Journal
BIOINFORMATICS
Volume 26, Issue 11, Pages 1391-1394Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btq150
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Funding
- National Key Basic Research and Development Program of China [2005CB120901]
- National High Technology Research and Development Program of China [2008AA10Z125]
- National Natural Sciences Foundation of China [30771326, 30971743]
- Program for New Century Excellent Talents in University of China [NCET-07-0740]
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High-throughput sequencing (HTS) has opened up a new era for small RNA (sRNA) exploration. Using HTS data for a global survey of sRNAs in 26 angiosperms, elevated GC contents were detected in the monocots, whereas the 5'-terminal compositions were quite uniform among the angiosperms. Chromosome-wide distribution patterns of sRNAs were investigated by using scrolling-window analysis. We performed de novo natural antisense transcript (NAT) prediction, and found that the overlapping regions of trans-NATs, but not cis-NATs, were hotspots for sRNA generation. One cis-NAT generates phased natural antisense short interfering RNAs (nat-siRNAs) specifically from flowers in Arabidopsis, while one in rice produces phased nat-siRNAs from grains, suggesting their organ-specific regulatory roles.
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