Multiplexmethoden zur Profilierung der MikroRNA‐Expression in biologischen Proben

Die Entdeckung kleiner nichtcodierender RNA-Molekule (MikroRNAs; miRNAs), die in der Lage sind, die Genexpression zu steuern, hat eine neue Komplexitatsebene bei der Regulation der Zellfunktionen aufgezeigt. Seit einigen Jahren wird nun versucht, die regulatorische Funktion von hunderten bis tausenden von miRNAs zu verstehen, die in pflanzlichen und tierischen Zellen exprimiert werden. Um hier entscheidend weiterzukommen, ist die Entwicklung quantitativer bioanalytischer Verfahren erforderlich, mit denen ein schneller, paralleler Nachweis aller miRNAs in einer bestimmten Zelle oder Gewebeprobe moglich ist. In diesem Kurzaufsatz beschreiben wir einige der neuesten Verfahren zur Hochdurchsatzprofilierung von miRNAs und schildern die besonderen technischen Herausforderungen, die dabei gemeistert werden mussen.

[1]  Pasko Rakic,et al.  Microarray analysis of microRNA expression in the developing mammalian brain , 2004, Genome Biology.

[2]  Anton J. Enright,et al.  Requirement of bic/microRNA-155 for Normal Immune Function , 2007, Science.

[3]  John Bracht,et al.  MicroRNAs: a developing story. , 2005, Current opinion in genetics & development.

[4]  R. Aharonov,et al.  Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.

[5]  D. Turner,et al.  Detection of mammalian microRNA expression by in situ hybridization with RNA oligonucleotides , 2006, Developmental dynamics : an official publication of the American Association of Anatomists.

[6]  R. Plasterk,et al.  RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. , 2005, RNA.

[7]  Shiping Fang,et al.  Attomole microarray detection of microRNAs by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions. , 2006, Journal of the American Chemical Society.

[8]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[9]  Vladimir Benes,et al.  A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). , 2006, RNA.

[10]  Sonal Patel,et al.  A single-molecule method for the quantitation of microRNA gene expression , 2005, Nature Methods.

[11]  S. Kajigaya,et al.  Nonisotopic detection of microRNA using digoxigenin labeled RNA probes. , 2006, Molecular and cellular probes.

[12]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature reviews genetics.

[13]  Francois Natt,et al.  A novel microarray approach reveals new tissue-specific signatures of known and predicted mammalian microRNAs , 2007, Nucleic acids research.

[14]  Zhiqiang Gao,et al.  Detection of microRNAs using electrocatalytic nanoparticle tags. , 2006, Analytical chemistry.

[15]  Wigard P Kloosterman,et al.  In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes , 2005, Nature Methods.

[16]  Zissimos Mourelatos,et al.  Microarray-based, high-throughput gene expression profiling of microRNAs , 2004, Nature Methods.

[17]  Ranit Aharonov,et al.  MicroRNA expression detected by oligonucleotide microarrays: system establishment and expression profiling in human tissues. , 2004, Genome research.

[18]  R. Carthew.  Gene regulation by microRNAs. , 2006, Current opinion in genetics & development.

[19]  C. Croce,et al.  MicroRNA signatures in human cancers , 2006, Nature Reviews Cancer.

[20]  K. Livak,et al.  Real-time quantification of microRNAs by stem–loop RT–PCR , 2005, Nucleic acids research.

[21]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[22]  F. Slack,et al.  Oncomirs — microRNAs with a role in cancer , 2006, Nature Reviews Cancer.

[23]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[24]  Yang Li,et al.  An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe , 2005, Nucleic acids research.

[25]  E. Winzeler,et al.  Genomics, gene expression and DNA arrays , 2000, Nature.

[26]  J. Hagstrom,et al.  MicroRNA Labeling Methods Directly Influence the Accuracy of Expression Profiling Detection , 2007 .

[27]  Ibtissem Grissa,et al.  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..

[28]  C. Croce,et al.  An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Nóra Varga,et al.  Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. , 2004, Nucleic acids research.

[30]  V. Kim.  MicroRNA biogenesis: coordinated cropping and dicing , 2005, Nature Reviews Molecular Cell Biology.

[31]  S. Lowe,et al.  A microRNA polycistron as a potential human oncogene , 2005, Nature.

[32]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

[33]  H. Horvitz,et al.  MicroRNA expression profiles classify human cancers , 2005, Nature.

[34]  Jørgen Kjems,et al.  A microRNA detection system based on padlock probes and rolling circle amplification. , 2006, RNA.

[35]  Eugene Berezikov,et al.  Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. , 2006, Genome research.

[36]  V. Ambros.  The functions of animal microRNAs , 2004, Nature.

[37]  R. Ach,et al.  Direct and sensitive miRNA profiling from low-input total RNA. , 2006, RNA.

[38]  Michael Famulok,et al.  Sequence-specific detection of MicroRNAs by signal-amplifying ribozymes. , 2004, Journal of the American Chemical Society.

[39]  C. Benz,et al.  Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies , 2006, Molecular Cancer.

[40]  Christoph Arenz.  MicroRNAs – zukünftige Wirkstoff‐Targets? , 2006 .

[41]  Qian Liu,et al.  A high-throughput method to monitor the expression of microRNA precursors. , 2004, Nucleic acids research.

[42]  Quaid Morris,et al.  Probing microRNAs with microarrays: tissue specificity and functional inference. , 2004, RNA.

[43]  Jeffrey Shelton,et al.  An optimized isolation and labeling platform for accurate microRNA expression profiling. , 2005, RNA.

[44]  Chris Sander,et al.  The developmental miRNA profiles of zebrafish as determined by small RNA cloning. , 2005, Genes & development.

[45]  C. Arenz,et al.  MicroRNAs--future drug targets? , 2006, Angewandte Chemie.

[46]  D. Bartel,et al.  Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. , 2005, RNA.

[47]  C. Sander,et al.  A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing , 2007, Cell.

[48]  H. Horvitz,et al.  MicroRNA Expression in Zebrafish Embryonic Development , 2005, Science.

[49]  L. Goff,et al.  Rational Probe Optimization and Enhanced Detection Strategy for MicroRNAs Using Microarrays , 2005, RNA biology.

[50]  R. Corn,et al.  Creating advanced multifunctional biosensors with surface enzymatic transformations. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[51]  Brian S. Roberts,et al.  Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. , 2005, RNA.

[52]  Sarah Olson,et al.  Quantitation of microRNAs using a modified Invader assay. , 2004, RNA.

[53]  R. Corn,et al.  Enzymatically amplified surface plasmon resonance imaging detection of DNA by exonuclease III digestion of DNA microarrays. , 2005, Analytical chemistry.

[54]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[55]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[56]  R. Corn,et al.  Long-range surface plasmon resonance imaging for bioaffinity sensors. , 2005, Analytical chemistry.

[57]  J. Weiler,et al.  NEW APPROACHES TOWARDS FLUORESCENCE LABELLING OF MESSENGER RNA TRANSCRIPTS , 2001, Nucleosides, nucleotides & nucleic acids.

[58]  C. Perou,et al.  A custom microarray platform for analysis of microRNA gene expression , 2004, Nature Methods.

[59]  T. Golub,et al.  Impaired microRNA processing enhances cellular transformation and tumorigenesis , 2007, Nature Genetics.