Unified translation repression mechanism for microRNAs and upstream AUGs

Abstract Background MicroRNAs (miRNAs) are endogenous small RNAs that modulate gene expression at the post-transcriptional level by binding complementary sites in the 3'-UTR. In a recent genome-wide study reporting a new miRNA target class (miBridge), we identified and validated interactions between 5'-UTRs and miRNAs. Separately, upstream AUGs (uAUGs) in 5'-UTRs are known to regulate genes translationally without affecting mRNA levels, one of the mechanisms for miRNA-mediated repression. Results Using sequence data from whole-genome cDNA alignments we identified 1418 uAUG sequences on the 5'-UTR that specifically interact with 3'-ends of conserved miRNAs. We computationally identified miRNAs that can target six genes through their uAUGs that were previously reported to suppress translation. We extended this meta-analysis by confirming expression of these miRNAs in cell-lines used in the uAUG studies. Similarly, seven members of the KLF family of genes containing uAUGs were computationally identified as interacting with several miRNAs. Using KLF9 as an example (whose protein expression is limited to brain tissue despite the mRNA being expressed ubiquitously), we show computationally that miRNAs expressed only in HeLa cells and not in neuroblastoma (N2A) cells can bind the uAUGs responsible for translation inhibition. Our computed results demonstrate that tissue- or cell-line specific repression of protein translation by uAUGs can be explained by the presence or absence of miRNAs that target these uAUG sequences. We propose that these uAUGs represent a subset of miRNA interaction sites on 5'-UTRs in miBridge, whereby a miRNA binding a uAUG hinders the progression of ribosome scanning the mRNA before it reaches the open reading frame (ORF). Conclusions While both miRNAs and uAUGs are separately known to down-regulate protein expression, we show that they may be functionally related by identifying potential interactions through a sequence-specific binding mechanism. Using prior experimental evidence that shows uAUG effects on translation repression together with miRNA expression data specific to cell lines, we demonstrate through computational analysis that cell-specific down-regulation of protein expression (while maintaining mRNA levels) correlates well with the simultaneous presence of miRNA and target uAUG sequences in one cell type and not others, suggesting tissue-specific translation repression by miRNAs through uAUGs.http://deepblue.lib.umich.edu/bitstream/2027.42/112383/1/12864_2009_Article_2749.pd

Imaging {Au 0 -PAMAM} Gold-dendrimer Nanocomposites in Cells

Dendrimer nanocomposites (DNC) are hybrid nanoparticles formed by the dispersion and immobilization of guest atoms or small clusters in dendritic polymer matrices. They have a great potential in biomedical applications due to their controlled composition, predetermined size, shape and variable surface functionalities. In this work, d =5–25 nm spherical nanoparticles composed of gold and poly(amidoamine) (PAMAM) dendrimers have been selected to demonstrate this nanoparticle based concept. {Au(0) n -PAMAM} gold dendrimer nanocomposites with a well-defined size were synthesized and imaged by transmission electron microscopy both in vitro and in vivo. DNC have also the potential to be used for imaging and drug delivery vehicles either by utilizing bioactive guests or through the incorporation of radioactive isotopes, such as Au-198.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43295/1/11051_2004_Article_5101884.pd

Early Growth Response 1-Dependent Downregulation of Matrix Metalloproteinase 9 and Mouse Double Minute 2 Attenuates Head and Neck Squamous Cell Carcinoma Metastasis

Background/Aims: The functional relevance of early growth response-1 (EGR1) on cancer invasion remains controversial. The effect of EGR1 on the expression of MMP9, which is important for HNSCC invasion, is still disputed. There is no previous data showing the effect of EGR1 on mouse double minute 2 (MDM2), an enhancer of matrix metalloproteinase 9 (MMP9) expression. Our aim is to clarify the negative correlation between EGR1 expression and head and neck squamous cell carcinoma (HNSCC) metastasis. Methods: EGR1 mRNA and protein expressions were compared in normal and HNSCC tissues using The Cancer Genome Atlas (TCGA) dataset analysis or immunohistochemistry (IHC), respectively. In vitro cell invasion was evaluated Matrigel invasion assay. EGR1-dependent inhibition of MDM2 transcription was assessed by promoter–luciferase assay and chromatin immunoprecipitation (ChIP). Results: TCGA data showed that EGR1 mRNA levels are significantly higher in normal oral tissues as compared with HNSCC tumor tissues (adjusted P = 1.64x10-16). In addition, nonmetastatic HNSCC tissues showed significantly higher EGR1 mRNA levels as compared with metastatic tissues (adjusted P = 0.023). IHC analysis showed that primary tumor tissues expressed significantly higher levels of nuclear EGR1 compared with paired metastatic lymph node tissues (P < 0.05). EGR1 overexpression downregulated MMP9 and MDM2 protein expression. Consistent with these observations, TCGA data analysis found significantly fewer metastatic patients among a subgroup of population presenting higher EGR1 expressions with lower MMP9 and/or MDM2. Conclusion: Our data suggests that EGR1 prevents HNSCC metastasis through downregulation of MMP9 and MDM2. EGR1 might be a potential candidate to attenuate HNSCC metastasis

Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)

MicroRNAs (miRNA) are endogenous tissue-specific short RNAs that regulate gene expression. Discriminating each let-7 family member expression is especially important due to let-7's abundance and connection with development and cancer. However, short lengths (22 nt) and similarities between multiple sequences have prevented identification of individual members. Here, we present ProDeG, a computational algorithm which designs imperfectly matched sequences (previously yielding only noise levels in microarray experiments) for genome-wide microarray “signal” probes to discriminate single nucleotide differences and to improve probe qualities. Our probes for the entire let-7 family are both homogeneous and specific, verified using microarray signals from fluorescent dye-tagged oligonucleotides corresponding to the let-7 family, demonstrating the power of our algorithm. In addition, false let-7c signals from conventional perfectly-matched probes were identified in lymphoblastoid cell-line samples through comparison with our probe-set signals, raising concerns about false let-7 family signals in conventional microarray platform

Design and Function of a Dendrimer-Based Therapeutic Nanodevice Targeted to Tumor Cells Through the Folate Receptor

Purpose . We sought to develop nanoscale drug delivery materials that would allow targeted intracellular delivery while having an imaging capability for tracking uptake of the material. A complex nanodevice was designed and synthesized that targets tumor cells through the folate receptor.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41493/1/11095_2004_Article_378868.pd

A p53/miRNA-34 axis regulates Snail1-dependent cancer cell epithelial–mesenchymal transition

Expression of the essential EMT inducer Snail1 is inhibited by miR-34 through a p53-dependent regulatory pathway

Development of BIM-Based Risk Rating Estimation Automation and a Design-for-Safety Review System

Various laws and guidelines on designing for safety have been developed world-wide, and these were used to identify risks at construction sites in advance through qualitative and quantitative safe management. In other words, attention is being paid to safe management based on design drawings and models rather than field visits. It was predicted that the introduction of the concept of design-for-safety would minimize risk at construction sites through safe management in the design phase. This is because the efficiency and reliability of such a strategy has been demonstrated in various cases abroad. However, domestic design-for-safety suggests a very limited range of evaluation items, so there is a limit to using such strategies in construction sites. Building information modeling (BIM) technology is attracting attention in situations when safe management must also be based on design proposals. Although previous studies on the identification of falling disasters and automatic identification of hazards have been conducted, these studies only deal with a limited range of items for identifying risk items. For example, BIM-based risk extraction, which is limited to falling disasters, is only at the level of risk recognition that can be derived based on the process table, and evaluation is not made accordingly. It is difficult to assess the overall disaster risk in many of the items required for risk rating estimation. In this paper, we solve the above problems by deriving a BIM-based risk rating estimation scenario based on the disaster scenario for automating BIM-based risk rating estimation, and we developed an evaluation system using this method. The BIM-based risk rating estimation methodology was presented through BIM-based hazard extraction, evaluation of requirement information, evaluation item selection, and using the evaluation system in a design-for-safety review

Small Non-coding Transfer RNA-Derived RNA Fragments (tRFs): Their Biogenesis, Function and Implication in Human Diseases

tRNA-derived RNA fragments (tRFs) are an emerging class of non-coding RNAs (ncRNAs). A growing number of reports have shown that tRFs are not random degradation products but are functional ncRNAs made of specific tRNA cleavage. They play regulatory roles in several biological contexts such as cancer, innate immunity, stress responses, and neurological disorders. In this review, we summarize the biogenesis and functions of tRFs

Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray

Sequence-specific oligonucleotide probes play a crucial role in hybridization techniques including PCR, DNA microarray and RNA interference. Once the entire genome becomes the search space for target genes/genomic sequences, however, cross-hybridization to non-target sequences becomes a problem. Large gene families with significant similarity among family members, such as the P450s, are particularly problematic. Additionally, accurate single nucleotide polymorphism (SNP) detection depends on probes that can distinguish between nearly identical sequences. Conventional oligonucleotide probes that are perfectly matched to target genes/genomic sequences are often unsuitable in such cases. Carefully designed mismatches can be used to decrease cross-hybridization potential, but implementing all possible mismatch probes is impractical. Our study provides guidelines for designing non-perfectly matched DNA probes to target DNA sequences as desired throughout the genome. These guidelines are based on the analysis of hybridization data between perfectly matched and non-perfectly matched DNA sequences (single-point or double-point mutated) calculated in silico. Large changes in hybridization temperature predicted by these guidelines for non-matched oligonucleotides fit independent experimental data very well. Applying the guidelines to find oligonucleotide microarray probes for P450 genes, we confirmed the ability of our point mutation method to differentiate the individual genes in terms of thermodynamic calculations of hybridization and sequence similarity