Mil Av, Vrijsen KR, Goumans M, Metz CH, Doevendans PA, Sluijter JP. (2013) microRNA-1 enhances the angiogenic differentiation of human cardiomyocyte progenitor cells. J Mol Med. [Epub ahead of print]. [abstract]
Sun Z, Han Q, Zhou N, Wang S, Lu S, Bai C, Zhao RC. (2013) MicroRNA-9 enhances migration and invasion through KLF17 in hepatocellular carcinoma. Molecular Oncology [Epub ahead of print] . [abstract]
Cheng K, Rai P, Plagov A, Lan X, Mathieson PW, Saleem MA, Husain M, Malhotra A, Singhal PC. (2013) Rapamycin-induced modulation of miRNA expression is associated with amelioration of HIV-associated nephropathy (HIVAN). Experimental Cell Research [Epub ahead of print]. [abstract]
Title: Recent Work & Current Methods in Immunology microRNA Research
Date: Tuesday – 05/0713
MicroRNAs have proven to be an extremely important part of the gene expression regulation mechanism. While the role of microRNAs in cancer was recognized early on, expression profiling and functional studies have now shown that microRNAs participate in the regulation of many biological systems. There is now strong evidence suggesting that miRNA signaling plays a significant role in both innate and adaptive immune responses and their dysregulation contributes to pathogenesis.
Presented by
Dr. Christoph EickenHead of Technical Services
LC Sciences LLC
Webinar Outline
- Brief review of microRNA basics: history, biogenesis, function
- Recent developments of microRNA research in the field of immunology
- Current methods for microRNA discovery and profiling
- Case studies and application examples
Please register for the webinar by selecting the presentation time that is most convenient for your location.
North, South America – 1:00 Central Standard Time
https://attendee.gotowebinar.com/register/4876096924603080192Europe, Asia – 2:00 PM Greenwich Mean Time
https://attendee.gotowebinar.com/register/5157900655290357248
After registering, you will receive a confirmation email containing information about joining the webinar.
After completion of the webinar, you will receive an email containing a link to the archived webinar.
Download the presentation slides.
microRNAs ‐ What We Know
- All miRNAs are small non‐coding RNAs, usually consisting of…
At the upcoming Plant & Animal Genomes Conference, Jan 12th-16th 2013 , San Diego, LC Sciences and Norgen Biotek will be hosting a workshop:
Workshop Summary:
This workshop will provide an overview of the degradome sequencing method for miRNA target identification, as well as practical information for performing degradome sequencing experiments. Additionally, we will discuss the importance of miRNA sample preparation from various plant species/tissue types for downstream applications including next-gen sequencing, microarray and others. Diverse case study and application examples will be provided.
Presenter : Dr. Qi Zhu
Presentation Title: Degradome Sequencing for Plant microRNA Target Identification.
Presentation Abstract:
MicroRNAs (miRNAs) are endogenous small noncoding RNAs that play crucial roles in the post-transcriptional regulation of gene expression in plants and animals. They function by binding to complementary mRNA molecules (targets) and acting as negative regulators of translation. This function is part of a complex web as a single miRNA might have several target genes and a single gene may be regulated by many miRNAs. Identification of these miRNA-target pairs is crucial to understanding the biology of the miRNA regulatory mechanism.
Recently, degradome sequencing, a modified 5′-rapid amplification of cDNA ends (RACE) performed with next-gen sequencing, has emerged as a comprehensive method of analyzing patterns of RNA degradation. This presentation will provide an overview of this emerging method for miRNA target identification, as well as practical information for performing degradome sequencing experiments and data analysis. Diverse case study examples will be provided to illustrate the usefulness of this latest application of next-gen sequencing technology to plant miRNA research.
Presenters: Dr. Won-Sik Kim & Nezar Rghei
Presentation Title: The Importance Of Sample Preparation For Down Stream Applications: NGS, Sequencing, Microarray, RT-PCR, MdX, etc.
Presentation Abstract:
MicroRNAs are endogenous 20 to 24 nucleotide noncoding RNAs that play crucial posttranscriptional regulatory roles in plant and animals. Tremendous efforts are currently being undertaken to understand the profile of the entire miRNA population of a biological sample, which will provide useful information on miRNA activity. Many miRNA discovery tools, including micro arrays and Next-gen-based sequencing, have made it possible to comprehensively and accurately assess the entire miRNA repertoire. This presentation deals with the importance of sample preparation on downstream applications. A prerequisite for obtaining successful results from these approaches is an efficient method for total RNA purification without bias. The choice of the method of RNA purification is critical to the outcome of downstream analysis. This is made more significant in variations of the plant specimens and the high phenolics, starch and other inhibitors co-isolating with the RNA. The three most popular RNA purification methods (spin columns using Silicon Carbide, spin columns employing silica membrane and phenol/chloroform extraction) are compared in this talk in terms of quality, quantity and small RNA recovery from difficult and moderately challenging plant samples. Examples of microRNA study cases will be also discussed to highlight the importance of the RNA purification method used for different plant species.
