title: A mammalian microRNA expression atlas based on small RNA library sequencing.
abstract: MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.
authors.affiliation: Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA.
authors.forename: Pablo
authors.initials: P
authors.lastname: Landgraf
authors.forename: Mirabela
authors.initials: M
authors.lastname: Rusu
authors.forename: Robert
authors.initials: R
authors.lastname: Sheridan
authors.forename: Alain
authors.initials: A
authors.lastname: Sewer
authors.forename: Nicola
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authors.lastname: Iovino
authors.forename: Alexei
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authors.lastname: Aravin
authors.forename: Sébastien
authors.initials: S
authors.lastname: Pfeffer
authors.forename: Amanda
authors.initials: A
authors.lastname: Rice
authors.forename: Alice O
authors.initials: AO
authors.lastname: Kamphorst
authors.forename: Markus
authors.initials: M
authors.lastname: Landthaler
authors.forename: Carolina
authors.initials: C
authors.lastname: Lin
authors.forename: Nicholas D
authors.initials: ND
authors.lastname: Socci
authors.forename: Leandro
authors.initials: L
authors.lastname: Hermida
authors.forename: Valerio
authors.initials: V
authors.lastname: Fulci
authors.forename: Sabina
authors.initials: S
authors.lastname: Chiaretti
authors.forename: Robin
authors.initials: R
authors.lastname: Foà
authors.forename: Julia
authors.initials: J
authors.lastname: Schliwka
authors.forename: Uta
authors.initials: U
authors.lastname: Fuchs
authors.forename: Astrid
authors.initials: A
authors.lastname: Novosel
authors.forename: Roman-Ulrich
authors.initials: RU
authors.lastname: Müller
authors.forename: Bernhard
authors.initials: B
authors.lastname: Schermer
authors.forename: Ute
authors.initials: U
authors.lastname: Bissels
authors.forename: Jason
authors.initials: J
authors.lastname: Inman
authors.forename: Quang
authors.initials: Q
authors.lastname: Phan
authors.forename: Minchen
authors.initials: M
authors.lastname: Chien
authors.forename: David B
authors.initials: DB
authors.lastname: Weir
authors.forename: Ruchi
authors.initials: R
authors.lastname: Choksi
authors.forename: Gabriella
authors.initials: G
authors.lastname: De Vita
authors.forename: Daniela
authors.initials: D
authors.lastname: Frezzetti
authors.forename: Hans-Ingo
authors.initials: HI
authors.lastname: Trompeter
authors.forename: Veit
authors.initials: V
authors.lastname: Hornung
authors.forename: Grace
authors.initials: G
authors.lastname: Teng
authors.forename: Gunther
authors.initials: G
authors.lastname: Hartmann
authors.forename: Miklos
authors.initials: M
authors.lastname: Palkovits
authors.forename: Roberto
authors.initials: R
authors.lastname: Di Lauro
authors.forename: Peter
authors.initials: P
authors.lastname: Wernet
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Macino
authors.forename: Charles E
authors.initials: CE
authors.lastname: Rogler
authors.forename: James W
authors.initials: JW
authors.lastname: Nagle
authors.forename: Jingyue
authors.initials: J
authors.lastname: Ju
authors.forename: F Nina
authors.initials: FN
authors.lastname: Papavasiliou
authors.forename: Thomas
authors.initials: T
authors.lastname: Benzing
authors.forename: Peter
authors.initials: P
authors.lastname: Lichter
authors.forename: Wayne
authors.initials: W
authors.lastname: Tam
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Brownstein
authors.forename: Andreas
authors.initials: A
authors.lastname: Bosio
authors.forename: Arndt
authors.initials: A
authors.lastname: Borkhardt
authors.forename: James J
authors.initials: JJ
authors.lastname: Russo
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
mesh_terms: D000818:Animals; D001483:Base Sequence / Q000235:genetics*; D019070:Cell Lineage / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation / Q000235:genetics*; D015723:Gene Library; D019337:Hematologic Neoplasms / Q000235:genetics; D006412:Hematopoietic Stem Cells / Q000378:metabolism; D006801:Humans; D051379:Mice; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012333:RNA, Messenger / Q000235:genetics; D051381:Rats; D012689:Sequence Homology, Nucleic Acid
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger