Jul

14

Featured Article – MicroRNAome of Porcine Pre- and Postnatal Development

Filed Under New Customer Publications | Leave a Comment

The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Read more

Jun

30

Featured Publication – Costimulation-Dependent Expression of MicroRNA-214 Increases the Ability of T Cells To Proliferate by Targeting Pten

Filed Under New Customer Publications | Leave a Comment

T cell activation requires signaling through the TCR and costimulatory molecules, such as CD28. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression posttranscriptionally and are also known to be involved in lymphocyte development and function. In this paper, we set out to examine potential roles of miRNAs in T cell activation, using genome-wide expression profiling to identify miRNAs differentially regulated following T cell activation. One of the miRNAs upregulated after T cell activation, miR-214, was predicted to be capable of targeting Pten based on bioinformatics and reports suggesting that it targets Pten in ovarian tumor cells. Upregulation of miR-214 in T cells inversely correlated with levels of phosphatase and tensin homolog deleted on chromosome 10. In vivo, transcripts containing the 3′ untranslated region of Pten, including the miR-214 target sequence, were negatively regulated after T cell activation, and forced expression of miR-214 in T cells led to increased proliferation after stimulation. Blocking CD28 signaling in vivo prevented miR-214 upregulation in alloreactive T cells. Stimulation of T cells through the TCR alone was not sufficient to result in upregulation of miR-214. Thus, costimulation-dependent upregulation of miR-214 promotes T cell activation by targeting the negative regulator Pten. Thus, the requirement for T cell costimulation is, in part, related to its ability to regulate expression of miRNAs that control T cell activation.

Jindra PT, Bagley J, Godwin JG, Iacomini J. (2010) Costimulation-Dependent Expression of MicroRNA-214 Increases the Ability of T Cells To Proliferate by Targeting Pten. J Immunol [Epub ahead of print]. [abstract]

Jun

10

Tooth, Tail, & Hair – Where would we be without microRNA?

Filed Under New Customer Publications | Leave a Comment

  1. Cao H, Wang J, Li X, Florez S, Huang Z, Venugopalan SR, Elangovan S, Skobe Z, Margolis HC, Martin JF, Amendt BA. (2010) MicroRNAs Play a Critical Role in Tooth Development. J Dent Res [Epub ahead of print]. [abstract]
  2. Sehm T, Sachse C, Frenzel C, Echeverri K. (2009) miR-196 is an essential early-stage regulator of tail regeneration, upstream of key spinal cord patterning events. Dev Biol 334(2), 468-80.  [abstract]
  3. Mardaryev AN, Ahmed MI, Vlahov NV, Fessing MY, Gill JH, Sharov AA, Botchkareva NV. (2010) Micro-RNA-31 controls hair cycle-associated changes in gene expression programs of the skin and hair follicle. FASEB J [Epub ahead of print]. [abstract]

May

5

Featured Customer Publication: Phloem small RNAs, nutrient stress responses, and systemic mobility

Filed Under New Customer Publications | Leave a Comment

Phloem small RNAs, nutrient stress responses, and systemic mobility

The authors used LC Sciences’ custom miRNA microarrays containing all known plant miRNAs and a set of unknown small (s) RNAs earlier cloned from Brassica phloem sap, to comprehensively analyze the phloem response to nutrient deficiency by removing sulfate, copper or iron, respectively, from the growth medium. They show that phloem sap contains a specific set of sRNAs that is distinct from leaves and roots, and that the phloem also responds specifically to stress. They further demonstrate that under nutrient starvation miR399 and miR395 can be translocated through graft unions from wild type scions to rootstocks of the miRNA processing hen1-1 mutant. In contrast, miR171 was not transported. Translocation of miR395 led to a down-regulation of one of its targets in rootstocks, suggesting that this transport is of functional relevance, and that miR395, in addition to the well characterized miR399, could potentially act as a long-distance information transmitter.

Buhtz A, Pieritz J, Springer F, Kehr J. (2010) Phloem small RNAs, nutrient stress responses, and systemic mobility. BMC Plant Biol 10(1), 64. [Article]

Mar

11

New microRNA Publications List Available

Filed Under New Customer Publications | Leave a Comment

mirna_pubs_listHere is the latest list of publications from our customers making use of our microRNA Discovery and Profiling Services.  The current list includes more than 140 publications by some of the leading researchers in the microRNA field.  Enjoy!

Feb

15

New Customer Publication – MicroRNA-19a mediates the suppressive effect of laminar flow on cyclin D1 expression in human umbilical vein endothelial cells

Filed Under New Customer Publications | Leave a Comment

MicroRNA-19a mediates the suppressive effect of laminar flow on cyclin D1 expression in human umbilical vein endothelial cells

Endothelial cells (ECs) respond to changes in mechanical forces, leading to the modulation of signaling networks and cell function; an example is the inhibition of EC proliferation by steady laminar flow. MicroRNAs (miRs) are short noncoding 20–22 nucleotide RNAs that negatively regulate the expression of target genes at the posttranscriptional level. This study demonstrates that miRs are involved in the flow regulation of gene expression in ECs. With the use of microRNA chip array, we found that laminar shear stress (12 dyn/cm2, 12 h) regulated the EC expression of manymiRs, including miR-19a.We further showed that stable transfection of miR-19a significantly decreased the expression of a reporter gene controlled by a conserved 3′-untranslated region of the cyclinD1 gene and also the protein level of cyclin D1, leading to an arrest of cell cycle at G1/S transition. Laminar flow suppressed cyclin D1 protein level, and this suppressive effect was diminished when the endogenous miR-19a was inhibited. In conclusion, we demonstrated that miR-19a plays an important role in the flow regulation of cyclin D1 expression. These results revealed a mechanism by which mechanical forces modulate endothelial gene expression.

Qin X, Wang X, Wang Y, Tang Z, Cui Q, Xi J, J Li YS, Chien S, Wang N. (2010) MicroRNA-19a mediates the suppressive effect of laminar flow on cyclin D1 expression in human umbilical vein endothelial cells. Proc Natl Acad Sci USA [Epub ahead of print]. [abstract]

Feb

12

Peptide Microarray Publication – Creating protein affinity reagents by combining peptide ligands on synthetic DNA scaffolds

Filed Under New Customer Publications | Leave a Comment

Williams BA, Diehnelt CW, Belcher P, Greving M, Woodbury NW, Johnston SA, Chaput JC. (2009) Creating protein affinity reagents by combining peptide ligands on synthetic DNA scaffolds. J Am Chem Soc 131(47), 17233-41. [abstract]

A full understanding of the proteome will require ligands to all of the proteins encoded by genomes. While antibodies represent the principle affinity reagents used to bind proteins, their limitations have created a need for new ligands to large numbers of proteins. Here we propose a general concept to obtain protein affinity reagents that avoids animal immunization and iterative selection steps. Central to this process is the idea that small peptide libraries contain sequences that will bind to independent regions on a protein surface and that these ligands can be combined on synthetic scaffolds to create high affinity bivalent reagents. To demonstrate the feasibility of this approach, an array of 4000 unique 12-mer peptides was screened to identify sequences that bind to nonoverlapping sites on the yeast regulatory protein Gal80. Individual peptide ligands were screened at different distances using a novel DNA linking strategy to identify the optimal peptide pair and peptide pair separation distance required to transform two weaker ligands into a single high affinity protein capture reagent. A synthetic antibody or synbody was created with 5 nM affinity to Gal80 that functions in conventional ELISA and pull-down assays. We validated our synthetic antibody approach by creating a second synbody to human transferrin. In both cases, we observed an increase in binding affinity of  ~1000-fold (ΔΔG = ~4.1 kcal/mol) between the individual peptides and final bivalent synbody construct.

