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Microarrays
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MicroRNA Microarrays
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MicroRNA Microarrays

A special issue of Microarrays (ISSN 2076-3905).

Deadline for manuscript submissions: closed (31 January 2013) | Viewed by 36677

Special Issue Editor

Dr. Veronica Soloveva

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Guest Editor
IP-Korea, Center for Core Technologies, 696 Sampyeong-dong, Bundang-gu, Seongnam-si, 463-400, South Korea
Interests: HCS; target free; siRNA microarrays; shRNA Lentivirus; cDNA microarrays; cellular assays; phenotypic assays; HTS; GPCR; cellular pathway; differentiation; primary cells; stem cells; automation; screening platforms

Special Issue Information

Dear Colleagues,

After the first microRNA was discovered in 1993, those 20-22nt size non-coding antisense inhibitory RNAs very quickly moved into spotlight as a new class of genes that is playing critical role in regulation of gene expression during development and normal functioning of cells and tissues in plants or animals. During last several years thousands of new micro-RNA molecules were discovered or predicted to be an essential regulatory genes in both normal and diseases states. Profiling for miRNAs expression and search for their mRNA targets are still very challenging tasks.

Microarray technology on other hand became a standard approach when there is a need for reliable screening technique applicable for multiple biological samples and particular for genomic materials. Thus the application of microarrays for microRNA studies became a useful tool in basic research and drug discovery.

In this issue we are inviting material about new developments and applications of microarray based technologies in field of microRNA expression profiling, in screening for targeted mRNAs, in discovery of new regulatory functions of those small noncoding genes. Information about new developments associated with annotations of miRNAs in databases and data analysis for miRNA microarrays is also critical in area of microarray technologies.

Dr. Veronica Soloveva
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microarrays is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 350 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • miRNA microarrays, microchips
  • miRNA expression
  • profiling
  • targets of miRNA
  • repression and induction by miRNA
  • viral miRNA
  • miRNA database

Published Papers (5 papers)

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Research

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924 KiB  
Article
Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays
by Juha K. Rantala, Sunjong Kwon, James Korkola and Joe W. Gray
Microarrays 2013, 2(2), 97-114; https://doi.org/10.3390/microarrays2020097 - 11 Apr 2013
Cited by 7 | Viewed by 8327
Abstract
Over the past decade, great strides have been made in identifying gene aberrations and deregulated pathways that are associated with specific disease states. These association studies guide experimental studies aimed at identifying the aberrant genes and networks that cause the disease states. This [...] Read more.
Over the past decade, great strides have been made in identifying gene aberrations and deregulated pathways that are associated with specific disease states. These association studies guide experimental studies aimed at identifying the aberrant genes and networks that cause the disease states. This requires functional manipulation of these genes and networks in laboratory models of normal and diseased cells. One approach is to assess molecular and biological responses to high-throughput RNA interference (RNAi)-induced gene knockdown. These responses can be revealed by immunofluorescent staining for a molecular or cellular process of interest and quantified using fluorescence image analysis. These applications are typically performed in multiwell format, but are limited by high reagent costs and long plate processing times. These limitations can be mitigated by analyzing cells grown in cell spot microarray (CSMA) format. CSMAs are produced by growing cells on small (~200 mm diameter) spots with each spot carrying an siRNA with transfection reagent. The spacing between spots is only a few hundred micrometers, thus thousands of cell spots can be arranged on a single cell culture surface. These high-density cell cultures can be immunofluorescently stained with minimal reagent consumption and analyzed quickly using automated fluorescence microscopy platforms. This review covers basic aspects of imaging-based CSMA technology, describes a wide range of immunofluorescence assays that have already been implemented successfully for CSMA screening and suggests future directions for advanced RNAi screening experiments. Full article
(This article belongs to the Special Issue MicroRNA Microarrays)
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1081 KiB  
Article
Phenotypic MicroRNA Microarrays
by Yong-Jun Kwon, Jin Yeong Heo, Hi Chul Kim, Jin Yeop Kim, Michel Liuzzi and Veronica Soloveva
Microarrays 2013, 2(2), 63-80; https://doi.org/10.3390/microarrays2020063 - 03 Apr 2013
Cited by 1 | Viewed by 6689
Abstract
Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects [...] Read more.
Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the biology of selected cellular models. After reverse-transfection of microRNAs and siRNA, the cellular phenotype generated by microRNAs regulated NF-κB expression comparably to the siRNA. The ability to print microRNA molecules for reverse transfection into cells is opening up the wide horizon for the phenotypic high content screening of microRNA libraries using cellular disease models. Full article
(This article belongs to the Special Issue MicroRNA Microarrays)
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261 KiB  
Communication
Profiling Pre-MicroRNA and Mature MicroRNA Expressions Using a Single Microarray and Avoiding Separate Sample Preparation
by Lin Gan and Bernd Denecke
Microarrays 2013, 2(1), 24-33; https://doi.org/10.3390/microarrays2010024 - 14 Mar 2013
Cited by 18 | Viewed by 6225 | Correction
Abstract
Mature microRNA is a crucial component in the gene expression regulation network. At the same time, microRNA gene expression and procession is regulated in a precise and collaborated way. Pre-microRNAs mediate products during the microRNA transcription process, they can provide hints of microRNA [...] Read more.
Mature microRNA is a crucial component in the gene expression regulation network. At the same time, microRNA gene expression and procession is regulated in a precise and collaborated way. Pre-microRNAs mediate products during the microRNA transcription process, they can provide hints of microRNA gene expression regulation or can serve as alternative biomarkers. To date, little effort has been devoted to pre-microRNA expression profiling. In this study, three human and three mouse microRNA profile data sets, based on the Affymetrix miRNA 2.0 array, have been re-analyzed for both mature and pre-microRNA signals as a primary test of parallel mature/pre-microRNA expression profiling on a single platform. The results not only demonstrated a glimpse of pre-microRNA expression in human and mouse, but also the relationship of microRNA expressions between pre- and mature forms. The study also showed a possible application of currently available microRNA microarrays in profiling pre-microRNA expression in a time and cost effective manner. Full article
(This article belongs to the Special Issue MicroRNA Microarrays)
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Review

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462 KiB  
Review
Comparative Analyses of MicroRNA Microarrays during Cardiogenesis: Functional Perspectives
by Fernando Bonet, Francisco Hernandez-Torres, Franciso J. Esteban, Amelia Aranega and Diego Franco
Microarrays 2013, 2(2), 81-96; https://doi.org/10.3390/microarrays2020081 - 03 Apr 2013
Cited by 6 | Viewed by 6634
Abstract
Cardiovascular development is a complex process in which several transcriptional pathways are operative, providing instructions to the developing cardiomyocytes, while coping with contraction and morphogenetic movements to shape the mature heart. The discovery of microRNAs has added a new layer of complexity to [...] Read more.
Cardiovascular development is a complex process in which several transcriptional pathways are operative, providing instructions to the developing cardiomyocytes, while coping with contraction and morphogenetic movements to shape the mature heart. The discovery of microRNAs has added a new layer of complexity to the molecular mechanisms governing the formation of the heart. Discrete genetic ablation of the microRNAs processing enzymes, such as Dicer and Drosha, has highlighted the functional roles of microRNAs during heart development. Importantly, selective deletion of a single microRNA, miR-1-2, results in an embryonic lethal phenotype in which both morphogenetic, as well as impaired conduction, phenotypes can be observed. In an effort to grasp the variability of microRNA expression during cardiac morphogenesis, we recently reported the dynamic expression profile during ventricular development, highlighting the importance of miR-27 on the regulation of a key cardiac transcription factor, Mef2c. In this review, we compare the microRNA expression profile in distinct models of cardiogenesis, such as ventricular chamber development, induced pluripotent stem cell (iPS)-derived cardiomyocytes and the aging heart. Importantly, out of 486 microRNAs assessed in the developing heart, 11% (55) displayed increased expression, many of which are also differentially expressed in distinct cardiogenetic experimental models, including iPS-derived cardiomyocytes. A review on the functional analyses of these differentially expressed microRNAs will be provided in the context of cardiac development, highlighting the resolution and power of microarrays analyses on the quest to decipher the most relevant microRNAs in the developing, aging and diseased heart. Full article
(This article belongs to the Special Issue MicroRNA Microarrays)
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272 KiB  
Review
Challenges for MicroRNA Microarray Data Analysis
by Bin Wang and Yaguang Xi
Microarrays 2013, 2(2), 34-50; https://doi.org/10.3390/microarrays2020034 - 25 Mar 2013
Cited by 28 | Viewed by 8528
Abstract
Microarray is a high throughput discovery tool that has been broadly used for genomic research. Probe-target hybridization is the central concept of this technology to determine the relative abundance of nucleic acid sequences through fluorescence-based detection. In microarray experiments, variations of expression measurements [...] Read more.
Microarray is a high throughput discovery tool that has been broadly used for genomic research. Probe-target hybridization is the central concept of this technology to determine the relative abundance of nucleic acid sequences through fluorescence-based detection. In microarray experiments, variations of expression measurements can be attributed to many different sources that influence the stability and reproducibility of microarray platforms. Normalization is an essential step to reduce non-biological errors and to convert raw image data from multiple arrays (channels) to quality data for further analysis. In general, for the traditional microarray analysis, most established normalization methods are based on two assumptions: (1) the total number of target genes is large enough (>10,000); and (2) the expression level of the majority of genes is kept constant. However, microRNA (miRNA) arrays are usually spotted in low density, due to the fact that the total number of miRNAs is less than 2,000 and the majority of miRNAs are weakly or not expressed. As a result, normalization methods based on the above two assumptions are not applicable to miRNA profiling studies. In this review, we discuss a few representative microarray platforms on the market for miRNA profiling and compare the traditional methods with a few novel strategies specific for miRNA microarrays. Full article
(This article belongs to the Special Issue MicroRNA Microarrays)
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