IMAGEtags: Quantifying mRNA Transcription in Real Time with Multiaptamer Reporters

2016-01-01
Ray, J.
SHIN, I.
İlgü, Müslüm
BENDICKSON, L.
GUPTA, V.
KRAUS, G. A.
NILSEN-HAMILTON, M.
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.
VISUALIZING RNA DYNAMICS IN THE CELL

Suggestions

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 ...
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...
Resonctructing signaling pathways from RNAi data using genetic algorithms
Ayaz, Eyüp Serdar; Can, Tolga; Department of Bioinformatics (2011)
Cell signaling is a list of chemical reactions that are used for intercellular and intracellular communication. Signaling pathways denote these chemical reactions in a systematic manner. Today, many signaling pathways are constructed by several experimental methods. However there are still many communication skills of cells that are needed to be discovered. RNAi system allows us to see the phenotypes when some genes are removed from living cells. By observing these phenotypes, we can build signaling pathway...
Intergenic and Repeat Transcription in Human, Chimpanzee and Macaque Brains Measured by RNA-Seq
Xu, Augix Guohua; He, Liu; Li, Zhongshan; Xu, Ying; Li, Mingfeng; Fu, Xing; Yan, Zheng; Yuan, Yuan; Menzel, Corinna; Li, Na; Somel, Mehmet; Hu, Hao; Chen, Wei; Paabo, Svante; Khaitovich, Philipp (Public Library of Science (PLoS), 2010-07-01)
Transcription is the first step connecting genetic information with an organism's phenotype. While expression of annotated genes in the human brain has been characterized extensively, our knowledge about the scope and the conservation of transcripts located outside of the known genes' boundaries is limited. Here, we use high-throughput transcriptome sequencing (RNA-Seq) to characterize the total non-ribosomal transcriptome of human, chimpanzee, and rhesus macaque brain. In all species, only 20-28% of non-ri...
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: https://hdl.handle.net/11511/36904.