IMAGEtags: Quantifying mRNA Transcription in Real Time with Multiaptamer Reporters

Ray, J.
İlgü, Müslüm
Cell communications are essential to the organization, development, and maintenance of multicellular organisms. Much of this communication involves changes in RNA transcription and is dynamic. Most methods for studying transcription require interrupting the continuity of cellular function by sacrificing the communicating cells and capturing gene expression information by periodic sampling of individual cells or the population. The IMAGEtag technology to quantify RNA levels in living cells, demonstrated here in yeast, allows individual cells to be tracked over time as they respond to different environmental cues. IMAGEtags are short RNAs consisting of strings of a variable number of tandem aptamers that bind small-molecule ligands. The aptamer strings can vary in length and in configuration of aptamer constituents, such as to contain multiples of the same aptamer or two or more different aptamers that alternate in their occurrence. A minimum effective length is about five aptamers. The maximum length is undefined. The small-molecule ligands are enabled for imaging as fluorophore conjugates. For each IMAGEtag, two fluorophore conjugates are provided, which are FRET pairs. When a cell expresses an RNA containing an IMAGEtag sequence, the aptamers bind their ligands and bring the fluorophores into sufficiently close proximity to allow FRET. The background fluorescence of both fluorophores is minimal in the FRET channel. These features endow IMAGEtags with the sensitivity to report on mRNA expression levels in living cells.


Trehalose metabolism in wheat and identification of trehalose metabolizing enzymes under abiotic stress conditions
El-Bashiti, Tarek; Yücel, Ayşe Meral; Hamamcı, Haluk; Department of Biotechnology (2003)
Trehalose (a-D-glucopyranosyl-1,1-a-D-glucopyranoside) is a non reducing disaccharide of glucose that occurs in a large variety of organisms, ranging from bacteria to invertebrate animals, where it serves as an energy source or stress protectant. Until recently, only few plant species, mainly desiccation tolerant ءresurrection̕ plants, were considered to synthesize trehalose. Although most plant species do not appear to accumulate easily detectable amounts of trehalose, the discovery of genes for trehalose ...
Induction and control of large-scale gene regulatory networks
Tan, Mehmet; Tan, Mehmet; Department of Computer Engineering (2009)
Gene regulatory networks model the interactions within the cell and thus it is essential to understand their structure and to develop some control mechanisms that could effectively deal with them. This dissertation tackles these two aspects. To handle the first problem, a new constraint-based modeling algorithm is proposed that can both increase the quality of the output and decrease the computational requirements for learning the structure of gene regulatory networks by integrating multiple biological data...
ARID3B expression in primary breast cancers and breast cancer-derived cell lines
ERDOGAN, Ayse Selcen Oguz; OZDEMIRLER, Nihan; ÖYKEN, MERVE; ALPER, Murat; Erson Bensan, Ayşe Elif (2014-08-01)
ARID3B (AT-rich interaction domain 3) is a member of the family of ARID proteins, which constitutes evolutionarily conserved transcription factors implicated in normal development, differentiation, cell cycle regulation and chromatin remodeling. In addition, ARID3B has been linked to cellular immortalization, epithelial-mesenchymal transition (EMT) and tumorigenesis. Given the emerging role of ARID3B in tumor development, we examined its expression in primary patient-derived breast cancer samples and breast...
Investigation of SNX3 in colon cancer
Cingöz, Harun; Erson Bensan, Ayşe Elif; Department of Biology (2019)
Sorting Nexin 3 (SNX3) is part of the retromer complex that recycles cargo receptors back to plasma membrane or to Trans Golgi Network. WNT ligand carrier protein Wntless (WLS) is a known SNX3 cargo protein. Our earlier data suggested over expression of SNX3 in colon cancer cells. Considering its importance in receptor recycling, we hypothesized SNX3 to be a potential modulator of cancer related receptors. To begin understanding the role of SNX3, we developed RNAi models of SNX3 in SW480 colon cancer cells ...
Comparative phosphoproteomic analysis reveals signaling networks regulating monopolar and bipolar cytokinesis.
KARAYEL, Ö; ŞANAL, E; GIESE, SH; Üretmen, Kagıalı; POLAT, AN; HU, CK; RENARD, BY; Tunçbağ, Nurcan; ÖZLÜ, N (2018-02-02)
The successful completion of cytokinesis requires the coordinated activities of diverse cellular components including membranes, cytoskeletal elements and chromosomes that together form partly redundant pathways, depending on the cell type. The biochemical analysis of this process is challenging due to its dynamic and rapid nature. Here, we systematically compared monopolar and bipolar cytokinesis and demonstrated that monopolar cytokinesis is a good surrogate for cytokinesis and it is a well-suited system ...
Citation Formats
J. Ray et al., “IMAGEtags: Quantifying mRNA Transcription in Real Time with Multiaptamer Reporters,” VISUALIZING RNA DYNAMICS IN THE CELL, pp. 193–213, 2016, Accessed: 00, 2020. [Online]. Available: