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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
- I. Ovcharenko, M. Nóbrega, G. Loots, L. Stubbs
- Biology, Computer ScienceNucleic Acids Res.
- 1 July 2004
The ECR Browser is presented, a tool that provides easy and dynamic access to whole genome alignments of human, mouse, rat and fish sequences and provides the starting point for discovery of novel genes, identification of distant gene regulatory elements and prediction of transcription factor binding sites.
A comprehensive catalog of human KRAB-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors.
Comparisons between the human genes and ZNF loci mined from the draft mouse, dog, and chimpanzee genomes identified 103 KRAB-ZNF genes that are conserved in mammals but also highlighted a substantial level of lineage-specific change.
Mulan: multiple-sequence local alignment and visualization for studying function and evolution.
The uses and applications of the Mulan tool are illustrated through multispecies comparisons of the GATA3 gene locus and the identification of elements that are conserved in a different way in avians than in other genomes, allowing speculation on the evolution of birds.
Evolution and functional classification of vertebrate gene deserts.
- I. Ovcharenko, G. Loots, M. Nóbrega, R. Hardison, W. Miller, L. Stubbs
- Biology, MedicineGenome research
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct…
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.
This map is based on a comparison of the sequences of three domestic chicken breeds with that of their wild ancestor, red jungle fowl, and indicates that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds.
Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution
To illuminate the function and evolutionary history of both genomes, mouse DNA related to human chromosome 19 is sequenced and breakpoints of all 15 evolutionary rearrangements are sequenced, providing a view of the forces that drive chromosome evolution in mammals.
Differential expansion of zinc-finger transcription factor loci in homologous human and mouse gene clusters.
- M. Shannon, A. Hamilton, L. Gordon, E. Branscomb, L. Stubbs
- Biology, MedicineGenome research
- 1 June 2003
It is deduced that duplication and loss of ancestral cluster members occurred independently in the primate and rodent lineages after divergence, yielding substantially different ZNF gene repertoires in humans and mice.
The ancestral gene for transcribed, low-copy repeats in the Prader-Willi/Angelman region encodes a large protein implicated in protein trafficking, which is deficient in mice with neuromuscular and…
The identification of the ancestral gene ( HERC2) and a family of duplicated, truncated copies that comprise these low-copy repeats suggest that Herc2 is an important gene encoding a GEF involved in protein trafficking and degradation pathways in the cell.
Methylation-sensitive binding of transcription factor YY1 to an insulator sequence within the paternally expressed imprinted gene, Peg3.
- Joomyeong Kim, A. Kollhoff, A. Bergmann, L. Stubbs
- Biology, MedicineHuman molecular genetics
- 1 February 2003
This study is the first report demonstrating the involvement of YY1 in methylation-sensitive insulator activity and suggests a potential role of this highly conserved protein in mammalian genomic imprinting.