The evolution of isochores

scientific article (publication date: July 2001)

The evolution of isochores is …
instance of (P31):
scholarly articleQ13442814
review articleQ7318358

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P6179Dimensions Publication ID1012015628
P356DOI10.1038/35080577
P3181OpenCitations bibliographic resource ID2269659
P698PubMed publication ID11433361

P2093author name stringL D Hurst
A Eyre-Walker
P2860cites workInitial sequencing and analysis of the human genomeQ21045365
The Sequence of the Human GenomeQ22065842
Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortiumQ22122334
Mutation rates differ among regions of the mammalian genomeQ24498019
Isochores result from mutation not selectionQ24498046
High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotesQ24522409
Human L1 retrotransposon encodes a conserved endonuclease required for retrotranspositionQ28114795
Warm-blooded isochore structure in Nile crocodile and turtleQ28137686
Isochores and the evolutionary genomics of vertebratesQ28141033
Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotesQ28239616
An analysis of eukaryotic genomes by density gradient centrifugationQ28257568
An approach to the organization of eukaryotic genomes at a macromolecular levelQ28257581
Compositional constraints and genome evolutionQ28290436
The mosaic genome of warm-blooded vertebratesQ28308096
Interspersed repeats and other mementos of transposable elements in mammalian genomesQ29615764
Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposonsQ30004188
Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic dataQ33376219
Directional mutation pressure and neutral molecular evolutionQ33567307
Compositional patterns in the nuclear genome of cold-blooded vertebratesQ33795655
High genomic deleterious mutation rates in hominidsQ34491535
The molecular basis of mutations induced by deoxyribonucleoside triphosphate pool imbalances in mammalian cellsQ34498295
Evolutionary consequences of nonrandom damage and repair of chromatin domainsQ35687509
Precise switching of DNA replication timing in the GC content transition area in the human major histocompatibility complex.Q36569378
A novel pathway for transversion mutation induced by dCTP misincorporation in a mutator strain of CHO cellsQ36764846
DNA precursor pools and ribonucleotide reductase activity: distribution between the nucleus and cytoplasm of mammalian cellsQ36952926
Evolution of a finite population under gene conversionQ37617861
Evolution of chromosome bands: molecular ecology of noncoding DNA.Q38285941
An isochore transition in the NF1 gene region coincides with a switch in the extent of linkage disequilibriumQ39807260
Evidence that both G + C rich and G + C poor isochores are replicated early and late in the cell cycleQ40421468
Correlation between molecular clock ticking, codon usage fidelity of DNA repair, chromosome banding and chromatin compactness in germline cellsQ41458110
The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolutionQ43586352
Cytosine deamination plays a primary role in the evolution of mammalian isochoresQ44875348
An analysis of the bovine genome by Cs2SO4-Ag density gradient centrifugationQ45276990
The genetic consequences of DNA precursor pool imbalance: sequence analysis of mutations induced by excess thymidine at the hamster aprt locusQ46283824
A model for the correlation of mutation rate with GC content and the origin of GC-rich isochores.Q52378242
Mammalian DNA replication: mutation biases and the mutation rate.Q52451474
Deleterious mutations and the evolution of sex.Q52583324
Chromosome localization-dependent compositional bias of point mutations in Alu repetitive sequences.Q52848459
Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells.Q52868583
Covariation of GC content and the silent site substitution rate in rodents: implications for methodology and for the evolution of isochores.Q52927789
Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans.Q52931680
Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequenceQ57234066
The gene-richest bands of human chromosomes replicate at the onset of the S-phaseQ57951190
Local Rates of Recombination Are Positively Correlated with GC Content in the Human GenomeQ60510887
The compositional distribution of coding sequences and DNA molecules in humans and muridsQ67235419
The role of DNA replication and isochores in generating mutation and silent substitution rate variance in mammalsQ67594027
Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteinsQ67994906
Recombination and mammalian genome evolutionQ70469993
Human coding and noncoding DNA: compositional correlationsQ71168152
Changes in ribo- and deoxyribonucleoside triphosphate pools within the cell cycle of a synchronized mouse fibroblast cell lineQ71660514
Pattern of selective constraint in C. elegans and C. briggsae genomesQ73039061
The correlation of protein hydropathy with the base composition of coding sequencesQ73203504
Comparative evolutionary rates of introns and exons in murine rodentsQ73542592
Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elementsQ73643695
Mutation pattern variation among regions of the primate genomeQ73709520
P433issue7
P407language of work or nameEnglishQ1860
P304page(s)549-55
P577publication date2001-07-01
P1433published inNature Reviews GeneticsQ1071824
P1476titleThe evolution of isochores
P478volume2

