazuharu ^a   Tomita, Masaru ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

Comparative genomics; Computational analysis; DNA replication; GC skew; Homologous recombination

Indexed keywords

OLIGOMER;

ARTICLE; BACILLUS SUBTILIS; DNA BASE COMPOSITION; DNA REPLICATION; ESCHERICHIA COLI; GENE LOCATION; GENE REPLICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; GENOME; HAEMOPHILUS INFLUENZAE; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL;

BACILLUS SUBTILIS; BASE COMPOSITION; BASE SEQUENCE; DATABASES, FACTUAL; DNA REPLICATION; DNA, BACTERIAL; ESCHERICHIA COLI; GENOME, BACTERIAL; GUANINE; HAEMOPHILUS INFLUENZAE; RECOMBINATION, GENETIC;

BACILLUS SUBTILIS; ESCHERICHIA COLI; HAEMOPHILUS; HAEMOPHILUS INFLUENZAE RD KW20;

EID: 0034707195     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(00)00430-3     Document Type: Article

References (36)

1. Correlation between transcription and C to T mutations in the non-transcribed DNA strand
2. Correlation of chi orientation with transcription indicates a fundamental relationship between recombination and transcription
3. Codon usage can explain GT-rich islands surrounding Chi sites on the Escherichia coli genome
4. A 7-base-pair sequence protects DNA from exonucleolytic degradation in Lactococcus lactis
5. The complete genome sequence of Escherichia coli K-12
6. A five-nucleotide sequence protects DNA from exonucleolytic degradation by AddAB, the RecBCD analogue of Bacillus subtilis
7. The Bacillus subtilis AddAB helicase/nuclease is regulated by its cognate Chi sequence in vitro
8. Genomics, Chi sites and codons: 'Islands of preferred DNA pairing' are oceans of ORFs
9. A broadening view of recombinational DNA repair in bacteria
10. Homologous pairing in vitro stimulated by the recombination hotspot, Chi
11. Recombination initiation: Easy as A, B, C, D... chi?
12. Identification of the lactococcal exonuclease/recombinase and its modulation by the putative Chi sequence
13. Characteristics of Chi distribution on different bacterial genomes
14. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd
15. Strand asymmetries in DNA evolution
16. Recombinational rescue of the stalled DNA replication fork: A model based on analysis of an Escherichia coli strain with a chromosome region difficult to replicate
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18. Biochemistry of homologous recombination in Escherichia coli
19. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis
20. Collapse and repair of replication forks in Escherichia coli
21. Crossover hot-spot instigator (Chi) sequences in Escherichia coli occupy distinct recombination/transcription islands
22. Asymmetric substitution patterns in the two DNA strands of bacteria
23. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression
24. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes
25. PriA-directed replication fork restart in Escherichia coli
26. Replication fork arrest and DNA recombination
27. Strand compositional asymmetry in bacterial and large viral genomes
28. Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces
29. Skewed oligomers and origins of replication
30. RuvAB acts at arrested replication forks
31. The initiation and control of homologous recombination in Escherichia coli
32. Identification of the Chi site of Haemophilus influenzae as several sequences related to the Escherichia coli Chi site
33. The contributions of replication orientation, gene direction, and signal sequences to base-composition asymmetries in bacterial genomes
34. In vitro selection of preferred DNA pairing sequences by the Escherichia coli RecA protein
35. The preference for GT-rich DNA by the yeast Rad51 protein defines a set of universal pairing sequences
36. The recombination hot spot chi is embedded within islands of preferred DNA pairing sequences in the E. coli genome