Genome dynamics最新文献

Being the major heterochromatin constituents, satellite DNAs serve important roles in heterochromatin establishment and regulation. Their transcripts act as epigenetic signals required for organization of pericentromeric heterochromatin during embryogenesis and are necessary for developmental progression. In addition, satellite DNAs and their transcripts potentially play an active role in modulating gene expression and epigenetic states of a genome. Due to the presence of promoter elements and transcription factor binding sites within a sequence, satellite DNAs can interfere with the expression of nearby genes. Gene activity can be directly controlled by the number of repeats in a section of satellite DNA. In the case of stress, transcriptional activation of pericentromeric satellite DNAs seems to be part of a general stress response program activated by environmental stimuli. Such diverse forms of genome regulation modulated by satellite DNAs may be controlled by selective pressures and could influence the adaptability of the organism.

Fish exhibit the greatest diversity of all vertebrates, making this group extremely attractive for the study of a number of evolutionary questions. Fish genomes have intrinsic characteristics that may be responsible for the amazing diversity of fish species observed, but little is known about their structure and organization. A large amount of data from mapping of repetitive DNA sequences of several species has been generated, providing an important source of information for better understanding the involvement of repetitive DNA sequences in chromosomal organization. Almost all classes of repeated DNAs have been mapped in fishes, and all fish genomes analyzed contain at least one, mostly all types of repetitive DNAs. DNA sequence data combined with the chromosomal mapping of these repeated elements by means of cytogenetic techniques can provide a clearer picture of the genome, which is not yet clearly defined, even if already sequenced. In this chapter, we do not aim to analyze all available data on the chromosomal distribution of repetitive DNAs in fish species, but instead wish to draw attention to the impact of repetitive DNA sequences on fish karyotyping and genome evolution, with a particular focus on B chromosome origin and maintenance and on the differentiation of sex chromosomes. We also discuss the integration of chromosome analysis and genomic data, which represents a promising tool for fish cytogenomics.

Satellite DNAs represent the most abundant fraction of repetitive sequences in genomes of almost all eukaryotic species. Long arrays of satellite DNA monomers form densely packed heterochromatic genome compartments and also span over the functionally important centromere locus. Many specific features can be ascribed to the evolution of tandemly repeated genomic components. This chapter focuses on the structural and evolutionary dynamics of satellite DNAs and the potential molecular mechanisms responsible for rapid changes of the genomic areas they constitute. Monomer sequences of a satellite DNA evolve concertedly through a process of molecular drive in which mutations are homogenized in a genome and fixed in a population. This process results in divergence of satellite sequences in reproductively isolated groups of organisms. However, some satellite DNA sequences are conserved over long evolutionary periods. Since many satellite DNAs exist in a genome, the evolution of species-specific satellite DNA composition can be directed by copy number changes within a library of satellite sequences common for a group of species. There are 2 important features of these satellite DNAs: long time sequence conservation and, at the same time, proneness to rapid changes through copy number alterations. Sequence conservation may be enhanced by constraints such as those imposed on functional motifs and/or architectural features of a satellite DNA molecule. Such features can limit the selection of sequences able to persist in a genome, and can direct the evolutionary course of satellite DNAs spanning the functional centromeres.

Telomeres have a DNA component composed of repetitive sequences. In most eukaryotes these repeats are very similar in length and sequence and are maintained by a highly conserved specialized cellular enzyme, telomerase. Some exceptions of the telomerase mechanism exist in eukaryotes of which the most studied are concentrated in insects, and from these, Drosophila species stand out in particular. The alternative mechanism of telomere maintenance in Drosophila is based on targeted transposition of 3 very special non-LTR retrotransposons, HeT-A, TART and TAHRE. The fingerprint of the co-evolution between the Drosophila genome and the telomeric retrotransposons is visible in special features of both. In this chapter, we will review the main aspects of Drosophila telomeres and the telomere retrotransposons that explain how this alternative mechanism works, is regulated, and evolves. By going through the different aspects of this symbiotic relationship, we will try to unravel which have been the necessary changes at Drosophila telomeres in order to exert their telomeric function analogously to telomerase telomeres, and also which particularities have been maintained in order to preserve the retrotransposon personality of HeT-A, TART and TAHRE. Drosophila telomeres constitute a remarkable variant that reminds us how exceptions should be treasured in order to widen our knowledge in any particular biological mechanism.

