Premium
Analysis of RDR 1 / RDR 2 / RDR 6 ‐independent small RNA s in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of short interfering RNA loci
Author(s) -
Polydore Seth,
Axtell Michael J.
Publication year - 2018
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13919
Subject(s) - arabidopsis thaliana , biology , genetics , gene , mutant
Summary Plant small RNA s ( sRNA s) modulate key physiological mechanisms through post‐transcriptional and transcriptional silencing of gene expression. Small RNA s fall into two major categories: those are reliant on RNA ‐dependent RNA polymerases ( RDR s) for biogenesis and those that are not. Known RDR 1 / 2 / 6 ‐dependent sRNA s include phased and repeat‐associated short interfering RNA s, while known RDR 1 / 2 / 6 ‐independent sRNA s are primarily micro RNA s (mi RNA ) and other hairpin‐derived sRNA s. In this study we produced and analyzed sRNA ‐seq libraries from rdr1 / rdr2 / rdr6 triple mutant plants. We found 58 previously annotated mi RNA loci that were reliant on RDR 1 , ‐ 2 , or ‐ 6 function, casting doubt on their classification. We also found 38 RDR 1 / 2 /6‐independent sRNA loci that are not MIRNA s or otherwise hairpin‐derived, and did not fit into other known paradigms for sRNA biogenesis. These 38 sRNA ‐producing loci have as‐yet‐undescribed biogenesis mechanisms, and are frequently located in the vicinity of protein‐coding genes. Altogether, our analysis suggests that these 38 loci represent one or more undescribed types of sRNA in Arabidopsis thaliana .