Small RNAs in angiosperms: sequence characteristics, distribution and generation | Zendy

Dijun Chen | Zendy; Yijun Meng | Zendy; Xiaoxia Ma | Zendy; Chuanzao Mao | Zendy; Youhuang Bai | Zendy; Junjie Cao | Zendy; Haibin Gu | Zendy; Ping Wu | Zendy; Ming Chen | Zendy

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Small RNAs in angiosperms: sequence characteristics, distribution and generation

Author(s) -

Dijun Chen,

Yijun Meng,

Xiaoxia Ma,

Chuanzao Mao,

Youhuang Bai,

Junjie Cao,

Haibin Gu,

Ping Wu,

Ming Chen

Publication year - 2010

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btq150

Subject(s) - nat , biology , small interfering rna , rna , arabidopsis , small rna , computational biology , scrolling , dna sequencing , transfer rna , genetics , gene , computer science , computer network , artificial intelligence , mutant

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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