Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3' trailers.
BACKGROUND
MicroRNAs (miRNAs) are approximately 22-nt small non-coding regulatory RNAs that have generally been considered to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in the nucleus.


RESULTS
To determine the number of miRNAs localized to the nucleus, we systematically investigated the subcellular distribution of small RNAs (sRNAs) by independent deep sequencing sequenced of the nuclear and cytoplasmic pools of 18- to 30-nucleotide sRNAs from human cells. We identified 339 nuclear and 324 cytoplasmic known miRNAs, 300 of which overlap, suggesting that the majority of miRNAs are imported into the nucleus. With the exception of a few miRNAs evidently enriched in the nuclear pool, such as the mir-29b, the ratio of miRNA abundances in the nuclear fraction versus in the cytoplasmic fraction vary to some extent. Moreover, our results revealed that a large number of tRNA 3' trailers are exported from the nucleus and accumulate in the cytoplasm. These tRNA 3' trailers accumulate in a variety of cell types, implying that the biogenesis of tRNA 3' trailers is conserved and that they have a potential functional role in vertebrate cells.


CONCLUSIONS
Our results provide the first comprehensive view of the subcellular distribution of diverse sRNAs and new insights into the roles of miRNAs and tRNA 3' trailers in the cell.
Liao
Jian-You
JY
State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, People's Republic of China.
Ma
Li-Ming
LM
Guo
Yan-Hua
YH
Zhang
Yu-Chan
YC
Zhou
Hui
H
Shao
Peng
P
Chen
Yue-Qin
YQ
Qu
Liang-Hu
LH
D000818:Animals; D001483:Base Sequence; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000235:genetics*; D002645:Chickens / Q000235:genetics; D004285:Dogs; D005786:Gene Expression Regulation; D006801:Humans; D035683:MicroRNAs / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D034443:RNA Transport / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA / Q000379:methods*; D018709:Statistics, Nonparametric; D013347:Subcellular Fractions / Q000378:metabolism
D035683:MicroRNAs; D012343:RNA, Transfer