title: Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants.
abstract: Many plant small RNAs are sequence-specific negative regulators of target mRNAs and/or chromatin. In angiosperms, the two most abundant endogenous small RNA populations are usually 21-nucleotide microRNAs (miRNAs) and 24-nucleotide heterochromatic short interfering RNAs (siRNAs). Heterochromatic siRNAs are derived from repetitive regions and reinforce DNA methylation at targeted loci. The existence and extent of heterochromatic siRNAs in other land plant lineages has been unclear. Using small RNA-sequencing (RNA-seq) of the moss Physcomitrella patens, we identified 1090 loci that produce mostly 23- to 24-nucleotide siRNAs. These loci are mostly in intergenic regions with dense DNA methylation. Accumulation of siRNAs from these loci depends upon P. patens homologs of DICER-LIKE3 (DCL3), RNA-DEPENDENT RNA POLYMERASE2, and the largest subunit of DNA-DEPENDENT RNA POLYMERASE IV, with the largest subunit of a Pol V homolog contributing to expression at a smaller subset of the loci. A MINIMAL DICER-LIKE (mDCL) gene, which lacks the N-terminal helicase domain typical of DCL proteins, is specifically required for 23-nucleotide siRNA accumulation. We conclude that heterochromatic siRNAs, and their biogenesis pathways, are largely identical between angiosperms and P. patens, with the notable exception of the P. patens-specific use of mDCL to produce 23-nucleotide siRNAs.
authors.affiliation: Plant Biology PhD Program, Penn State University, University Park, Pennsylvania 16802 Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 Department of Biology, Penn State University, University Park, Pennsylvania 16802.
authors.forename: Ceyda
authors.initials: C
authors.lastname: Coruh
authors.affiliation: Department of Biology, Penn State University, University Park, Pennsylvania 16802.
authors.forename: Sung Hyun
authors.identifier: http://orcid.org/0000-0002-8191-7181
authors.initials: SH
authors.lastname: Cho
authors.affiliation: Plant Biology PhD Program, Penn State University, University Park, Pennsylvania 16802 Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 Department of Biology, Penn State University, University Park, Pennsylvania 16802.
authors.forename: Saima
authors.initials: S
authors.lastname: Shahid
authors.affiliation: Plant Biology PhD Program, Penn State University, University Park, Pennsylvania 16802 Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 Department of Biology, Penn State University, University Park, Pennsylvania 16802.
authors.forename: Qikun
authors.identifier: http://orcid.org/0000-0003-2489-2907
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Wierzbicki
authors.affiliation: Plant Biology PhD Program, Penn State University, University Park, Pennsylvania 16802 Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802 Department of Biology, Penn State University, University Park, Pennsylvania 16802 mja18@psu.edu.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D053898:Biosynthetic Pathways / Q000235:genetics; D019068:Bryopsida / Q000235:genetics*; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D055786:Gene Knockout Techniques; D017343:Genes, Plant / Q000235:genetics; D006570:Heterochromatin / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D010802:Phylogeny; D010944:Plants / Q000145:classification / Q000235:genetics*; D034741:RNA, Small Interfering / Q000145:classification / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid
chemical_list: D006570:Heterochromatin; D035683:MicroRNAs; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated