title: Transcriptome-Wide Discovery of PASRs (Promoter-Associated Small RNAs) and TASRs (Terminus-Associated Small RNAs) in Arabidopsis thaliana.
abstract: Hints from animals point to the existence of two novel small RNA (sRNA) species surrounding the transcription start sites (TSSs) and the termini of the genes, respectively. In this study, we performed a comprehensive search for the two sRNA species named promoter-associated sRNAs (PASRs) and terminus-associated sRNAs (TASRs) in Arabidopsis. By using sRNA sequencing data from wild type plants and several mutants related to the sRNA biogenesis, Argonaute (AGO) 1- and AGO4-associated sRNA sequencing data, double-stranded RNA sequencing (dsRNA-seq) data, and DNA methylation profiling data, the biogenesis and action pathways of the PASRs and the TASRs were investigated. PASR and TASR peaks were identified on hundreds of the protein-coding genes. Deep analysis uncovered that some of the sRNA peaks were covered by dsRNA-seq reads, and these peaks were significantly repressed in specific mutants. Besides, certain PASRs and TASRs were preferentially recruited by AGO4, and site-specific DNA methylation signals encompassing the genomic loci of these sRNAs were also detected. Accordingly, we proposed a model that certain PASRs and TASRs were generated through a specific Pol IV-, RDR-, DCL-dependent pathway, and they were associated with AGO4 to perform site-specific DNA methylation on their host genes. The above results indicate the existence of PASRs and TASRs in plants. The proposed biogenesis pathway and action mode of the PASRs and TASRs could facilitate us to perform in-depth functional studies on these novel sRNA species.
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China.
authors.forename: Xiaoxia
authors.initials: X
authors.lastname: Ma
authors.affiliation: Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, PR China.
authors.forename: Ning
authors.initials: N
authors.lastname: Han
authors.affiliation: College of Life Sciences, Huzhou University, Huzhou, PR China.
authors.forename: Chaogang
authors.initials: C
authors.lastname: Shao
authors.affiliation: College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, PR China.
authors.forename: Yijun
authors.initials: Y
authors.lastname: Meng
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D060565:Argonaute Proteins / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D061125:Genes, Chloroplast / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012330:RNA, Double-Stranded / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D012330:RNA, Double-Stranded; D018749:RNA, Plant