Feb

3

Recent Customer Publications – microRNA

Filed Under New Customer Publications | Leave a Comment

  1. Greene SB, Gunaratne PH, Hammond SM, Rosen JM. (2010) A putative role for microRNA-205 in mammary epithelial cell progenitors. J Cell Sci [Epub ahead of print] [abstract]
  2. Pogribny IP, Filkowski JN, Tryndyak VP, Golubov A, Shpyleva SI, Kovalchuk O. (2010) Alterations of microRNAs and their targets are associated with acquired resistance of MCF-7 breast cancer cells to cisplatin. Int J Cancer [Epub ahead of print] [abstract]
  3. Sluijter JP, van Mil A, van Vliet P, Metz CH, Liu J, Doevendans PA, Goumans MJ. (2009) MicroRNA-1 and -499 Regulate Differentiation and Proliferation in Human-Derived Cardiomyocyte Progenitor Cells. Arterioscler Thromb Vasc Biol [Epub ahead of print] [abstract]
  4. Curtale G, Citarella F, Carissimi C, Goldoni M, Carucci N, Fulci V, Franceschini D, Meloni F, Barnaba V, Macino G. (2009) An emerging player in the adaptive immune response: microRNA-146a is a modulator of IL-2 expression and activation-induced cell death in T lymphocytes. Blood [Epub ahead of print] [abstract]
  5. Filkowski J, Ilnytskyy Y, Tamminga J, Koturbash I, Golubov A, Bagnyukova T, Pogribny I, Kovalchuk O. (2009) Hypomethylation and genome instability in the germline of exposed parents and their progeny is associated with altered miRNA expression. Carcinogenesis [Epub ahead of print] [abstract]
  6. Liu W, Gong YH, Chao TF, Peng XZ, Yuan JG, Ma ZY, Jia G, Zhao JZ. (2009) Identification of differentially expressed microRNAs by microarray: a possible role for microRNAs gene in medulloblastomas. Chin Med J (Engl) 122(20), 2405-411. [abstract]
  7. Duan Z, Choy E, Nielsen GP, Rosenberg A, Iafrate J, Yang C, Schwab J, Mankin H, Xavier R, Hornicek FJ. (2009) Differential expression of microRNA (miRNA) in chordoma reveals a role for miRNA-1 in Met expression. J Orthop Res [Epub ahead of print] [abstract]
  8. Lau P, Verrier JD, Nielsen JA, Johnson KR, Notterpek L, Hudson LD. (2008) Identification of dynamically regulated microRNA and mRNA networks in developing oligodendrocytes. J Neurosci 28(45), 11720-730. [abstract]

Jan

25

Customer Publication – Peptide Microarrays

Filed Under New Customer Publications | Leave a Comment

Identification and Sequence Composition Characterization of Chondroitin Sulfate-Binding Peptides through Peptide Array Screening

Researchers at Arizona State University made use of LC Sciences Custom Peptide Microarray Service and demonstrated an effective methodology to identify and characterize Chrondroitin sulfate (CS) binding peptides for sequence composition. 

Butterfield K, Caplan M, Panitch A. (2010) Identification and Sequence Composition Characterization of Chondroitin Sulfate-Binding Peptides through Peptide Array Screening. Biochemistry [Epub ahead of print]. [abstract]

Dec

21

LC Sciences’ Customers Publish in Science Magazine

Filed Under New Customer Publications | Leave a Comment

One of the highlights in the Dec 11th issue of Science Magazine was a paper published by LC Sciences’ customers Andrew H. Williams and Eric N. Olsen from the Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas. 

Williams AH, Valdez G, Moresi V, Qi X, McAnally J, Elliott JL, Bassel-Duby R, Sanes JR, Olson EN.  (2009) MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice.  Science 326(5959), 1549-54 [abstract]

This groundbreaking work identified miR-206 as a modifier of Amyotrophic lateral sclerosis (ALS)  pathogenesis  and provides a new perspective on the mechanisms underlying this neurodegenerative disease.  More broadly, the findings provide insight into the molecular basis of neuromuscular junction plasticity and also into determinants of rates of disease progression in motor neuron disease.

Additionally, a perspective on these important findings was published in the same Dec 11th issue of Science, by Robert H. Brown of the UMASS Medical School.

Brown, RH. (2009) A Reinnervating  MicroRNA. Science 326(5959), 1494-95. [abstract]

Next Page →