Dr. Lucrecia Alvarez is currently editing one of the Springer Book Series on Methods in Molecular Biology entitled “Structural and Functional RNA Mapping” and is looking for contributions:

“All I am asking the authors to do is to present their routinely laboratory protocols in a define format and, therefore, there is not too much work involved. I am looking for potential authors interested in writing a book chapter on experimental or in silico methods related to the study of microRNA and long non-coding RNAs. Each chapter will appear indexed in PubMed and on Web of Science.”

If you are interested, please contact her at [email protected] and state the title and a brief summary of the book chapter that you would like to contribute. You will receive the Instructions for Authors and a sample of a book chapter. Thanks!


The hippocampus is a part of the brain critically involved in memory formation and spatial navigation. Shinohara et al. (2011,) used deep sequencing for  miRNA profiling of multiple samples of the mature male rat hippocampal CA3 region. According to their study, the let-7 family miRNA represents about half of the small RNA cDNA library. Major let-7 family miRNAs are  let-7c (23%), let-7a (9%), let-7f (9%), and let-7b (7%). The authors found miR134, a miRNA previously reported to be related to synaptic plasticity and morphology, only modestly expressed (~0.05%). The miRNA profiles of the left and right hippocampi were similar.  The sequence data derived from 3 pooled data sets and each data set contained corresponding left and right hippocampal CA3 samples. This study is one of the fewest studies in which miRNA expression profiles were quantitatively assessed in a specific region of the brain. The raw sequence reads and cross-mapped results are available in the DDJB sequence archive with the accession number DRA000379 (

miRNA profiling of bilateral rat hippocampal CA3 by deep sequencing.
Shinohara Y, Yahagi K, Kawano M, Nishiyori H, Kawazu C, Suzuki N, Manabe RI, Hirase H.
Biochem Biophys Res Commun. 2011 May 13. [Epub ahead of print]
PMID:  21575607 [PubMed – as supplied by publisher]

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The mechanism of regulation by microRNA (miRNA) is complex in that miRNAs are frequently transcribed together as primary transcripts that are then processed into multiple individual mature miRNAs and, that each individual miRNA may target many different mRNAs.  Thus miRNA represents a network of control over cellular functions.  Additionally, the organization of many clusters of miRNAs is highly conserved and this suggests an important role for coordinated programmable function.  Expression profiling of complete “microRNA-omes” enables researchers to look at this network on a broad scale and better understand the interrelationship of factors at work.

It has now been well established that miRNAs are important for the regulation of many cellular activities including cell development and differentiation.  MicroRNAs play particularly important roles in human embryonic stem cells (hESC), possibly regulating self-renewal, pluripotency and differentiation.  Furthermore, a better understanding of the molecular circuitry involved with reprogramming of adult cells into induced pluripotent stem cells (iPSCs) could lead to better methods of which would circumvent the need to use human embryos for research and possibly lead to the creation of disease-specific stem cells as model systems. [click to continue…]


The study of microRNA (miRNA) is growing rapidly as researchers discover new miRNA sequences and uncover the importance of these small regulatory elements linked to a wide range of biological functions. The miRBase sequence database (1) is the primary public repository for newly discovered miRNAs and the number of miRBase entries has grown rapidly from a mere 218 in 2002 to almost 10,000 in the latest version, suggesting the existence of many more miRNAs yet to be discovered.
Contributing to the rapid rate of new discoveries is the development of several new advanced technologies such as high-throughput sequencing and custom microfluidic arrays. The increasing availability of these technologies makes the discovery of new sequences in lesser understood organisms now routinely possible. A straightforward process of discovery, confirmation, and validation is commonly employed:

Deep Sequencing – Discovery —> Microarray – Confirmation —> QPCR – Validation

In a recent study, many novel miRNAs were experimentally verified in the silkworm Bombyx mori, an industrially important insect, by researchers at the Chinese Academy of Sciences, Shanghai using this three step process (2).
Deep sequencing (Illumina GA sequencing-by-synthesis platform) revealed a total of 95,184 non-redundant tags that matched to the silkworm genome, and computational pipeline analysis identified 3,750 potential miRNA precursors. Probes for these candidate miRNAs in situ synthesized on a custom microfluidic microarray (3) (LC Sciences µParaflo® microfluidic platform) confirmed 354 of the candidates. Further microarray experiments profiled the expression level of these miRNAs at the various developmental stages of the silkworm (egg, larvae, pupa, and adult). QPCR (GenePharma, molecular beacon platform) validated several highly differentially expressed miRNAs, thought to be important for embryogenesis and metamorphosis.
It is well known that miRNAs are important players for regulation of cellular activities. Therefore, the establishment of miRNAs in traditional industrial or agriculturally important species such as the silkworm should lead to better understanding of the fundamentals of their growth, maturation, and disease-resistance.

1. The miRBase sequence database is a comprehensive database of miRNA sequence data, annotation, and predicted gene targets and is the primary public repository for these data. miRBase also provides a gene-naming service for assigning official miRNA names to novel miRNAs before they are published. It is freely available to all at

2. Zhang Y, Zhou X, Ge X, Jiang J, Li M, Jia S, Yang X, Kan Y, Miao X, Zhao G, Li F, Huang Y. (2009) Insect-Specific microRNA Involved in the Development of the Silkworm Bombyx mori. PLoS ONE 4(3), e4677.

3. More information about LC Sciences miRNA discovery and analysis services is available at:

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While much progress has been made in computational target prediction of miRNAs in recent years and more than 10 miRNA target prediction programs have been established, the prediction of miRNA targets remains a challenging task.
The group of Dr. Tongbin Li from the Department of Neuroscience, University of Minnesota has developed miRecords, an integrated resource for animal miRNA–target interactions. The validated targets component of this resource hosts a large, high-quality manually curated database of experimentally validated miRNA–target interactions with systematic documentation of experimental support for each interaction. The current release of this database includes 1135 records of validated miRNA–target interactions between 301 miRNAs and 902 target genes in seven animal species. The Predicted Targets component of miRecords stores predicted miRNA targets produced by 11 established miRNA target prediction programs:

Read the Full Text Version of the article here:

miRecords: an integrated resource for microRNA-target interactions.
Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T.
Nucleic Acids Res. 2008 Nov 7. [Epub ahead of print]

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