title: Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.
abstract: Many studies on conserved noncoding sequences (CNSs) have found that CNSs are enriched significantly in regulatory sequence elements. We conducted whole-genome analysis on plant CNSs to identify lineage-specific CNSs in eudicots, monocots, angiosperms,and vascular plants based on the premise that lineage-specific CNSs define lineage-specific characters and functions in groups of organisms. We identified 27 eudicot, 204 monocot, 6,536 grass, 19 angiosperm, and 2 vascular plant lineage-specific CNSs(lengths range from 16 to 1,517 bp) that presumably originated in their respective common ancestors. A stronger constraint on the CNSs located in the untranslated regions was observed. The CNSs were often flanked by genes involved in transcription regulation. A drop of A+T content near the border of CNSs was observed and CNS regions showed a higher nucleosome occupancy probability. These CNSs are candidate regulatory elements, which are expected to define lineage-specific features of various plant groups.
authors.forename: Nilmini
authors.initials: N
authors.lastname: Hettiarachchi
authors.forename: Kirill
authors.initials: K
authors.lastname: Kryukov
authors.forename: Kenta
authors.initials: K
authors.lastname: Sumiyama
authors.forename: Naruya
authors.initials: N
authors.lastname: Saitou
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D018745:Genome, Plant; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000235:genetics / Q000378:metabolism*; D010944:Plants / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics*; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D016415:Sequence Alignment; D013045:Species Specificity; D020506:Untranslated Regions
chemical_list: D009707:Nucleosomes; D018749:RNA, Plant; D022661:RNA, Untranslated; D020506:Untranslated Regions