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.


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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...
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NAC-type plant-specific transcription factor genes encode proteins that play important roles in abiotic stress responses, as well as regulation of plant development. In the current study, expression profiles of wheat NAC-type transcription factor genes, TaNAC69-1 and TtNAMB-2, were examined under drought, salt, cold, and heat stress conditions in wheat. Based on reverse transcription quantitative PCR results, TaNAC69-1 was strongly expressed under drought, salinity, and high-temperature stress conditions. C...
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Ran binding proteins (RanBPs) are highly conserved members of the GTP-binding protein family that are involved in nuclear protein export between the nucleus and the cytoplasm. In this study, a CmRanBP gene from a melon was isolated (Cucumis melo L.) using the RACE (rapid amplification of cDNA ends) method. The 778 basepair long melon, with a RanBP cDNA encoding consisting of 197 amino acids (22.2 kDa protein), was characterized (GenBank accession no: EU853459). The predicted amino acid sequence of CmRanBP w...
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Gene regulatory networks (GRNs) govern the protein transcription process in the cell and interactions among genes play a vital role in determining the biosynthesis rate of proteins. By using intervention techniques discovered by biological research it is possible to control a GRN, thus promoting or demoting the expression rate of a certain gene. In this work, this control task is studied in a partially observable setting where interventions lack perfect knowledge of the expression level of all genes. Moreov...
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The recent advancement of omic technologies provides snapshots of cells, tissues, or patients identifying prominent genes, proteins, metabolites, and small molecules. However, accumulated big data on various omic data types may inherently make diseases or perturbations incomprehensible. Network inference or reconstruction methods map a set of significantly altered proteins/genes/metabolites to a given reference network that is composed of already known relations or interactions. Followingly, the signals fro...
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: