| References |
|
|
Belle EMS,
Smith N and
Eyre-Walker A
(2002)
Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis.
Journal of Molecular Evolution
55:
356–363.
|
|
|
Bentley SD and
Parkhill J
(2004)
Comparative genomic structure of prokaryotes.
Annual Review of Genetics
38:
771–792.
|
|
|
Bernardi G
(1986)
Compositional constraints and genome evolution.
Journal of Molecular Evolution
24:
1–11.
|
|
|
Bernardi G
(1995)
The human genome: organization and evolutionary history.
Annual Review of Genetics
29:
445–476.
|
|
|
Brown TC and
Jiricny J
(1988)
Different base mispairs are corrected with different efficiencies and specificities in monkey kidney cells.
Cell
54:
705–711.
|
|
|
Deschavanne P and
Filipski J
(1995)
Correlation of GC content with replication timing and repair mechanisms in weakly expressed Escherichia coli genes.
Nucleic Acids Research
23:
1350–1353.
|
|
|
Duret L and
Arndt PF
(2008)
The impact of recombination on nucleotide substitutions in the human genome.
PLoS Genetics
4(5):
e1000071.
|
|
|
Duret L and
Galtier N
(2009)
Biased gene conversion and the evolution of mammalian genomic landscapes.
Annual Review of Genomics and Human Genetics
10:
285–311.
|
|
|
Eyre-Walker A and
Hurst LD
(2001)
The evolution of isochores.
Nature Reviews. Genetics
2:
549–555.
|
|
|
Filatov DA
(2004)
A gradient of silent substitution rate in the human pseudoautosomal region.
Molecular Biology and Evolution
21:
410–417.
|
|
|
Filipski J
(1987)
Correlation between molecular clock ticking, codon usage, fidelity of DNA-repair, chromosome-banding and chromatin compactness in germline cells.
FEBS Letters
217:
184–186.
|
|
|
Francino MP and
Ochman H
(1997)
Strand asymmetries in DNA evolution.
Trends in Genetics
13:
240–245.
|
|
|
Galtier N and
Lobry JR
(1997)
Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes.
Journal of Molecular Evolution
44:
632–636.
|
|
|
Gilbert N,
Boyle S,
Fiegler H,
Woodfine K and
Carter NP
(2004)
Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers.
Cell
118:
555–566.
|
|
|
Green P,
Ewing B,
Miller W,
Thomas PJ and
Green ED
(2003)
Transcription-associated mutational asymmetry in mammalian evolution.
Nature Genetics
33:
514–517.
|
|
|
Haywood-Farmer E and
Otto SP
(2003)
The evolution of genomic base composition in bacteria.
Evolution
57:
1783–1792.
|
|
|
Hillier LW,
Miller W,
Birney E,
Warren W and
Hardison RC
(2004)
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Nature
432:
695–716.
|
|
|
Hughes S,
Zelus D and
Mouchiroud D
(1999)
Warm-blooded isochore structure in Nile crocodile and turtle.
Molecular Biology and Evolution
16:
1521–1527.
|
|
|
Hurst LD,
Pal C and
Lercher MJ
(2004)
The evolutionary dynamics of eukaryotic gene order.
Nature Reviews. Genetics
5:
299–310.
|
|
|
Kerr ARW,
Peden JF and
Sharp PM
(1997)
Systematic base composition variation around the genome of Mycoplasma genitalium, but not Mycoplasma pneumoniae.
Molecular Microbiology
25:
1177–1179.
|
|
|
Ko WY,
Piao S and
Akashi H
(2006)
Strong regional heterogeneity in base composition evolution on the Drosophila X chromosome.
Genetics
174:
349–362.
|
|
|
Kong A,
Gudbjartsson DF,
Sainz J,
Jonsdottir GM and
Gudjonsson SA
(2002)
A high-resolution recombination map of the human genome.
Nature Genetics
31:
241–247.
|
|
|
Kudla G,
Lipinski L,
Caffin F,
Helwak A and
Zylicz M
(2006)
High guanine and cytosine content increases mRNA levels in mammalian cells.
PLoS Biology
4:
e180.
|
|
|
Kunkel TA
(2004)
DNA replication fidelity.
Journal of Biological Chemistry
279:
16895–16898.
|
|
|
Kunkel TA and
Alexander PS
(1986)
The base substitution fidelity of eukaryotic DNA-polymerases: mispairing frequencies, site preferences, insertion preferences, and base substitution by dislocation.
Journal of Biological Chemistry
261:
160–166.
|
|
|
Kunz BA and
Kohalmi SE
(1991)
Modulation of mutagenesis by deoxyribonucleotide levels.
