Sep, 2014
Lineage-Specific Conserved Noncoding Sequences of Plant Genomes: Their Possible Role in Nucleosome Positioning
GENOME BIOLOGY AND EVOLUTION
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- Volume
- 6
- Number
- 9
- First page
- 2527
- Last page
- 2542
- Language
- English
- Publishing type
- Research paper (scientific journal)
- DOI
- 10.1093/gbe/evu188
- Publisher
- OXFORD UNIV PRESS
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, angio-sperms, 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.
- Link information
- ID information
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- DOI : 10.1093/gbe/evu188
- ISSN : 1759-6653
- Pubmed ID : 25364802
- Web of Science ID : WOS:000343249300028