Reverse relations

cites work (P2860)
Q36208865A Novel Type Pathway-Specific Regulator and Dynamic Genome Environments of a Solanapyrone Biosynthesis Gene Cluster in the Fungus Ascochyta rabiei
Q36882213A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales
Q92690745A century of bias in genetics and evolution
Q34041667A comprehensive reference transcriptome resource for the common house spider Parasteatoda tepidariorum
Q41977055A genomic basis for the evolution of vertebrate transcription factors containing amino Acid runs
Q51915507A markovian approach for the prediction of mouse isochores.
Q34382796A new framework for studying the isochore evolution: estimation of the equilibrium GC content based on the temporal mutation rate model
Q33530134A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes
Q30393184Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes
Q44764026Amino acids runs and genomic compositional biases in vertebrates
Q36242543An Isochore Framework Underlies Chromatin Architecture.
Q35854846An analysis of the gene complement of a marsupial, Monodelphis domestica: evolution of lineage-specific genes and giant chromosomes
Q24546063An isochore map of human chromosomes
Q79266821An isochore map of the human genome based on the Z curve method
Q81007603An isochore transition zone in the NF1 gene region is a conserved landmark of chromosome structure and function
Q37642080Analytical Biases Associated with GC-Content in Molecular Evolution
Q30000333Ancestral alleles in the human genome based on population sequencing data
Q30482794Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
Q28202367Base compositions of genes encoding alpha-actin and lactate dehydrogenase-A from differently adapted vertebrates show no temperature-adaptive variation in G + C content
Q33279052Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content
Q37557286Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
Q36004666Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion
Q35047548Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates
Q24655865Both selective and neutral processes drive GC content evolution in the human genome
Q57251625Can mutation or fixation biases explain the allele frequency distribution of human single nucleotide polymorphisms (SNPs)?
Q41934881Changing effective population size and the McDonald-Kreitman test
Q34382808Chromosomal G + C content evolution in yeasts: systematic interspecies differences, and GC-poor troughs at centromeres
Q35855816Chromosome Architecture and Genome Organization
Q46258124Codon usage and codon pair patterns in non-grass monocot genomes
Q30684148Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data
Q30478840Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species
Q34389299Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes
Q37318383Comparative genomic study reveals a transition from TA richness in invertebrates to GC richness in vertebrates at CpG flanking sites: an indication for context-dependent mutagenicity of methylated CpG sites
Q37322300Comparative recombination rates in the rat, mouse, and human genomes
Q28763574Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage
Q24558319Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes
Q34618898Compositional biases and polyalanine runs in humans
Q34411619Compositional gradients in Gramineae genes
Q35031378Compositional patterns in the genomes of unicellular eukaryotes
Q34309873Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence
Q24603486Contrasting GC-content dynamics across 33 mammalian genomes: relationship with life-history traits and chromosome sizes
Q35024015Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution
Q39744481DNA helix: the importance of being GC-rich
Q33719158Deciphering heterogeneity in pig genome assembly Sscrofa9 by isochore and isochore-like region analyses
Q22065757Deterministic mutation rate variation in the human genome
Q35794410Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation
Q37695589Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-rich isochores
Q37538168Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes
Q43267755Distribution of DNA methylation, CpGs, and CpG islands in human isochores
Q35212663Distribution of meiotic recombination sites
Q34618832Duplication-dependent CG suppression of the seed storage protein genes of maize
Q28742103Dynamic evolution of base composition: causes and consequences in avian phylogenomics
Q28654800Ecological and evolutionary significance of genomic GC content diversity in monocots
Q22122100Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
Q33654627Estimates of the effect of natural selection on protein-coding content
Q41903111Evidence for deep phylogenetic conservation of exonic splice-related constraints: splice-related skews at exonic ends in the brown alga Ectocarpus are common and resemble those seen in humans.
Q24814018Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
Q34713978Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura.
Q36089885Evidence of selection for an accessible nucleosomal array in human
Q53017853Evidence of selectively driven codon usage in rice: implications for GC content evolution of Gramineae genes.
Q33654639Evidence that localized variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair.
Q64120104Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals
Q36052327Evolution of gene sequence in response to chromosomal location.
Q33265509Evolution of proteomes: fundamental signatures and global trends in amino acid compositions
Q35145835Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes
