title: Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants.
abstract: Noncoding RNAs have been extensively described in plant and animal transcriptomes by using high-throughput sequencing technology. Of these noncoding RNAs, a growing number of long intergenic noncoding RNAs (lincRNAs) have been described in multicellular organisms, however the origins and functions of many lincRNAs remain to be explored. In many eukaryotic genomes, transposable elements (TEs) are widely distributed and often account for large fractions of plant and animal genomes yet the contribution of TEs to lincRNAs is largely unknown. By using strand-specific RNA-sequencing, we profiled the expression patterns of lincRNAs in Arabidopsis, rice and maize, and identified 47 611 and 398 TE-associated lincRNAs (TE-lincRNAs), respectively. TE-lincRNAs were more often derived from retrotransposons than DNA transposons and as retrotransposon copy number in both rice and maize genomes so did TE-lincRNAs. We validated the expression of these TE-lincRNAs by strand-specific RT-PCR and also demonstrated tissue-specific transcription and stress-induced TE-lincRNAs either after salt, abscisic acid (ABA) or cold treatments. For Arabidopsis TE-lincRNA11195, mutants had reduced sensitivity to ABA as demonstrated by longer roots and higher shoot biomass when compared to wild-type. Finally, by altering the chromatin state in the Arabidopsis chromatin remodelling mutant ddm1, unique lincRNAs including TE-lincRNAs were generated from the preceding untranscribed regions and interestingly inherited in a wild-type background in subsequent generations. Our findings not only demonstrate that TE-associated lincRNAs play important roles in plant abiotic stress responses but lincRNAs and TE-lincRNAs might act as an adaptive reservoir in eukaryotes.
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
authors.affiliation: Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
authors.forename: Zhipeng
authors.initials: Z
authors.lastname: Qu
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Lan
authors.initials: L
authors.lastname: Yang
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Qingzhu
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, 200032, China.
authors.forename: Zhi-Hong
authors.initials: ZH
authors.lastname: Liu
authors.affiliation: Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
authors.forename: Trung
authors.initials: T
authors.lastname: Do
authors.affiliation: Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
authors.forename: David L
authors.initials: DL
authors.lastname: Adelson
authors.affiliation: Hainan Key laboratory for Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou, China.
authors.forename: Zhen-Yu
authors.initials: ZY
authors.lastname: Wang
authors.affiliation: Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
authors.forename: Iain
authors.initials: I
authors.lastname: Searle
authors.affiliation: Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, 200032, China.|Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
authors.forename: Jian-Kang
authors.initials: JK
authors.lastname: Zhu
mesh_terms: D000040:Abscisic Acid / Q000494:pharmacology; D017360:Arabidopsis / Q000187:drug effects / Q000235:genetics; D003080:Cold Temperature; D004251:DNA Transposable Elements / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects / Q000235:genetics; D012275:Oryza / Q000187:drug effects / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D012965:Sodium Chloride / Q000494:pharmacology; D003313:Zea mays / Q000187:drug effects / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D062085:RNA, Long Noncoding; D018749:RNA, Plant; D012965:Sodium Chloride; D000040:Abscisic Acid
keywords: abiotic stress; long intergenic noncoding RNAs; noncoding RNAs; transposable element; transposable elements-associated lincRNAs