@article {48595, title = {mRNA quantification using single-molecule FISH in Drosophila embryos.}, journal = {Nature Protocols}, volume = {12}, year = {2017}, month = {2017 Jul}, pages = {1326-1348}, abstract = {

Spatial information is critical to the interrogation of developmental and tissue-level regulation of gene expression. However, this information is usually lost when global mRNA levels from tissues are measured using reverse transcriptase PCR, microarray analysis or high-throughput sequencing. By contrast, single-molecule fluorescence in situ hybridization (smFISH) preserves the spatial information of the cellular mRNA content with subcellular resolution within tissues. Here we describe an smFISH protocol that allows for the quantification of single mRNAs in Drosophila embryos, using commercially available smFISH probes (e.g., short fluorescently labeled DNA oligonucleotides) in combination with wide-field epifluorescence, confocal or instant structured illumination microscopy (iSIM, a super-resolution imaging approach) and a spot-detection algorithm. Fixed Drosophila embryos are hybridized in solution with a mixture of smFISH probes, mounted onto coverslips and imaged in 3D. Individual fluorescently labeled mRNAs are then localized within tissues and counted using spot-detection software to generate quantitative, spatially resolved gene expression data sets. With minimum guidance, a graduate student can successfully implement this protocol. The smFISH procedure described here can be completed in 4-5 d.

}, issn = {1750-2799}, doi = {10.1038/nprot.2017.030}, author = {Trcek, Tatjana and Lionnet, Timoth{\'e}e and Shroff, Hari and Lehmann, Ruth} } @article {46975, title = {Drosophila germ granules are structured and contain homotypic mRNA clusters.}, journal = {Nature Communications}, volume = {6}, year = {2015}, month = {2015 Aug 5}, pages = {7962}, abstract = {

Germ granules, specialized ribonucleoprotein particles, are a hallmark of all germ cells. In Drosophila, an estimated 200 mRNAs are enriched in the germ plasm, and some of these have important, often conserved roles in germ cell formation, specification, survival and migration. How mRNAs are spatially distributed within a germ granule and whether their position defines functional properties is unclear. Here we show, using single-molecule FISH and structured illumination microscopy, a super-resolution approach, that mRNAs are spatially organized within the granule whereas core germ plasm proteins are distributed evenly throughout the granule. Multiple copies of single mRNAs organize into {\textquoteright}homotypic clusters{\textquoteright} that occupy defined positions within the center or periphery of the granule. This organization, which is maintained during embryogenesis and independent of the translational or degradation activity of mRNAs, reveals new regulatory mechanisms for germ plasm mRNAs that may be applicable to other mRNA granules.

}, issn = {2041-1723}, doi = {10.1038/ncomms8962}, author = {Trcek, Tatjana and Grosch, Markus and York, Andrew and Shroff, Hari and Lionnet, Timoth{\'e}e and Lehmann, Ruth} } @article {46714, title = {The fate of the messenger is pre-determined: a new model for regulation of gene expression.}, journal = {Biochimica et Biophysica Acta (BBA)}, volume = {1829}, year = {2013}, month = {2013 Jun-Jul}, pages = {643-53}, abstract = {

Recent years have seen a rise in publications demonstrating coupling between transcription and mRNA decay. This coupling most often accompanies cellular processes that involve transitions in gene expression patterns, for example during mitotic division and cellular differentiation and in response to cellular stress. Transcription can affect the mRNA fate by multiple mechanisms. The most novel finding is the process of co-transcriptional imprinting of mRNAs with proteins, which in turn regulate cytoplasmic mRNA stability. Transcription therefore is not only a catalyst of mRNA synthesis but also provides a platform that enables imprinting, which coordinates between transcription and mRNA decay. Here we present an overview of the literature, which provides the evidence of coupling between transcription and decay, review the mechanisms and regulators by which the two processes are coupled, discuss why such coupling is beneficial and present a new model for regulation of gene expression. This article is part of a Special Issue entitled: RNA Decay mechanisms.

}, keywords = {Cytoplasm, Gene Expression Regulation, Fungal, Genomic Imprinting, Humans, Poly(A)-Binding Proteins, Ribonucleases, RNA Polymerase II, RNA Stability, RNA, Messenger, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic}, issn = {0006-3002}, doi = {10.1016/j.bbagrm.2013.01.004}, author = {Haimovich, Gal and Choder, Mordechai and Singer, Robert H and Trcek, Tatjana} } @article {46713, title = {Temporal and spatial characterization of nonsense-mediated mRNA decay.}, journal = {Genes \& Development}, volume = {27}, year = {2013}, month = {2013 Mar 1}, pages = {541-51}, abstract = {

Nonsense-mediated mRNA decay (NMD) is a quality control mechanism responsible for "surveying" mRNAs during translation and degrading those that harbor a premature termination codon (PTC). Currently the intracellular spatial location of NMD and the kinetics of its decay step in mammalian cells are under debate. To address these issues, we used single-RNA fluorescent in situ hybridization (FISH) and measured the NMD of PTC-containing β-globin mRNA in intact single cells after the induction of β-globin gene transcription. This approach preserves temporal and spatial information of the NMD process, both of which would be lost in an ensemble study. We determined that decay of the majority of PTC-containing β-globin mRNA occurs soon after its export into the cytoplasm, with a half-life of \<1 min; the remainder is degraded with a half-life of \>12 h, similar to the half-life of normal PTC-free β-globin mRNA, indicating that it had evaded NMD. Importantly, NMD does not occur within the nucleoplasm, thus countering the long-debated idea of nuclear degradation of PTC-containing transcripts. We provide a spatial and temporal model for the biphasic decay of NMD targets.