The domestic pig is of enormous agricultural significance and a valuable model organism for human biological and biomedical studies. Elucidation of the pig microRNAome will permit an atlas of microRNA regulation functions and networks to be constructed.
Our customers, through a combination of next-gen sequencing and microarray experiments have take taken large steps towards this end and provided significant contributions to the miRNA body of knowledge for this important animal.
Guo XK, Zhang Q, Gao L, Li N, Chen XX, Feng WH. (2012) Additional expression of microRNA-181 inhibits Porcine Reproductive and Respiratory Syndrome Virus replication and its implications for controlling virus infection. J Virol [Epub ahead of print]. [abstract]
Li R, Sun Q, Jia Y, Cong R, Ni Y, et al. (2012) Coordinated miRNA/mRNA Expression Profiles for Understanding Breed-Specific Metabolic Characters of Liver between Erhualian and Large White Pigs. PLoS ONE 7(6), e38716. [abstract]
Lin F, Li R, Pan Zx, Zhou B, Yu Db, et al. (2012) miR-26b Promotes Granulosa Cell Apoptosis by Targeting ATM during Follicular Atresia in Porcine Ovary. PLoS ONE 7(6), e38640. [abstract]
Li M, Liu Y, Wang T, Guan J, Luo Z, Chen H, Wang X, Chen L, Ma J, Mu Z, Jiang AA, Zhu L, Lang Q, Zhou X, Wang J, Zeng W, Li N, Li K, Gao X, Li X (2011) Repertoire of Porcine MicroRNAs in Adult Ovary and Testis by Deep Sequencing. Int J Biol Sci 7(7), 1045-55. [abstract]
Li M, Xia Y, Gu Y, Zhang K, Lang Q, et al. (2010) MicroRNAome of Porcine Pre- and Postnatal Development. PLoS ONE 5(7), e11541. [abstract
Zhou B, Liu HL, Shi FX, Wang JY. (2010) MicroRNA expression profiles of porcine skeletal muscle. Anim Genet 41(5), 499-508. [abstract]
Luo L, Ye L, Liu G, Shao G, Zheng R, Ren Z, Zuo B, Xu D, Lei M, Jiang S, Deng C, Xiong Y, Li F. (2010) Microarray-based approach identifies differentially expressed microRNAs in porcine sexually immature and mature testes. PLoS ONE 5(8), e11744. [abstract]
Curry E, Ellis SE, Pratt SL. (2009) Detection of porcine sperm microRNAs using a heterologous microRNA microarray and reverse transcriptase polymerase chain reaction. Mol Reprod Dev 76 (3), 218-19. [abstract]
Next-gen sequencing has provided new insight into the microRNAome, is accerating the rate of discovery of new small RNAs, and is responsible for many of the changes to the miRBase sequence database in recent updates. But a miRBase update is not merely the adding of new sequences. Though that is a large part of it, sequences are also updated, corrected, or in some cases deleted.
Deleting Sequences
- Misannotated sequences are deleted – next-gen sequencing data will enable more of this
- Cases of duplicate entries mapping to a single genomic locus are cleaned up – some enabled by new genome assembly releases
- Ex – Drosophila pseudoobscura V18 – 211 database entries, V19 – 210 database entries.
Renaming Sequences
- The process of retiring the miR/miR* nomenclature, in favour of the -5p/-3p nomenclature began with version 17 of the database.
- Version 17 – Drosophila sequences renamed.
- Version 18 – Human, Mouse, and Zebrafish sequences renamed.
- Version 19 – the miR* nomenclature is finally retired for all species.
- The miRBase curators note that the names are meant to be useful, but are not formally stable. They recommend that sequence names shouldn’t be used to convey complex information. Instead they recommend to use miRNA accession numbers, which do remain stable between releases, or you can always quote the sequence to be truly unambiguous. (miRBase Blog post regarding naming)
Adding Sequences
- Version 19 includes 3171 new hairpins and 3625 novel mature products. That’s an 18% increase in the database size in a single update.
Because the rate of increase in size of the database is accelerating, it is making it more and more difficult for array manufacturers (that use the miRBase sequence database for probe content) to keep their microarrays up-to-date with the latest sequence information. Often, pre-made arrays, sitting on the shelf, contain only a fraction of the known content for a particular species.
In comparison, LC Sciences’ microRNA microarrays are produced only as needed. This is made possible by our µParaflo® Biochip Technology – a high performance microfluidic custom microarray platform, enables on demand synthesis of microarrays.
Our microRNA arrays cover all species for which sequence data are available in the miRBase Sequence Database and the Plant MicroRNA Database.
Comparison of miRBase Versions
Supplier miRBase Version Available Total miRBase Entries miRBase Release Date LC Sciences 19 21264 Aug 2012 Exiqon 18 18226 Nov 2011 Phalanx 18 18226 Nov 2011 Agilent 17 16772 April 2011 Affymetrix 17 16772 April 2011 ABI qPCR Cards 14 10883 Sept 2009
A comparison of the array versions available from various suppliers shows a significant amount of miRNA expression information is missed when using these out of date arrays for miRNA expression profiling analysis.
