Publication Date: 2008 Jan PMID: 18059368
Authors: Henikoff, S.
Journal: Nat Rev Genet

Assembly, mobilization and disassembly of nucleosomes can influence the regulation of gene expression and other processes that act on eukaryotic DNA. Distinct nucleosome-assembly pathways deposit dimeric subunits behind the replication fork or at sites of active processes that mobilize pre-existing nucleosomes. Replication-coupled nucleosome assembly appears to be the default process that maintains silent chromatin, counteracted by active processes that destabilize nucleosomes. Nucleosome stability is regulated by the combined effects of nucleosome-positioning sequences, histone chaperones, ATP-dependent nucleosome remodellers, post-translational modifications and histone variants. Recent studies suggest that histone turnover helps to maintain continuous access to sequence-specific DNA-binding proteins that regulate epigenetic inheritance, providing a dynamic alternative to histone-marking models for the propagation of active chromatin.

MeSH Categories: Adenosine Triphosphate/metabolism, Chromatin/metabolism, DNA/metabolism, *Epigenesis, Genetic, *Gene Expression Regulation, Nucleosomes/*metabolism, Protein Processing, Post-Translational

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Publication Date: 2008 Jan PMID: 18040271
Authors: Barzel, A. - Kupiec, M.
Journal: Nat Rev Genet

Decades of research into homologous recombination have unravelled many of the details concerning the transfer of information between two homologous sequences. By contrast, the processes by which the interacting molecules initially colocalize are largely unknown. How can two homologous needles find each other in the genomic haystack? Is homologous pairing the result of a damage-induced homology search, or is it an enduring and general feature of the genomic architecture that facilitates homologous recombination whenever and wherever damage occurs? This Review presents the homologous-pairing enigma, delineates our current understanding of the process and offers guidelines for future research.

MeSH Categories: DNA Damage, DNA Repair, *Recombination, Genetic, Saccharomyces cerevisiae/genetics, *Sequence Homology, Nucleic Acid

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Publication Date: 2007 Dec PMID: 18007648
Authors: Raff, R. A.
Journal: Nat Rev Genet

Fossils give evo-devo a past. They inform phylogenetic trees to show the direction of evolution of developmental features, and they can reveal ancient body plans. Fossils also provide the primary data that are used to date past events, including divergence times needed to estimate molecular clocks, which provide rates of developmental evolution. Fossils can set boundaries for hypotheses that are generated from living developmental systems, and for predictions of ancestral development and morphologies. Finally, although fossils rarely yield data on developmental processes directly, informative examples occur of extraordinary preservation of soft body parts, embryos and genomic information.

MeSH Categories: Animals, Biodiversity, Developmental Biology, *Evolution, Molecular, *Fossils, Gene Duplication, Genes/*physiology, Genetics, Population, Phylogeny, Variation (Genetics)

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Publication Date: 2007 Dec PMID: 18007649
Authors: Wagner, G. P. - Pavlicev, M. - Cheverud, J. M.
Journal: Nat Rev Genet

A network of interactions is called modular if it is subdivided into relatively autonomous, internally highly connected components. Modularity has emerged as a rallying point for research in developmental and evolutionary biology (and specifically evo-devo), as well as in molecular systems biology. Here we review the evidence for modularity and models about its origin. Although there is an emerging agreement that organisms have a modular organization, the main open problem is the question of whether modules arise through the action of natural selection or because of biased mutational mechanisms.

MeSH Categories: Animals, Biodiversity, *Developmental Biology, *Evolution, Molecular, Fossils, Gene Duplication, Genes, Genetics, Population, Variation (Genetics)

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Publication Date: 2007 Dec PMID: 18007651
Authors: Ferguson-Smith, M. A. - Trifonov, V.
Journal: Nat Rev Genet

The chromosome complements (karyotypes) of animals display a great diversity in number and morphology. Against this background, the genomes of all species are remarkably conserved, not only in transcribed sequences, but also in some chromosome-specific non-coding sequences and in gene order. A close examination with chromosome painting shows that this conservation can be resolved into small numbers of large chromosomal segments. Rearrangement of these segments into different combinations explains much of the observed diversity in species karyotypes. Here we discuss how these rearrangements come about, and show how their analysis can determine the evolutionary relationships of all mammals and their descent from a common ancestor.

MeSH Categories: Animals, *Chromosome Banding, *Chromosome Mapping, *Evolution, Gene Rearrangement, *Karyotyping, Phylogeny

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