Advances in Fluorescent Tracking of Nucleic Acids in Living Cell

Dirks, Roeland W.; Tanke, Hans J.

doi:10.2144/000112121

Cited by 61 publications

(39 citation statements)

References 63 publications

(61 reference statements)

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“…Visualizing patterns of gene expression within the intact tissues of transgenic organisms containing gene expression reporters may be the most general method (Tomancak et al 2002). Epitope tagging, enhancer trapping, and gene trapping all have the added advantage that gene expression can subsequently be observed in living tissues, revealing dynamic processes that are largely beyond the reach of methods based on fixed material (reviewed in Herschman 2003;Dirks and Tanke 2006).…”

Section: T He Central Challenge Of Postsequence Genomics Ismentioning

confidence: 99%

The Carnegie Protein Trap Library: A Versatile Tool for Drosophila Developmental Studies

et al. 2007

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Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were found in 256 additional genes. At least 8 novel genes were also identified. Our results demonstrate that the Carnegie collection will be useful as a discovery tool in diverse areas of cell and developmental biology and suggest new strategies for greatly increasing the coverage of the Drosophila proteome with protein trap insertions.

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Section: T He Central Challenge Of Postsequence Genomics Ismentioning

confidence: 99%

The Carnegie Protein Trap Library: A Versatile Tool for Drosophila Developmental Studies

et al. 2007

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“…One of the simplest methods used to visualize endogenous RNA in single living cells involves introducing fluorescently labeled antisense linear oligonucleotide probes (Figure 1 a ) into cells (19, 20, 50, 51, 56). In general, this approach requires the use of multiple probes targeting the same RNA transcript so that a high local concentration of hybridized probes can be seen above the high background of unbound probes (51).…”

Section: Fluorescent Probes For Live-cell Rna Detectionmentioning

confidence: 99%

Fluorescent Probes for Live-Cell RNA Detection

Bao

Rhee

Tsourkas

2009

Annu. Rev. Biomed. Eng.

223

175

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Commonly used techniques for analyzing gene expression, such as polymerase chain reaction (PCR), microarrays, and in situ hybridization, have proven invaluable in understanding RNA processing and regulation. However, these techniques rely on the use of lysed and/or fixed cells and are therefore limited in their ability to provide important spatial-temporal information. This has led to the development of numerous techniques for imaging RNA in living cells, some of which have already provided important insight into the dynamic role RNA plays in dictating cell behavior. Here we review the fluorescent probes that have allowed for RNA imaging in living cells and discuss their utility and limitations. Common challenges faced by fluorescent probes, such as probe design, delivery, and target accessibility, are also discussed. It is expected that continued advancements in live cell imaging of RNA will open new and exciting opportunities in a wide range of biological and medical applications.

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“…These studies regarding the organization of chromosome territories, genes, and intracellular RNA dynamics have been based on cytogenetics conducted mainly in fixed cells through in situ hybridization (ISH) which, although still a powerful tool to study nuclear architecture, only provides restricted information on existing structures at the time of fixation. Thus, there is a growing interest in live-cell imaging techniques and one possible strategy to follow the dynamics of intracellular RNA and proteins in living cells may involve fluorescent labelling [17,18]. Studies on living plant cells can benefit from the use of an optical imaging chamber that enables visualization for long periods [19].…”

Section: Introduction: the Structural Chromatin Organizationmentioning

confidence: 99%

Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses

Santos

Ferreira

Oliveira

2017

Biology

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The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.

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Advances in Fluorescent Tracking of Nucleic Acids in Living Cell

Cited by 61 publications

References 63 publications

The Carnegie Protein Trap Library: A Versatile Tool for Drosophila Developmental Studies

The Carnegie Protein Trap Library: A Versatile Tool for Drosophila Developmental Studies

Fluorescent Probes for Live-Cell RNA Detection

Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses

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