title: Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development.
abstract: BACKGROUND
  In eukaryotes, microRNAs (miRNAs) have emerged as critical regulators of gene expression. The Silkworm (Bombyx mori L.) is one of the most suitable lepidopteran insects for studying the molecular aspects of metamorphosis because of its large size, availability of mutants and genome sequence. Besides, this insect also has been amply studied from a physiological and biochemical perspective. Deep sequencing of small RNAs isolated from different stages of silkworm is a powerful tool not only for measuring the changes in miRNA profile but also for discovering novel miRNAs.
  
  
  RESULTS
  We generated small RNA libraries from feeding larvae, spinning larvae, pupae and adults of B. mori and obtained approximately 2.5 million reads of 18-30 nt. Sequence analysis identified 14 novel and 101 conserved miRNAs. Most novel miRNAs are preferentially expressed in pupae, whereas more than 95% of the conserved miRNAs are dynamically regulated during different developmental stages. Remarkably, the miRNA-star (miR*) of four miRNAs are expressed at much higher levels than their corresponding miRNAs, and their expression profiles are distinct from their corresponding miRNA profiles during different developmental stages. Additionally, we detected two antisense miRNA loci (miR-263-S and miR-263-AS; miR-306-S and miR-306-AS) that are expressed in sense and antisense directions. Interestingly, miR-263 and miR-306 are preferentially and abundantly expressed in pupae and adults, respectively.
  
  
  CONCLUSIONS
  We identified 101 homologs of conserved miRNAs, 14 species-specific and two antisense miRNAs in the silkworm. Our results provided deeper insights into changes in conserved and novel miRNA and miRNA* accumulation during development.
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
authors.forename: Guru
authors.initials: G
authors.lastname: Jagadeeswaran
authors.forename: Yun
authors.initials: Y
authors.lastname: Zheng
authors.forename: Niranji
authors.initials: N
authors.lastname: Sumathipala
authors.forename: Haobo
authors.initials: H
authors.lastname: Jiang
authors.forename: Estela L
authors.initials: EL
authors.lastname: Arrese
authors.forename: Jose L
authors.initials: JL
authors.lastname: Soulages
authors.forename: Weixiong
authors.initials: W
authors.lastname: Zhang
authors.forename: Ramanjulu
authors.initials: R
authors.lastname: Sunkar
mesh_terms: D000818:Animals; D001483:Base Sequence; D012831:Bombyx / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D007814:Larva / Q000235:genetics / Q000254:growth & development; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011679:Pupa / Q000235:genetics / Q000254:growth & development; D016372:RNA, Antisense; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D013045:Species Specificity
chemical_list: D035683:MicroRNAs; D016372:RNA, Antisense