title: Identification of small non-coding RNAs in the planarian Dugesia japonica via deep sequencing.
abstract: Freshwater planarian flatworm possesses an extraordinary ability to regenerate lost body parts after amputation; it is perfect organism model in regeneration and stem cell biology. Recently, small RNAs have been an increasing concern and studied in many aspects, including regeneration and stem cell biology, among others. In the current study, the large-scale cloning and sequencing of sRNAs from the intact and regenerative planarian Dugesia japonica are reported. Sequence analysis shows that sRNAs between 18nt and 40nt are mainly microRNAs and piRNAs. In addition, 209 conserved miRNAs and 12 novel miRNAs are identified. Especially, a better screening target method, negative-correlation relationship of miRNAs and mRNA, is adopted to improve target prediction accuracy. Similar to miRNAs, a diverse population of piRNAs and changes in the two samples are also listed. The present study is the first to report on the important role of sRNAs during planarian Dugesia japonica regeneration.
authors.affiliation: Department of Bioengineering, Zhengzhou University, Zhengzhou, Henan 450001, China.
authors.forename: Yun-Fei
authors.initials: YF
authors.lastname: Qin
authors.forename: Jin-Mei
authors.initials: JM
authors.lastname: Zhao
authors.forename: Zhen-Xia
authors.initials: ZX
authors.lastname: Bao
authors.forename: Zhao-Yu
authors.initials: ZY
authors.lastname: Zhu
authors.forename: Jia
authors.initials: J
authors.lastname: Mai
authors.forename: Yi-Bo
authors.initials: YB
authors.lastname: Huang
authors.forename: Jian-Biao
authors.initials: JB
authors.lastname: Li
authors.forename: Ge
authors.initials: G
authors.lastname: Chen
authors.forename: Ping
authors.initials: P
authors.lastname: Lu
authors.forename: San-Jun
authors.initials: SJ
authors.lastname: Chen
authors.forename: Lin-Lin
authors.initials: LL
authors.lastname: Su
authors.forename: Hui-Min
authors.initials: HM
authors.lastname: Fang
authors.forename: Ji-Ke
authors.initials: JK
authors.lastname: Lu
authors.forename: Yi-Zhe
authors.initials: YZ
authors.lastname: Zhang
authors.forename: Shou-Tao
authors.initials: ST
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D049751:Genome, Helminth / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics; D008969:Molecular Sequence Data; D010932:Planarians / Q000235:genetics* / Q000502:physiology; D018510:RNA, Helminth / Q000235:genetics*; D034741:RNA, Small Interfering / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D012038:Regeneration / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D035683:MicroRNAs; D018510:RNA, Helminth; D034741:RNA, Small Interfering; D058727:RNA, Small Untranslated