Speaker: Prof. Saitou Naruya (Division of Population Genetics, National Institute of Genetics, Mishima, Japan)
Title: Evolutionarily conserved nonconding sequences (CNSs) may bridge gap between DNA and morphology
Time:October 31 (Wednesday) 2018, 15: 00pm
Venue:Conference 327, KIZ main campus
Everyone is welcome!
State Key Laboratory of Genetic Resources and Evolution
Laboratory of Comparative Genomics
Conserved non-coding sequences (CNSs) of Eukaryotes are known to be significantly enriched in regulatory sequences. CNSs of diverse lineages follow different patterns in abundance, sequence composition, and location. Hettiarachchi and Saitou (2016; Genome Biology and Evolution, 8: 3377–3392) reported CNSs in diverse groups of Eukaryote genomes (24 fungi, 19 invertebrates, and 12 nonmammalian vertebrates) with respect to GC content heterogeneity. They found that fungi and invertebrate CNSs are predominantly GC rich as in plants they previously observed, whereas vertebrate CNSs are GC poor. This result suggests that CNS GC content transition occurred from ancestral GC rich state of Eukaryotes to GC poor in vertebrate lineage due to enrollment of GC poor transcription factor binding sites that are lineage specific. CNS GC content is closely linked with nucleosome occupancy that determines location and structural architecture of DNAs.
Babarinde and Saitou (2016; Molecular Biology and Evolution, 33: 1807-1817) extracted CNSs conserved between chicken and four mammalian species (human, mouse, dog, and cattle) To test the importance of the CNS genomic location. Intergenic CNSs are often found in clusters in gene deserts, where protein-coding genes are in paucity. ChIP-Seq and RNA-Seq data suggested that CNSs are more likely to be regulatory elements. Physical distances between CNS and their nearest protein coding genes were well conserved between human and mouse genomes, and CNS-flanking genes were often found in evolutionarily conserved genomic neighborhoods. These results suggest that genomic locations of CNSs are important for their regulatory functions. In fact, various kinds of evolutionary constraints may be acting to maintain the genomic locations of CNSs and protein-coding genes in mammals to ensure proper regulation.
Saber and Saitou (2017; Genome Biology and Evolution, 9: 2037–2048) identified 679 Hominoidea restricted highly conserved noncoding sequences (HCNSs) to decipher the underlying genomic basis of Hominoidea-restricted phenotypes. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting intervention of positive Darwinian selection for creating those HCNSs. Their putative target genes are enriched in the nervous system, development and transcription. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development.