Q33769248Evolutionary forces affecting synonymous variations in plant genomes.
Q53051252Evolutionary genomics: A positive becomes a negative.
Q35476330Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems
Q34399488Evolutionary rates and gene dispensability associate with replication timing in the archaeon Sulfolobus islandicus
Q33883121Fast evolution of core promoters in primate genomes
Q21145252Forces shaping the fastest evolving regions in the human genome
Q22122007Fundamental concepts in genetics: Genetics and the understanding of selection
Q54920383GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes.
Q37351818GC content and recombination: reassessing the causal effects for the Saccharomyces cerevisiae genome
Q83921204GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates
Q33384130GC content increased at CpG flanking positions of fish genes compared with sea squirt orthologs as a mechanism for reducing impact of DNA methylation
Q36119885GC-Content of Synonymous Codons Profoundly Influences Amino Acid Usage
Q34974317GC-Profile: a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences
Q42598099GC-biased gene conversion and selection affect GC content in the Oryza genus (rice).
Q34587185GC-biased segregation of noncoding polymorphisms in Drosophila
Q85347814GC-made protein disorder sheds new light on vertebrate evolution
Q37273284Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays.
Q37585028Gene conversion in angiosperm genomes with an emphasis on genes duplicated by polyploidization
Q34335541Gene conversion occurs within the mating-type locus of Cryptococcus neoformans during sexual reproduction
Q40877299Genes on human chromosome 19 show extreme divergence from the mouse orthologs and a high GC content
Q38708379Genome Organization and Chromosome Architecture
Q34273327Genome evolution in filamentous plant pathogens: why bigger can be better
Q37241262Genome size and GC content evolution of Festuca: ancestral expansion and subsequent reduction
Q37421075Genome-wide colonization of gene regulatory elements by G4 DNA motifs
Q50961941Genome-wide copy number profiling using high-density SNP array in chickens.
Q37625484Genomes as documents of evolutionary history
Q28611281Genomic Analysis of an Ascomycete Fungus from the Rice Planthopper Reveals How It Adapts to an Endosymbiotic Lifestyle
Q33668518GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolution
Q35458052Guanine quadruplexes are formed by specific regions of human transposable elements
Q34485607Hearing silence: non-neutral evolution at synonymous sites in mammals
Q33243412High guanine and cytosine content increases mRNA levels in mammalian cells
Q47398534High mutation rates in human and ape pseudoautosomal genes
Q37158110High-Throughput Sequencing Reveals Single Nucleotide Variants in Longer-Kernel Bread Wheat
Q21145834Hotspots of biased nucleotide substitutions in human genes
Q42119657Hotspots of mutation and breakage in dog and human chromosomes
Q35018004Human genome replication proceeds through four chromatin states.
Q30476270Human microRNAs target a functionally distinct population of genes with AT-rich 3' UTRs
Q42073649Human-specific CpG "beacons" identify loci associated with human-specific traits and disease
Q79202075Identification of isochore boundaries in the human genome using the technique of wavelet multiresolution analysis
Q41043683Immunocytological analysis of meiotic recombination in two anole lizards (Squamata, Dactyloidae).
Q36808815Impact of GC content on gene expression pattern in chicken
Q55153017Impact of mating systems on patterns of sequence polymorphism in flowering plants.
Q33762440Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes
Q34994441Informatics for unveiling hidden genome signatures
Q34135136Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution
Q44861956Interspecific and intragenic differences in codon usage bias among vertebrate myosin heavy-chain genes.
Q52710198Intronic AT skew is a defendable proxy for germline transcription but does not predict crossing-over or protein evolution rates in Drosophila melanogaster.
Q82741662Introns form compositional clusters in parallel with the compositional clusters of the coding sequences to which they pertain
Q41010776IsoFinder: computational prediction of isochores in genome sequences
Q39504815IsoPlotter(+): A Tool for Studying the Compositional Architecture of Genomes
Q52026892Isochore chromosome maps of the human genome.
Q28307507Isochore patterns and gene distributions in fish genomes
Q44598570Isochore structures in the genome of the plant Arabidopsis thaliana
Q28245084Isochore structures in the mouse genome
Q36247591Isochores and tissue-specificity
Q28767148Isochores exhibit evidence of genes interacting with the large-scale genomic environment
Q44240026Isochores, GC3 and mutation biases in the human genome
Q74083861Isochores: dream or reality?
Q36001682Large homogeneous genome regions (isochores) in soybean [glycine max (L.) merr].
Q52806484Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans.
Q34354530Less is more in mammalian phylogenomics: AT-rich genes minimize tree conflicts and unravel the root of placental mammals
Q42136150Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models.
Q39690641Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability
Q33467737Measuring the rates of spontaneous mutation from deep and large-scale polymorphism data
Q45786550Meiotic recombination strongly influences GC-content evolution in short regions in the mouse genome
Q28190897Misunderstandings about isochores. Part 1
Q42857437Models for the evolution of GC content in asexual fungi Candida albicans and C. dubliniensis
