ABSTRACT
Dispersed genetic elements, such as retrotransposons and Pol-III-transcribed genes, including tRNA and 5S rRNA, cluster and associate with centromeres in fission yeast through the function of condensin. However, the dynamics of these condensin-mediated genomic associations remains unknown. We have examined the 3D motions of genomic loci including the centromere, telomere, rDNA repeat locus, and the loci carrying Pol-III-transcribed genes or long-terminal repeat (LTR) retrotransposons in live cells at as short as 1.5-second intervals. Treatment with carbendazim (CBZ), a microtubule-destabilizing agent, not only prevents centromeric motion, but also reduces the mobility of the other genomic loci during interphase. Further analyses demonstrate that condensin-mediated associations between centromeres and the genomic loci are clonal, infrequent and transient. However, when associated, centromeres and the genomic loci migrate together in a coordinated fashion. In addition, a condensin mutation that disrupts associations between centromeres and the genomic loci results in a concomitant decrease in the mobility of the loci. Our study suggests that highly mobile centromeres pulled by microtubules in cytoplasm serve as 'genome mobility elements' by facilitating physical relocations of associating genomic regions.
Subject(s)
Centromere/genetics , Interphase/genetics , Mitosis/genetics , Schizosaccharomyces/genetics , Adenosine Triphosphatases/genetics , Adenosine Triphosphatases/ultrastructure , Benzimidazoles/pharmacology , Carbamates/pharmacology , DNA, Ribosomal/genetics , DNA, Ribosomal/ultrastructure , DNA-Binding Proteins/genetics , DNA-Binding Proteins/ultrastructure , Genome, Fungal , Microtubules/drug effects , Microtubules/ultrastructure , Mitosis/drug effects , Multiprotein Complexes/genetics , Multiprotein Complexes/ultrastructure , RNA, Ribosomal, 5S/genetics , RNA, Ribosomal, 5S/ultrastructure , RNA, Transfer/genetics , RNA, Transfer/ultrastructure , Retroelements/genetics , Schizosaccharomyces/cytology , Telomere/genetics , Telomere/ultrastructureABSTRACT
We have comprehensively mapped long-range associations between chromosomal regions throughout the fission yeast genome using the latest genomics approach that combines next generation sequencing and chromosome conformation capture (3C). Our relatively simple approach, referred to as enrichment of ligation products (ELP), involves digestion of the 3C sample with a 4 bp cutter and self-ligation, achieving a resolution of 20 kb. It recaptures previously characterized genome organizations and also identifies new and important interactions. We have modeled the 3D structure of the entire fission yeast genome and have explored the functional relationships between the global genome organization and transcriptional regulation. We find significant associations among highly transcribed genes. Moreover, we demonstrate that genes co-regulated during the cell cycle tend to associate with one another when activated. Remarkably, functionally defined genes derived from particular gene ontology groups tend to associate in a statistically significant manner. Those significantly associating genes frequently contain the same DNA motifs at their promoter regions, suggesting that potential transcription factors binding to these motifs are involved in defining the associations among those genes. Our study suggests the presence of a global genome organization in fission yeast that is functionally similar to the recently proposed mammalian transcription factory.
