title: Genome-wide analysis of single non-templated nucleotides in plant endogenous siRNAs and miRNAs.
abstract: Plant small RNAs are subject to various modifications. Previous reports revealed widespread 3' modifications (truncations and non-templated tailing) of plant miRNAs when the 2'-O-methyltransferase HEN1 is absent. However, non-templated nucleotides in plant heterochromatic siRNAs have not been deeply studied, especially in wild-type plants. We systematically studied non-templated nucleotide patterns in plant small RNAs by analyzing small RNA sequencing libraries from Arabidopsis, tomato, Medicago, rice, maize and Physcomitrella Elevated rates of non-templated nucleotides were observed at the 3' ends of both miRNAs and endogenous siRNAs from wild-type specimens of all species. 'Off-sized' small RNAs, such as 25 and 23 nt siRNAs arising from loci dominated by 24 nt siRNAs, often had very high rates of 3'-non-templated nucleotides. The same pattern was observed in all species that we studied. Further analysis of 24 nt siRNA clusters in Arabidopsis revealed distinct patterns of 3'-non-templated nucleotides of 23 nt siRNAs arising from heterochromatic siRNA loci. This pattern of non-templated 3' nucleotides on 23 nt siRNAs is not affected by loss of known small RNA 3'-end modifying enzymes, and may result from modifications added to longer heterochromatic siRNA precursors.
authors.affiliation: Intercollege Plant Biology PhD Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA Department of Biology, Penn State University, University Park, PA 16802, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.affiliation: Intercollege Plant Biology PhD Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA Department of Biology, Penn State University, University Park, PA 16802, USA.
authors.forename: Nathan R
authors.initials: NR
authors.lastname: Johnson
authors.affiliation: Intercollege Plant Biology PhD Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA Department of Biology, Penn State University, University Park, PA 16802, USA.
authors.forename: Ceyda
authors.initials: C
authors.lastname: Coruh
authors.affiliation: Intercollege Plant Biology PhD Program, Huck Institutes of the Life Sciences, Penn State University, University Park, PA 16802, USA Department of Biology, Penn State University, University Park, PA 16802, USA mja18@psu.edu.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000378:metabolism; D060565:Argonaute Proteins / Q000378:metabolism; D020137:Base Pair Mismatch; D018745:Genome, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D009693:Nucleic Acid Hybridization; D009711:Nucleotides / Q000378:metabolism*; D010944:Plants / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism*; D013698:Templates, Genetic
chemical_list: C471209:AGO4 protein, Arabidopsis; D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D035683:MicroRNAs; D009711:Nucleotides; D018749:RNA, Plant; D034741:RNA, Small Interfering