Annual Review of Genetics
25:
339–359.
|
|
|
Lercher MJ and
Hurst LD
(2002)
Human SNP variability and mutation rate are higher in regions of high recombination.
Trends in Genetics
18:
337–340.
|
|
|
Mancera E,
Bourgon R,
Brozzi A,
Huber W and
Steinmetz LM
(2008)
High-resolution mapping of meiotic crossovers and non-crossovers in yeast.
Nature
454:
479–485.
|
|
|
Mathews CK
(2006)
DNA precursor metabolism and genomic stability.
FASEB Journal
20:
1300–1314.
|
|
|
Meunier J and
Duret L
(2004)
Recombination drives the evolution of GC-content in the human genome.
Molecular Biology and Evolution
21:
984–990.
|
|
|
Montoya-Burgos JI,
Boursot P and
Galtier N
(2003)
Recombination explains isochores in mammalian genomes.
Trends in Genetics
19:
128–130.
|
|
|
Nekrutenko A and
Li WH
(2000)
Assessment of compositional heterogeneity within and between eukaryotic genomes.
Genome Research
10:
1986–1995.
|
|
|
Rocha EP and
Feil EJ
(2010)
Mutational patterns cannot explain genome composition: are there any neutral sites in the genomes of bacteria?
PLoS Genetics
6(9):
e1001104.
|
|
|
Rocha EPC and
Danchin A
(2002)
Base composition bias might result from competition for metabolic resources.
Trends in Genetics
18:
291–294.
|
|
|
Sharp PM,
Emery LR and
Zeng K
(2010)
Forces that influence the evolution of codon bias.
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
365:
1203–1212.
|
|
|
Sharp PM and
Lloyd AT
(1993)
Regional base composition variation along yeast chromosome III: evolution of chromosome primary structure.
Nucleic Acids Research
21:
179–183.
|
|
|
Spencer CCA,
Deloukas P,
Hunt S,
Mullikin J and
Myers S
(2006)
The influence of recombination on human genetic diversity.
PLoS Genetics
2:
1375–1385.
|
|
|
Sueoka N
(1961)
Variation and heterogeneity of base composition of deoxyribonucleic acids: a compilation of Old and New Data.
Journal of Molecular Biology
3:
31–31.
|
|
|
Touchon M,
Hoede C,
Tenaillon O et al.
(2009)
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.
PLoS Genetics
5:
e1000344.
|
|
|
Ussery DW and
Hallin PF
(2004)
Genome update: AT content in sequenced prokaryotic genomes.
Microbiology
150:
749–752.
|
|
|
Vinogradov AE
(2005)
Noncoding DNA, isochores and gene expression: nucleosome formation potential.
Nucleic Acids Research
33:
559–563.
|
|
|
Webster MT,
Smith NGC and
Ellegren H
(2003)
Compositional evolution of noncoding DNA in the human and chimpanzee genomes.
Molecular Biology and Evolution
20:
278–286.
|
|
|
Wolfe KH
(1991)
Mammalian DNA replication: mutation biases and the mutation rate.
Journal of Theoretical Biology
149:
441–451.
|
|
|
Wolfe KH,
Sharp PM and
Li WH
(1989)
Mutation-rates differ among regions of the mammalian genome.
Nature
337:
283–285.
|
|
|
Woodfine K,
Fiegler H,
Beare DM,
Collins JE and
McCann OT
(2004)
Replication timing of the human genome.
Human Molecular Genetics
13:
191–202.
|
| Further Reading |
|
|
Berglund J,
Pollard KS and
Webster MT
(2009)
Hotspots of biased nucleotide substitutions in human genes.
PLoS Biology
7:
e26.
|
|
|
Galtier N and
Duret L
(2007)
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution.
Trends in Genetics
23:
273–277.
|
|
|
Hershberg R and
Petrov DA
(2010)
Evidence that mutation is universally biased towards AT in bacteria.
PLoSs Genetics
6(9):
e1001115.
|
|
|
Hildebrand F,
Meyer A and
Eyre-Walker A
(2010)
Evidence of selection upon genomic GC-content in bacteria.
PLoS Genetics
6(9):
e1001107.
|
|
|
Marais G
(2003)
Biased gene conversion: implications for genome and sex evolution.
Trends in Genetics
19:
330–338.
|
|
|
Myers S,
Bottolo L,
Freeman C,
McVean G and
Donnelly P
(2005)
A fine-scale map of recombination rates and hotspots across the human genome.
Science
310:
321–324.
|