}, keywords = {Animals, beta-Globins, Cell Line, Cell Nucleus, Cytoplasm, Humans, In Situ Hybridization, Fluorescence, Nonsense Mediated mRNA Decay, RNA, Messenger, Time Factors}, issn = {1549-5477}, doi = {10.1101/gad.209635.112}, author = {Trcek, Tatjana and Sato, Hanae and Singer, Robert H and Maquat, Lynne E} } @article {46725, title = {Single-mRNA counting using fluorescent in situ hybridization in budding yeast.}, journal = {Nature Protocols}, volume = {7}, year = {2012}, month = {2012 Feb 2}, pages = {408-19}, abstract = {

Fluorescent in situ hybridization (FISH) allows the quantification of single mRNAs in budding yeast using fluorescently labeled single-stranded DNA probes, a wide-field epifluorescence microscope and a spot-detection algorithm. Fixed yeast cells are attached to coverslips and hybridized with a mixture of FISH probes, each conjugated to several fluorescent dyes. Images of cells are acquired in 3D and maximally projected for single-molecule analysis. Diffraction-limited labeled mRNAs are observed as bright fluorescent spots and can be quantified using a spot-detection algorithm. FISH preserves the spatial distribution of cellular RNA distribution within the cell and the stochastic fluctuations in individual cells that can lead to phenotypic differences within a clonal population. This information, however, is lost if the RNA content is measured on a population of cells by using reverse transcriptase PCR, microarrays or high-throughput sequencing. The FISH procedure and image acquisition described here can be completed in 3 d.

}, keywords = {Algorithms, Antisense Elements (Genetics), In Situ Hybridization, Fluorescence, RNA, Fungal, RNA, Messenger, Saccharomyces cerevisiae}, issn = {1750-2799}, doi = {10.1038/nprot.2011.451}, author = {Trcek, Tatjana and Chao, Jeffrey A and Larson, Daniel R and Park, Hye Yoon and Zenklusen, Daniel and Shenoy, Shailesh M and Singer, Robert H} } @article {46722, title = {An unbiased analysis method to quantify mRNA localization reveals its correlation with cell motility.}, journal = {Cell Reports}, volume = {1}, year = {2012}, month = {2012 Feb 23}, pages = {179-84}, abstract = {

Localization of mRNA is a critical mechanism used by a large fraction of transcripts to restrict its translation to specific cellular regions. Although current high-resolution imaging techniques provide ample information, the analysis methods for localization have either been qualitative or employed quantification in nonrandomly selected regions of interest. Here, we describe an analytical method for objective quantification of mRNA localization using a combination of two characteristics of its molecular distribution, polarization and dispersion. The validity of the method is demonstrated using single-molecule FISH images of budding yeast and fibroblasts. Live-cell analysis of endogenous β-actin mRNA in mouse fibroblasts reveals that mRNA polarization has a half-life of ~16 min and is cross-correlated with directed cell migration. This novel approach provides insights into the dynamic regulation of mRNA localization and its physiological roles.

}, keywords = {Actins, Animals, Cell Movement, Chick Embryo, Computer Simulation, Embryo, Mammalian, Fibroblasts, Green Fluorescent Proteins, Imaging, Three-Dimensional, In Situ Hybridization, Mice, Monte Carlo Method, RNA Transport, RNA, Messenger, Saccharomyces cerevisiae}, issn = {2211-1247}, doi = {10.1016/j.celrep.2011.12.009}, author = {Park, Hye Yoon and Trcek, Tatjana and Wells, Amber L and Chao, Jeffrey A and Singer, Robert H} } @article {46734, title = {Single-molecule mRNA decay measurements reveal promoter- regulated mRNA stability in yeast.}, journal = {Cell}, volume = {147}, year = {2011}, month = {2011 Dec 23}, pages = {1484-97}, abstract = {

Messenger RNA decay measurements are typically performed on a population of cells. However, this approach cannot reveal sufficient complexity to provide information on mechanisms that may regulate mRNA degradation, possibly on short timescales. To address this deficiency, we measured cell cycle-regulated decay in single yeast cells using single-molecule FISH. We found that two genes responsible for mitotic progression, SWI5 and CLB2, exhibit a mitosis-dependent mRNA stability switch. Their transcripts are stable until mitosis, when a precipitous decay eliminates the mRNA complement, preventing carryover into the next cycle. Remarkably, the specificity and timing of decay is entirely regulated by their promoter, independent of specific cis mRNA sequences. The mitotic exit network protein Dbf2p binds to SWI5 and CLB2 mRNAs cotranscriptionally and regulates their decay. This work reveals the promoter-dependent control of mRNA stability, a regulatory mechanism that could be employed by a variety of mRNAs and organisms.

}, keywords = {Cell Cycle, Cell Cycle Proteins, Cyclin B, Gene Expression Regulation, Fungal, In Situ Hybridization, Fluorescence, Kinetics, Promoter Regions, Genetic, Protein-Serine-Threonine Kinases, RNA Stability, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription Factors, Transcription, Genetic}, issn = {1097-4172}, doi = {10.1016/j.cell.2011.11.051}, author = {Trcek, Tatjana and Larson, Daniel R and Mold{\'o}n, Alberto and Query, Charles C and Singer, Robert H} }