Annual Review of Genetics
Vol. 28:27-47 (Volume publication date December 1994)
https://doi.org/10.1146/annurev.ge.28.120194.000331
Simon Alberti and Dorothee Dormann
Vol. 53, 2019
We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
Figure 1: The phase diagram depicted is obtained by systematically changing two conditions (e.g., concentration, salt, pH) and determining the regions in which the system switches from a one-phase sta...
Figure 2: Theoretical possibilities of how disease phenotypes can arise from aberrant phase separation and condensate formation. Diseases can arise because of alterations to the mechanism of assembly,...
Figure 3: Evidence for disturbed phase separation and condensate formation in neurodegeneration, cancer, and infectious diseases. In neurodegenerative diseases, mutations or repeat expansions, abnorma...
Kenneth S. Zaret
Vol. 54, 2020
Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA sequence motifs that are exposed on the surface of a nucleosome and thus access silent genes that are inaccessible to other transcription factors. Pioneer factors ...Read More
Figure 1: Actions of pioneer transcription factors. (a) The pioneer transcription factor (gold sphere) scans laterally across chromatin and targets a nucleosome. (b) The pioneer transcription factor e...
Figure 2: Transcription factor DNA-binding domains (spheres) bind to nucleosomes in diverse methods, such as (a) edge binding, (b) near dyad axis, (c) around the nucleosome, (d) dyad axis, and (e) bin...
Figure 3: DNA-binding domain structures that enable or limit binding to nucleosomes. (a) Two different DNA-binding domain structures are shown interacting with DNA orthogonal to the long axis of the d...
Figure 4: Pioneer transcription factors perturb nucleosome structure in different ways. (a) Pioneer factor binding can facilitate the freeing of its target site from the nucleosome. (b) Binding can ca...
Ana Bošković and Oliver J. Rando
Vol. 52, 2018
Inheritance of genomic DNA underlies the vast majority of biological inheritance, yet it has been clear for decades that additional epigenetic information can be passed on to future generations. Here, we review major model systems for transgenerational ...Read More
Eugene V. Koonin
Vol. 39, 2005
AbstractOrthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Figure 1: The time dynamics of the usage of the terms “ortholog” and “paralog”. The PubMed database was searched using the Entrez search engine with the following queries: “ortholog or orthologs or or...
Figure 2: A hypothetical phylogenetic tree illustrating orthologous and paralogous relationships between three ancestral genes and their descendants in three species. LCA, last common ancestor (of the...
Figure 3: A hypothetical phylogenetic tree illustrating emergence of pseudoorthologs via lineage-specific gene loss.
Figure 4: Effect of horizontal gene transfer on orthology and paralogy. (a) A hypothetical evolutionary scenario with HGT leading to xenology. (b) A hypothetical evolutionary scenario with HGT leading...
Figure 5: Orthology and genome-specific best hits. (A) An evolutionary scheme illustrating the connection between orthology and symmetrical best hits (SymBets). X and Y represent two paralogous genes....
Figure 6: Coverage of selected genomes with clusters of orthologous groups of proteins (C/KOGs). (a) Prokaryotic genomes. (b) Eukaryotic genomes. The data are from (88). Filled volume, genes in C/KOGs...
Figure 7: Distribution of the number of paralogs in COGs for selected prokaryotic genomes. The data were extracted from the current COG version (88). The plot is shown in the double-logarithmic scale.
Figure 8: Xenologous displacement in situ of the ruvB gene in the mycoplasmas. (A) Organization of the Holliday junction resolvasome operon and surrounding genes in bacteria. COG0632, Holliday junctio...
Figure 9: Horizontal gene transfer leading to pseudoparalogy. The two pseudoparalogous peroxiredoxins from Aquifex aeolicus are shown in red, the three pseudoparalogs from the Thermoplasmas in blue, a...
Figure 10: Rearrangements of gene structure and orthology. (a) Domain architectures of bacterial and archaeal DnaG-like primases. (b) Independent fission of the DNA polymerase I gene in multiple bacte...
Jonathan N. Wells and Cédric Feschotte
Vol. 54, 2020
Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic ...Read More
Figure 1: Summary of replication mechanisms and transposition intermediates, including proposed transposition intermediates and key replication steps for five TE subclasses. YR retrotransposons and Ma...
Figure 2: Structure and taxonomy of eukaryotic transposable elements. The left panel lists unrooted cladograms showing putative relationships between the major TE superfamilies, based on phylogenies o...
Figure 3: Distribution of TEs across the eukaryote phylogeny. Reference genome size (sea green circles) varies dramatically across eukaryotes and is loosely correlated with TE content. Here, the honey...
