MicroRNA Expression Profiling of Single Whole Embryonic Stem Cells

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2006 Jan 26

PMID 16434699

Citations 141

Authors

Fuchou Tang

Petra Hajkova

Sheila C Barton

Kaiqin Lao

M Azim Surani

Affiliations

Soon will be listed here.

Abstract

MicroRNAs (miRNAs) are a class of 17-25 nt non-coding RNAs that have been shown to have critical functions in a wide variety of biological processes during development. Recently developed miRNA microarray techniques have helped to accelerate research on miRNAs. However, in some instances there is only a limited amount of material available for analysis, which requires more sensitive techniques that can preferably work on single cells. Here we demonstrate that it is possible to analyse miRNA in single cells by using a real-time PCR-based 220-plex miRNA expression profiling method. Development of this technique will greatly facilitate miRNA-related research on cells, such as the founder population of primordial germ cells where rapid and dynamic changes occur in a few cells, and for analysing heterogeneous population of cells. In these and similar cases, our method of single cell analysis is critical for elucidating the diverse roles of miRNAs.

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References

Miska E, Alvarez-Saavedra E, Townsend M, Yoshii A, Sestan N, Rakic P . Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 2004; 5(9):R68. PMC: 522875. DOI: 10.1186/gb-2004-5-9-r68. View

Calin G, Liu C, Sevignani C, Ferracin M, Felli N, Dumitru C . MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci U S A. 2004; 101(32):11755-60. PMC: 511048. DOI: 10.1073/pnas.0404432101. View

Babak T, Zhang W, Morris Q, Blencowe B, Hughes T . Probing microRNAs with microarrays: tissue specificity and functional inference. RNA. 2004; 10(11):1813-9. PMC: 1370668. DOI: 10.1261/rna.7119904. View

Sioud M, Rosok O . Profiling microRNA expression using sensitive cDNA probes and filter arrays. Biotechniques. 2004; 37(4):574-6, 578-80. DOI: 10.2144/04374ST01. View

Barad O, Meiri E, Avniel A, Aharonov R, Barzilai A, Bentwich I . MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. Genome Res. 2004; 14(12):2486-94. PMC: 534673. DOI: 10.1101/gr.2845604. View

Sun Y, Koo S, White N, Peralta E, Esau C, Dean N . Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res. 2004; 32(22):e188. PMC: 545483. DOI: 10.1093/nar/gnh186. View

Liang R, Li W, Li Y, Tan C, Li J, Jin Y . An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res. 2005; 33(2):e17. PMC: 548377. DOI: 10.1093/nar/gni019. View

Baskerville S, Bartel D . Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA. 2005; 11(3):241-7. PMC: 1370713. DOI: 10.1261/rna.7240905. View

Thomson J, Parker J, Perou C, Hammond S . A custom microarray platform for analysis of microRNA gene expression. Nat Methods. 2005; 1(1):47-53. DOI: 10.1038/nmeth704. View

10.

Nelson P, Baldwin D, Marie Scearce L, Oberholtzer J, Tobias J, Mourelatos Z . Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods. 2005; 1(2):155-61. DOI: 10.1038/nmeth717. View

11.

Lu J, Getz G, Miska E, Alvarez-Saavedra E, Lamb J, Peck D . MicroRNA expression profiles classify human cancers. Nature. 2005; 435(7043):834-8. DOI: 10.1038/nature03702. View

12.

Wang J, Dick J . Cancer stem cells: lessons from leukemia. Trends Cell Biol. 2005; 15(9):494-501. DOI: 10.1016/j.tcb.2005.07.004. View

13.

Jiang J, Lee E, Gusev Y, Schmittgen T . Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res. 2005; 33(17):5394-403. PMC: 1236977. DOI: 10.1093/nar/gki863. View

14.

Chen C, Ridzon D, Broomer A, Zhou Z, Lee D, Nguyen J . Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005; 33(20):e179. PMC: 1292995. DOI: 10.1093/nar/gni178. View

15.

Saitou M, Barton S, Surani M . A molecular programme for the specification of germ cell fate in mice. Nature. 2002; 418(6895):293-300. DOI: 10.1038/nature00927. View

16.

Houbaviy H, Murray M, Sharp P . Embryonic stem cell-specific MicroRNAs. Dev Cell. 2003; 5(2):351-8. DOI: 10.1016/s1534-5807(03)00227-2. View

17.

Krichevsky A, King K, Donahue C, Khrapko K, Kosik K . A microRNA array reveals extensive regulation of microRNAs during brain development. RNA. 2003; 9(10):1274-81. PMC: 1370491. DOI: 10.1261/rna.5980303. View

18.

Ying Q, Nichols J, Chambers I, Smith A . BMP induction of Id proteins suppresses differentiation and sustains embryonic stem cell self-renewal in collaboration with STAT3. Cell. 2003; 115(3):281-92. DOI: 10.1016/s0092-8674(03)00847-x. View

19.

Griffiths-Jones S . The microRNA Registry. Nucleic Acids Res. 2003; 32(Database issue):D109-11. PMC: 308757. DOI: 10.1093/nar/gkh023. View

20.

Sempere L, Freemantle S, Pitha-Rowe I, Moss E, Dmitrovsky E, Ambros V . Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 2004; 5(3):R13. PMC: 395763. DOI: 10.1186/gb-2004-5-3-r13. View