3 research outputs found
Elucidating Genome Structure Evolution by Analysis of Isoapostatic Gene Clusters using Statistics of Variance of Gene Distances
Identifying genomic regions that descended from a common ancestor is important
for understanding the function and evolution of genomes. In related genomes,
clusters of homologous gene pairs serve as evidence for candidate homologous
regions, which make up genomic core. Previous studies on the structural
organization of bacterial genomes revealed that basic backbone of genomic core
is interrupted by genomic islands. Here, we applied statistics using variance of
distances as a measure to classify conserved genes within a set of genomes
according to their “isoapostatic” relationship, which keeps
nearly identical distances of genes. The results of variance statistics analysis
of cyanobacterial genomes including Prochlorococcus,
Synechococcus, and Anabaena indicated that
the conserved genes are classified into several groups called “virtual
linkage groups (VLGs)” according to their positional conservation of
orthologs over the genomes analyzed. The VLGs were used to define mosaic domain
structure of the genomic core. The current model of mosaic genomic domains can
explain global evolution of the genomic core of cyanobacteria. It also
visualizes islands of lateral gene transfer. The stability and the robustness of
the variance statistics are discussed. This method will also be useful in
deciphering the structural organization of genomes in other groups of
bacteria
Identification and Characterization of Novel Genotoxic Stress-Inducible Nuclear Long Noncoding RNAs in Mammalian Cells
Whole transcriptome analyses have revealed a large number of novel transcripts including long and short noncoding RNAs (ncRNAs). Currently, there is great interest in characterizing the functions of the different classes of ncRNAs and their relevance to cellular processes. In particular, nuclear long ncRNAs may be involved in controlling various aspects of biological regulation, such as stress responses. By a combination of bioinformatic and experimental approaches, we identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Some nuclear long ncRNAs were conserved among vertebrates, whereas others were found only among primates. Expression profiling of the nuclear long ncRNAs in human tissues revealed that most were expressed ubiquitously. A subset of the identified nuclear long ncRNAs was induced by the genotoxic agents mitomycin C or doxorubicin, in HeLa Tet-off cells. There were no commonly altered nuclear long ncRNAs between mitomycin C- and doxorubicin-treated cells. These results suggest that distinct sets of nuclear long ncRNAs play roles in cellular defense mechanisms against specific genotoxic agents, and that particular long ncRNAs have the potential to be surrogate indicators of a specific cell stress