Transposable elements (TEs) are ubiquitous components of eukaryotic genomes. They have considerably affected their size, structure and function. The sequencing of a multitude of eukaryote genomes has revealed some striking differences in the abundance and diversity of TEs among eukaryotes. Protists, plants, insects and vertebrates contain species with large numbers of TEs and species with small numbers, as well as species with diverse repertoires of TEs and species with a limited diversity of TEs. There is no apparent relationship between the complexity of organisms and their TE profile. The profile of TE diversity and abundance results from the interaction between the rate of transposition, the intensity of selection against new inserts, the demographic history of populations and the rate of DNA loss. Recent population genetics studies suggest that selection against new insertions, mostly caused by the ability of TEs to mediate ectopic recombination events, is limiting the fixation of TEs, but that reduction in effective population size, caused by population bottlenecks or inbreeding, significantly reduces the efficacy of selection. These results emphasize the importance of drift in shaping genomic architecture.

SINEs are short interspersed elements derived from cellular RNAs that repetitively retropose via RNA intermediates and integrate more or less randomly back into the genome. SINEs propagate almost entirely vertically within their host cells and, once established in the germline, are passed on from generation to generation. As non-autonomous elements, their reverse transcription (from RNA to cDNA) and genomic integration depends on the activity of the enzymatic machinery of autonomous retrotransposons, such as long interspersed elements (LINEs). SINEs are widely distributed in eukaryotes, but are especially effectively propagated in mammalian species. For example, more than a million Alu-SINE copies populate the human genome (approximately 13% of genomic space), and few master copies of them are still active. In the organisms where they occur, SINEs are a challenge to genomic integrity, but in the long term also can serve as beneficial building blocks for evolution, contributing to phenotypic heterogeneity and modifying gene regulatory networks. They substantially expand the genomic space and introduce structural variation to the genome. SINEs have the potential to mutate genes, to alter gene expression, and to generate new parts of genes. A balanced distribution and controlled activity of such properties is crucial to maintaining the organism's dynamic and thriving evolution.

Tandem repeats are intrinsically highly variable sequences since repeat units are often lost or gained during replication or following unequal recombination events. Because of their low complexity and their instability, these repeats, which are also called satellite repeats, are often considered to be useless 'junk' DNA. However, recent findings show that tandem repeats are frequently found within promoters of stress-induced genes and within the coding regions of genes encoding cell-surface and regulatory proteins. Interestingly, frequent changes in these repeats often confer phenotypic variability. Examples include variation in the microbial cell surface, rapid tuning of internal molecular clocks in flies, and enhanced morphological plasticity in mammals. This suggests that instead of being useless junk DNA, some variable tandem repeats are useful functional elements that confer 'evolvability', facilitating swift evolution and rapid adaptation to changing environments. Since changes in repeats are frequent and reversible, repeats provide a unique type of mutation that bridges the gap between rare genetic mutations, such as single nucleotide polymorphisms, and highly unstable but reversible epigenetic inheritance.

Telomeres are specialized structures found at the end of linear chromosomes. Telomere structure and functions are conserved throughout evolution and are essential for genome stability, preventing chromosome ends from being recognized as damaged DNA and from being fused or degraded by the DNA repair machinery. The structure of telomeres is intrinsically dynamic and affected by multiple processes that impact their length and nucleoprotein composition, thus leading to functional and structural heterogeneity. We review here the most significant facets of telomere metabolism and its dynamics, with an emphasis on human biology.

Eukaryotic genomes are composed of both unique and repetitive DNA sequences. These latter form families of different classes that may be organized in tandem or may be dispersed within genomes with a moderate to high degree of repetitiveness. The repetitive DNA fraction may represent a high proportion of a particular genome due to correlation between genome size and abundance of repetitive sequences, which would explain the differences in genomic DNA contents of different species. In this review, we analyze repetitive DNA diversity and abundance as well as its impact on genome structure, function, and evolution.