The colorectal microRNAome.
MicroRNAs (miRNAs) are a class of small noncoding RNAs that have important regulatory roles in multicellular organisms. The public miRNA database contains 321 human miRNA sequences, 234 of which have been experimentally verified. To explore the possibility that additional miRNAs are present in the human genome, we have developed an experimental approach called miRNA serial analysis of gene expression (miRAGE) and used it to perform the largest experimental analysis of human miRNAs to date. Sequence analysis of 273,966 small RNA tags from human colorectal cells allowed us to identify 200 known mature miRNAs, 133 novel miRNA candidates, and 112 previously uncharacterized miRNA* forms. To aid in the evaluation of candidate miRNAs, we disrupted the Dicer locus in three human colorectal cancer cell lines and examined known and novel miRNAs in these cells. These studies suggest that the human genome contains many more miRNAs than currently identified and provide an approach for the large-scale experimental cloning of novel human miRNAs in human tissues.
Cummins
Jordan M
JM
The Sidney Kimmel Comprehensive Cancer Center and Howard Hughes Medical Institute, Johns Hopkins University Medical Institutions, Baltimore, MD 21231, USA.
He
Yiping
Y
Leary
Rebecca J
RJ
Pagliarini
Ray
R
Diaz
Luis A
LA
Sjoblom
Tobias
T
Barad
Omer
O
Bentwich
Zvi
Z
Szafranska
Anna E
AE
Labourier
Emmanuel
E
Raymond
Christopher K
CK
Roberts
Brian S
BS
Juhl
Hartmut
H
Kinzler
Kenneth W
KW
Vogelstein
Bert
B
Velculescu
Victor E
VE
D001483:Base Sequence; D045744:Cell Line, Tumor; D003106:Colon / Q000378:metabolism; D015179:Colorectal Neoplasms / Q000235:genetics*; D053487:DEAD-box RNA Helicases; D004722:Endoribonucleases / Q000235:genetics; D015870:Gene Expression; D018390:Gene Targeting; D015894:Genome, Human; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D020365:RNA Helicases / Q000235:genetics; D012334:RNA, Neoplasm / Q000737:chemistry / Q000235:genetics*; D012007:Rectum / Q000378:metabolism; D043244:Ribonuclease III
D035683:MicroRNAs; D012334:RNA, Neoplasm; D004722:Endoribonucleases; C408087:DICER1 protein, human; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases