MicroRNA detection by microarray

MicroRNAs (miRNAs) are a class of small noncoding RNAs ∼22 nt in length that regulate gene expression and play fundamental roles in multiple biological processes, including cell differentiation, proliferation and apoptosis as well as disease processes. The study of miRNA has thus become a rapidly emerging field in life science. The detection of miRNA expression is a very important first step in miRNA exploration. Several methodologies, including cloning, northern blotting, real-time RT-PCR, microRNA arrays and ISH (in situ hybridization), have been developed and applied successfully in miRNA profiling. This review discusses the main existing microRNA detection technologies, while emphasizing microRNA arrays.

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

[2]  B. Reinhart,et al.  The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans , 2000, Nature.

[3]  V. Ambros,et al.  An Extensive Class of Small RNAs in Caenorhabditis elegans , 2001, Science.

[4]  L. Lim,et al.  An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.

[5]  T. Tuschl,et al.  Identification of Tissue-Specific MicroRNAs from Mouse , 2002, Current Biology.

[6]  Hajime Sakai,et al.  Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.016238. , 2003, The Plant Cell Online.

[7]  V. Ambros,et al.  Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation , 2004, Genome Biology.

[8]  Konstantin Khrapko,et al.  A microRNA array reveals extensive regulation of microRNAs during brain development. , 2003, RNA.

[9]  C. Burge,et al.  Vertebrate MicroRNA Genes , 2003, Science.

[10]  R. Russell,et al.  bantam Encodes a Developmentally Regulated microRNA that Controls Cell Proliferation and Regulates the Proapoptotic Gene hid in Drosophila , 2003, Cell.

[11]  G. Church,et al.  Computational and experimental identification of C. elegans microRNAs. , 2003, Molecular cell.

[12]  Javier F. Palatnik,et al.  Control of leaf morphogenesis by microRNAs , 2003, Nature.

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

[14]  M. Hentze,et al.  Molecular mechanisms of translational control , 2004, Nature Reviews Molecular Cell Biology.

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

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

[17]  Xuemei Chen,et al.  A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development , 2004, Science.

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

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

[20]  Oliver Hobert,et al.  MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode , 2004, Nature.

[21]  Y. Yatabe,et al.  Reduced Expression of the let-7 MicroRNAs in Human Lung Cancers in Association with Shortened Postoperative Survival , 2004, Cancer Research.

[22]  D. Bartel,et al.  MicroRNAs Modulate Hematopoietic Lineage Differentiation , 2004, Science.

[23]  Seongjoon Koo,et al.  Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. , 2004, Nucleic acids research.

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

[25]  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.

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

[27]  C. Croce,et al.  MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[28]  G. Hannon,et al.  miRNAs on the move: miRNA biogenesis and the RNAi machinery. , 2004, Current opinion in cell biology.

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

[30]  Eugene Berezikov,et al.  Phylogenetic Shadowing and Computational Identification of Human microRNA Genes , 2005, Cell.

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

[32]  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.

[33]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[34]  W. Filipowicz,et al.  RNAi: The Nuts and Bolts of the RISC Machine , 2005, Cell.

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

[36]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

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

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

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

[40]  W. Filipowicz,et al.  Post-transcriptional gene silencing by siRNAs and miRNAs. , 2005, Current opinion in structural biology.

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

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

[43]  S. Kauppinen,et al.  Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues. , 2006, The Plant journal : for cell and molecular biology.

[44]  E. Haralambieva,et al.  Lack of BIC and microRNA miR‐155 expression in primary cases of Burkitt lymphoma , 2006, Genes, chromosomes & cancer.

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

[46]  Y. Kato,et al.  Detection of the mature, but not precursor, RNA using a fluorescent DNA probe. , 2006, Nucleic acids symposium series.

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

[48]  Gurman Singh Pall,et al.  Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot , 2007, Nucleic acids research.

[49]  Yukio Kitade,et al.  Downregulation of microRNAs‐143 and ‐145 in B‐cell malignancies , 2007, Cancer science.

[50]  Y. Chai,et al.  Direct electrochemistry of horseradish peroxidase immobilized on DNA/electrodeposited zirconium dioxide modified, gold disk electrode , 2007, Biotechnology Letters.

[51]  Chaoqian Xu,et al.  The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2 , 2011, Nature Medicine.

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

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

[54]  E. F. Walton,et al.  Plant Methods Protocol: a Highly Sensitive Rt-pcr Method for Detection and Quantification of Micrornas , 2022 .

[55]  Jing Wang,et al.  Lymphoproliferative disease and autoimmunity in mice with increased miR-17-92 expression in lymphocytes , 2008, Nature Immunology.