Novel Small RNAs Discovered, Contribute to Significant miRBase
on: September 17, 2008, 9:34 am
Release Author: Chris Hebel
Release Summary: Several research groups have recently made discoveries
of novel non-coding small RNAs. The small RNA discoveries were
made possible, in part, by LC Sciences’ small RNA discovery
service. The new microRNA sequences were included as part of the
latest update to the miRBase sequence database of experimentally
verified miRNAs. The Sanger Institute released the latest version
(12.0) of miRBase
on September 1st. The number of verified miRNAs has been increased
from 6396 to 8619 hairpin precursor miRNAs expressing 8273 mature
miRNA products. With the addition of 2062 new mature miRNA sequences,
this represents the largest update in miRBase history.
Release Body: Non-coding (ncRNAs) are a large class of RNAs which
do not encode proteins but possess regulatory functions at the
level of translation in cells of various species. There are an
increasing amount of data suggesting that there are likely many
more ncRNAs that exist, yet to be discovered. Custom small RNA
discovery microarrays have been shown to be an effective approach
for uncovering novel ncRNAs experimentally1 and/or to validate
predicted candidate ncRNAs2. Recently, researchers at Baylor College
of Medicine employed a discovery strategy of computational prediction
and microarray expression profiling to uncover a large number
of novel small RNAs in embryonic stem (ES) cells3. Dr.
Preethi Gunaratne and co-workers reported using computation,
custom small RNA microarray from LC Sciences,
and validation experiments to uncover hundreds of novel small
RNAs in ES cells. These small non-coding RNAs (ncRNAs) were from
adult tissue progenitor transcript sequences and are micro-conserved
elements. The detection probes were designed for custom array
synthesis by LC Sciences,
Houston, TX and included the standard microRNA (miRNA) sequences
in miRBase4, a comprehensive panel of 2,617 micro-conserved ncRNA
sequences, and several hundreds of literature reported small RNAs
or miRNAs. Two generations of custom array designs were used for
optimizing the probes. These profiling studies using ES cell lines
as well as normal adult mouse tissues identified 545 small RNAs
that are enriched in ES cells over adult cells. Of these, more
than 100 exhibited down-regulation in ES gene-knockout cells typical
In a similar way, LC Sciences’ custom small
RNA arrays have provided means for validation of computational
predictions of Bombyx mori (silkworm) 5 and Solanum lycopersicum
(Tomato) 6 miRNAs. These are species whose genomes are incomplete
at the present time. It is well known that miRNAs are important
players for regulation of cellular activities. Therefore, the
establishment of miRNAs in these traditional industrial or agricultural
important species should lead to better understanding of the fundamentals
of their growth, maturation, and disease-resistance.
The small RNA discoveries were made possible, in part, by LC Sciences’
small RNA discovery service. Using an innovative µParaflo®
platform technology and proprietary probe design, it enables highly
sensitive and specific direct detection of small RNAs in your
sample. This service is comprehensive; from array design to sample
to complete data set, allowing efficient and reliable discovery
of novel miRNA and other types of ncRNAs.
The new Bombyx and Solanum sequences were included as part of
the latest update to the miRBase sequence database of experimentally
verified miRNAs. The Sanger Institute released the latest version
(12.0) of miRBase on September 1st.
The number of verified miRNAs
has been increased from 6396 to 8619 hairpin precursor miRNAs
expressing 8273 mature miRNA products. With the addition of 2062
new mature miRNA sequences, this represents the largest update
in miRBase history.
Many sequences have been updated or revised. For the first time,
miRNAs are reported from: eleven new Drosophila species, Platypus,
Tomato, Red Flour Bettle, and two Polyomaviruses. There has been
a significant increase in the number of miRNAs reported for Human
and model species such as Chimpanzee, Mouse, and Arabidopsis as
well as agriculturally important species such as Rice, Soybean,
Pig, and Chicken.
The updated probe content from miRBase version 12.0 is currently
available on all of our standard or custom small RNA microarrays.
More information about LC Sciences’ Small
Non-coding RNA Discovery Service and the µParaflo® technology
is available at: http://www.lcsciences.com/small_non_coding.html.
About LC Sciences - LC Sciences is a genomics
and proteomics products company offering a comprehensive line
of DNA, RNA, and peptide microarrays for nucleic acid/protein
profiling and functional analysis, biomarker-discovery, novel
drug screening, and the custom development of miniaturized assay
devices for diagnostics and biosensing applications. Based on
the µParaflo® microfluidics technology, LC Sciences’
innovative products offer significant flexibility and customization
capability for rapidly evolving, diverse customer needs. In an
era of rapid technological advancement, LC Sciences offers service
products which enable efficient one-stop solution for assays of
DNA, RNA, protein, enzymes, antibodies, or small molecules. LC
Sciences also provides unique synthetic DNA and RNA products such
as OligoMix®, generated using their microfludic biochip synthesizer.
These innovative products drive synthetic biology and systems
biology applications by reducing the cost and increasing the speed
of highly multiplexing large-scale nucleic acid and protein engineering
More information about LC Sciences is available at www.lcsciences.com.
1. Vagin VV, Sigova A, Li C, Seitz H, Gvozdev V, Zamore PD. (2006)
A distinct small RNA pathway silences selfish genetic elements
in the germline. Science 313(5785), 320-324.
2. Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz L.A Jr, Sjoblom
T, Barad O,
Bentwich Z, Szafranska AE, Labourier E, et al. (2006) The colorectal
microRNAome. Proc Natl Acad Sci USA 103, 3687-92.
3. Gu P, Reid JG, Gao X, Shaw CA, Creighton C, Tran PL, Zhou X,
Drabek RB, Steffen DL, Hoang DM, Weiss MK, Naghavi AO, El-daye
J, Khan MF, Legge GB, Wheeler DA, Gibbs RA, Miller JN, Cooney
AJ, Gunaratne PH. (2008) Novel MicroRNA Candidates and miRNA-mRNA
Pairs in Embryonic Stem (ES) Cells. PloS One 3(7), e2548.
4. Griffiths-Jones S, Grocock R, van Dongen S, Bateman A, Enright
A. miRBase: microRNA sequences, targets and gene nomenclature.
Nucleic Acids Res 34 (Database issue), D140–D144.
5. He PA, Nie Z, Chen J, Chen J, Lv Z, Sheng Q, Zhou S, Gao X,
Kong L, Wu X, Jin Y, Zhang Y. (2008) Identification and characteristics
of microRNAs from Bombyx mori. BMC Genomics 9(1), 248.
6. Zhang J, Zeng R, Chen J, Liu X, Liao Q. (2008) Identification
of conserved microRNAs and their targets from Solanum lycopersicum
Mill. Gene [Epub ahead of print].
Details: LC Sciences LLC
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Houston, TX 77054