Comparison of miRBase Coverage
Supplier Species miRBase Version Unique Mature miRNAs Information Missed on Earlier Array Versions LC Sciences Human 19 2019 Mouse 19 1265 Rat 19 722 Exiqon / Phalanx Human 18 1921 5% Mouse 18 1157 9% Rat 18 680 6% Agilent Human 16 1212 40% Mouse 17 1111 12% Rat 16 679 6% Affymetrix Human 17 1733 14% Mouse 17 1111 12% Rat 17 680 6% ABI qPCR Cards Human 14 894 56% Mouse 14 700 44% Rat 14 388 46%
Ribonucleic acid (RNA) design offers unique opportunities for engineering genetic networks and nanostructures that self-assemble within living cells. Recent years have seen the creation of increasingly complex RNA devices, including proof-of-concept applications for in vivo three-dimensional scaffolding, imaging, computing, and control of biological behaviors. Expert intuition and simple design rules-the stability of double helices, the modularity of noncanonical RNA motifs, and geometric closure-have enabled these successful applications.
Going beyond heuristics, emerging algorithms may enable automated design of RNAs with nucleotide-level accuracy but, as illustrated on a recent RNA square design, are not yet fully predictive. Looking ahead, technological advances in RNA synthesis and interrogation are poised to radically accelerate the discovery and stringent testing of design methods.
Perspective: an impending acceleration
In recent years, RNA designers have leveraged simple rules for secondary structure formation, the modularity of small RNA motifs, and three-dimensional closure to produce devices and nanostructures of growing complexity.
It is particularly exciting to see these designs deployed into biological systems, suggesting future routes to biomedical devices that sense and perhaps correct cellular dysfunction. We are optimistic about the development of more quantitative and predictive theories for RNA structure design and eventually RNA functional design due to the explosion of RNA data expected in upcoming years.
The cycle of RNA design and testing can be short, especially compared to protein engineering — arbitrary RNA sequences up to hundreds of nucleotides in length are experimentally straightforward to synthesize, purify, interrogate, and evolve on the timescale of days. Current technologies offer the parallel synthesis of thousands of arbitrary DNA templates (Figure 4a and b), which can be transcribed into RNA in vitro and, in principle, in vivo (Figure 4c). Further, multiplexed single-nucleotide- resolution chemical mapping and elegant selection strategies can provide information-rich data on all of these molecules’ structures and functions, using deep-sequencing platforms with turn-around times of hours (Figure 4d). The key challenges will then be to distribute and accurately analyze these data, to update RNA modeling algorithms, and to feed back these insights into the next rounds of synthesis and mapping.
The result, a massively parallel design cycle, would offer unprecedented opportunities for squaring theory with practice in RNA design.
- Bida J, Das R. (2012) Squaring theory with practice in RNA design. Curr Opin Struct Biol [Epub ahead of print]. [article]
Title: Recent Work & Current Methods in Cancer microRNA Research
Date: Wed 7/11/12
Please register for the webinar by selecting the presentation time that is most convenient for your timezone.
North America – 1:00 Central Daylight Time
https://attendee.gotowebinar.com/185mk/register/4023113389282809344Europe – 1:00 PM Greenwich Mean Time
https://attendee.gotowebinar.com/185mk/register/8611379810038688768Far East – 10:00 AM China Standard Time (GMT +8hrs)
https://attendee.gotowebinar.com/185mk/register/1867106327144438016Webinar Outline
- Brief review of microRNA basics: history, biogenesis, function
- Recent developments of microRNA research in the field of cancer genomics
- Current methods for microRNA discovery and profiling
- Case studies and application examples
After registering, you will receive a confirmation email containing information about joining the webinar.
After completion of the webinar, you will receive an email containing a link to the archived webinar.
LC Sciences will be exhibiting this week in San Diego for the Drug Discovery Chemistry Conference.
Booth #19
We will also be presenting a poster: Phosphopeptide Array Platform for Cellular Signaling Network Protein Profiling in Breast Cancer Cells
Peptide Microarray technology for studying protein-protein interactions.
Microarray-Synthesized Oligos for Targeted Sequencing
Thu, 04/12/2012 – 3:28pmThough next-generation DNA sequencing (NGS) provides very high levels of coverage even on complex genomes, it is still advantageous to reduce the complexity of samples and sequence smaller targeted regions—in particular, when sample numbers are very high and the goal is detection of less prevalent mutations. Several academic and commercial groups have developed a variety of capture methods for enriching or selectively amplifying subsets of the genome for targeted sequencing. (read more…)
The Plant and Animal Genomes conference will be held in San Diego, CA January 14-18, 2012. LC Sciences will be exhibiting at the conference. Please visit us in booth #133 to learn more about our RNA sequencing services, microRNA discovery and profiling services, and our unique Seq-Array service for studying non-model plant and animal transcriptomes.
Happy Thanksgiving from LC Sciences.
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