A mammalian microRNA expression atlas based on small RNA library sequencing.
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.
Landgraf
Pablo
P
Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA.
Rusu
Mirabela
M
Sheridan
Robert
R
Sewer
Alain
A
Iovino
Nicola
N
Aravin
Alexei
A
Pfeffer
Sébastien
S
Rice
Amanda
A
Kamphorst
Alice O
AO
Landthaler
Markus
M
Lin
Carolina
C
Socci
Nicholas D
ND
Hermida
Leandro
L
Fulci
Valerio
V
Chiaretti
Sabina
S
Foà
Robin
R
Schliwka
Julia
J
Fuchs
Uta
U
Novosel
Astrid
A
Müller
Roman-Ulrich
RU
Schermer
Bernhard
B
Bissels
Ute
U
Inman
Jason
J
Phan
Quang
Q
Chien
Minchen
M
Weir
David B
DB
Choksi
Ruchi
R
De Vita
Gabriella
G
Frezzetti
Daniela
D
Trompeter
Hans-Ingo
HI
Hornung
Veit
V
Teng
Grace
G
Hartmann
Gunther
G
Palkovits
Miklos
M
Di Lauro
Roberto
R
Wernet
Peter
P
Macino
Giuseppe
G
Rogler
Charles E
CE
Nagle
James W
JW
Ju
Jingyue
J
Papavasiliou
F Nina
FN
Benzing
Thomas
T
Lichter
Peter
P
Tam
Wayne
W
Brownstein
Michael J
MJ
Bosio
Andreas
A
Borkhardt
Arndt
A
Russo
James J
JJ
Sander
Chris
C
Zavolan
Mihaela
M
Tuschl
Thomas
T
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
D035683:MicroRNAs; D012333:RNA, Messenger