discovery

miRNEST database: an integrative approach in microRNA search and annotation

by Christoph on December 8, 2011

Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to search for new microRNAs.

Izabela Makałowska’s Laboratory of Evolutionary Genomics at The Adam Mickiewicz University in Poznan just published miRNEST, a comprehensive database of animal, plant and virus microRNAs. The core part of the database is built from the author’s miRNA predictions conducted on Expressed Sequence Tags of 225 animal and 202 plant species. The miRNA search was performed based on sequence similarity and as many as 10 004 miRNA candidates in 221 animal and 199 plant species were discovered. Out of them only 299 have already been deposited in miRBase. Additionally, miRNEST has been integrated with external miRNA data from literature and 13 databases, which includes miRNA sequences, small RNA sequencing data, expression, polymorphisms and targets data as well as links to external miRNA resources, whenever applicable. All this makes miRNEST a considerable miRNA resource in a sense of number of species (544) that integrates a scattered miRNA data into a uniform format with a user-friendly web interface.

miRNEST: http://mirnest.amu.edu.pl

Michal Wojciech Szczesniak, Sebastian Deorowicz, Jakub Gapski, Lukasz Kaczynski, and Izabela Makalowska
miRNEST database: an integrative approach in microRNA search and annotation
Nucleic Acids Res. 2011

http://nar.oxfordjournals.org/content/early/2011/11/30/nar.gkr1159

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Yale spinout 3PrimiR pulls in $2M in funding

by Chris on September 16, 2009

Spawned by Yale University, biotech company 3PrimiR Inc., which is focused on applying microRNA discoveries to cancer diagnostics, has raised $2 million in a planned $4 million equity financing, according to federal documents.

According to the website of Yale’s Office of Cooperative Research, Westport, Conn.-based 3PrimiR was founded by Yale scientists based on their discoveries of the predictive roles of mutations affecting microRNA in cancers. The filing with the U.S. Securities and Exchange Commission notes the two company executives as Barbara Mignogna-Korus and Andrew Weidhaas.  (read more)

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RNA Discovery

by Chris on September 16, 2009

By Rachel Gilmore
Published Wednesday, September 16, 2009

In the three decades since RNA was first sequenced in 1975, scientists have been intrigued by how the genome relates to life, studying has been limited to looking at only one gene at a time. Now Erik Sperling GRAD ’11, a graduate student in the Yale Geology and Geophysics Department, and his colleagues have changed that. Staff reporter Rachel Gilmore investigates.

In research published Tuesday, the team reported their findings that microRNA or miRNA, single-stranded regulators of gene expression, can help us chart evolutionary history — and they used it to correct a misunderstood evolutionary fact.  (read more)

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MicroRNA Discovery and Validation in Silkworm – Case Study

by Christoph on May 4, 2009

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 http://microrna.sanger.ac.uk/.

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: http://www.lcsciences.com/mirna_discovery.html.

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