Q46269573Mutational Biases and GC-Biased Gene Conversion Affect GC Content in the Plastomes of Dendrobium Genus
Q33332467Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation
Q24801512Noncoding DNA, isochores and gene expression: nucleosome formation potential
Q57161881Numerous potentially functional but non-genic conserved sequences on human chromosome 21
Q35169862Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots
Q33407926Partial correlation analysis indicates causal relationships between GC-content, exon density and recombination rate in the human genome
Q43415916Patterns and evolution of nucleotide landscapes in seed plants
Q57228180Patterns of Vertebrate Isochore Evolution Revealed by Comparison of Expressed Mammalian, Avian, and Crocodilian Genes
Q75316265Phylogenetic analysis of vertebrate fibrillar collagen locates the position of zebrafish alpha3(I) and suggests an evolutionary link between collagen alpha chains and hox clusters
Q43623113Phylogenetic patterns of GC-biased gene conversion in placental mammals and the evolutionary dynamics of recombination landscapes
Q36082288Phylogenomic analysis of the emergence of GC-rich transcription elements
Q50225360Plasmodium vivax Biology: Insights Provided by Genomics, Transcriptomics and Proteomics.
Q57675399Quantifying the Slightly Deleterious Mutation Model of Molecular Evolution
Q37208453Radial chromatin positioning is shaped by local gene density, not by gene expression
Q24805150Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana
Q35076941Recombination explains isochores in mammalian genomes
Q36397980Recombination is associated with the evolution of genome structure and worker behavior in honey bees
Q35199917Reduced representation genome sequencing suggests low diversity on the sex chromosomes of tonkean macaque monkeys
Q25257867Regions of extreme synonymous codon selection in mammalian genes
Q81384054Repeats and correlations in human DNA sequences
Q42152783Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema
Q36838253Sensory genes and mate choice: evidence that duplications, mutations, and adaptive evolution alter variation in mating cue genes and their receptors
Q22122484Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
Q35204488Sex chromosomes: how X-Y recombination stops
Q30316555Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.
Q33988573Spatial analyses of mono, di and trinucleotide trends in plant genes
Q40949205Species-specific class I gene expansions formed the telomeric 1 mb of the mouse major histocompatibility complex
Q38442406Structural organization of human replication timing domains.
Q52937994Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects.
Q35111424Substitution patterns are GC-biased in divergent sequences across the metazoans
Q28741528Substitution patterns are under different influences in primates and rodents
Q48302388Substitution rates in the X- and Y-linked genes of the plants, Silene latifolia and S. dioica
Q31058303Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals
Q36882197The Anolis Lizard Genome: An Amniote Genome without Isochores?
Q33973441The Anolis lizard genome: an amniote genome without isochores
Q33395879The GC-heterogeneity of teleost fishes
Q64921319The Interaction of Natural Selection and GC Skew May Drive the Fast Evolution of a Sand Rat Homeobox Gene.
Q39153845The Isochores as a Fundamental Level of Genome Structure and Organization: A General Overview
Q35134468The Plasmodium vivax genome sequencing project
Q78617751The base composition of the genes is correlated with the secondary structures of the encoded proteins
Q35047552The bimodal distribution of genic GC content is ancestral to monocot species
Q36935355The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC
Q79266826The correlation between GC3 and hydropathy in human genes
Q28285823The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny
Q41940536The evolution of isochore patterns in vertebrate genomes
Q42534424The evolution of isochores: evidence from SNP frequency distributions
Q60302690The formation of chromatin domains involves a primary step based on the 3-D structure of DNA
Q53919277The genome: an isochore ensemble and its evolution.
Q33332585The impact of recombination on nucleotide substitutions in the human genome
Q37357996The influence of genomic context on mutation patterns in the human genome inferred from rare variants.
Q30891556The isochore patterns of invertebrate genomes
Q28602553The mutation spectrum in genomic late replication domains shapes mammalian GC content
Q35785915The neoselectionist theory of genome evolution
Q43003763The rate, not the spectrum, of base pair substitutions changes at a GC-content transition in the human NF1 gene region: implications for the evolution of the mammalian genome structure
Q60302712The short-sequence design of DNA and its involvement in the 3-D structure of the genome
Q34049625Transcriptome map of mouse isochores.
Q34410000Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens
Q42160320Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype
Q43159836Unexpected selection to retain high GC content and splicing enhancers within exons of multiexonic lncRNA loci
Q34616500Vanishing GC-rich isochores in mammalian genomes.
Q34598376Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans
Q33932596Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee
Q47345644cDNA-based gene mapping and GC3 profiling in the soft-shelled turtle suggest a chromosomal size-dependent GC bias shared by sauropsids.

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