title: Mouse microRNA profiles determined with a new and sensitive cloning method.
abstract: MicroRNAs (miRNAs) are noncoding RNA molecules of 21 to 24 nt that regulate the expression of target genes in a post-transcriptional manner. Although evidence indicates that miRNAs play essential roles in embryogenesis, cell differentiation and pathogenesis of human diseases, extensive miRNA profiling in cells or tissues has been hampered by the lack of sensitive cloning methods. Here we describe a highly efficient profiling method, termed miRNA amplification profiling (mRAP), as well as its application both to mouse embryos at various developmental stages and to adult mouse organs. A total of 77,436 Small-RNA species was sequenced, with 11,776 of these sequences found to match previously described miRNAs. With the use of a newly developed computational prediction algorithm, we further identified 229 independent candidates for previously unknown miRNAs. The expression of some of these candidate miRNAs was confirmed by northern blot analysis and whole-mount in situ hybridization. Our data thus indicate that the total number of miRNAs in vertebrates is larger than previously appreciated and that the expression of these molecules is tightly controlled in a tissue- and developmental stage-specific manner.
authors.affiliation: Division of Functional Genomics, Jichi Medical University, 3311-1 Yakushiji, Shimotsukeshi, Tochigi 329-0498, Japan.
authors.forename: Shuji
authors.initials: S
authors.lastname: Takada
authors.forename: Eugene
authors.initials: E
authors.lastname: Berezikov
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Yamashita
authors.forename: Mariana
authors.initials: M
authors.lastname: Lagos-Quintana
authors.forename: Wigard P
authors.initials: WP
authors.lastname: Kloosterman
authors.forename: Munehiro
authors.initials: M
authors.lastname: Enomoto
authors.forename: Hisashi
authors.initials: H
authors.lastname: Hatanaka
authors.forename: Shin-ichiro
authors.initials: S
authors.lastname: Fujiwara
authors.forename: Hideki
authors.initials: H
authors.lastname: Watanabe
authors.forename: Manabu
authors.initials: M
authors.lastname: Soda
authors.forename: Young Lim
authors.initials: YL
authors.lastname: Choi
authors.forename: Ronald H A
authors.initials: RH
authors.lastname: Plasterk
authors.forename: Edwin
authors.initials: E
authors.lastname: Cuppen
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Mano
mesh_terms: D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular / Q000379:methods*; D004622:Embryo, Mammalian / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D019169:Jurkat Cells; D051379:Mice; D035683:MicroRNAs / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D014018:Tissue Distribution
chemical_list: D035683:MicroRNAs