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The ability to visualize RNA in situ is essential to dissect mechanisms for the temporal and spatial regulation of gene expression that drives development. Although considerable attention has been focused on transcriptional control, studies in model organisms like Drosophila have highlighted the importance of post-transcriptional mechanisms - most notably intracellular mRNA localization - in the formation and patterning of the body axes, specification of cell fates, and polarized cell functions. Our understanding of both types of regulation has been greatly advanced by technological innovations that enable a combination of highly quantitative and dynamic analysis of RNA. This review presents two methods, single molecule fluorescence in situ hybridization for high resolution quantitative RNA detection in fixed Drosophila oocytes and embryos and genetically encoded fluorescent RNA labeling for detection in live cells.

Intracellular mRNA localization critically contributes to proper brain development and function. A recent study demonstrates that mRNAs are actively transported in radial glial cells from the soma to the distal basal endfeet, where they are locally translated.

Intracellular mRNA localization directs protein synthesis to particular subcellular domains to establish embryonic polarity in a wide range of vertebrates and invertebrates. In Drosophila, bicoid (bcd) mRNA is pre-localized at the anterior of the oocyte. After fertilization, this RNA is translated to produce a Bcd protein gradient that determines anterior cell fates [1, 2]. Recent analysis of bcd mRNA during late stages of oogenesis led to a model for steady-state localization of bcd by continual active transport [3]. Here, we elucidate the path and mechanism of sustained bcd mRNA transport by direct observation of bcd RNA particle translocation in living oocytes. However, this mechanism cannot explain maintenance of bcd localization throughout the end of oogenesis, when microtubules disassemble in preparation for embryogenesis [4, 5] or retention of bcd at the anterior in mature oocytes, which can remain dormant, but developmentally competent, for weeks prior to fertilization [6]. Through temporal analysis of bcd RNA particle dynamics, we show that bcd mRNA shifts from continuous active transport to stable actin-dependent anchoring at the end of oogenesis, ensuring the developmental integrity of the oocyte during dormancy. Egg activation triggers release of bcd from the anterior cortex for proper deployment in the fertilized egg, probably through reorganization of the actin cytoskeleton. These findings uncover a surprising parallel between flies and frogs, as cortically tethered Xenopus Vg1mRNA undergoes a similar redistribution during oocyte maturation [7]. Our results highlight a conserved mechanism used by invertebrates and vertebrates to regulate mRNA anchoring and redeployment during the oocyte-to-embryo transition.

We previously described the cDNA cloning and expression patterns of actin genes from amphioxus Branchiostoma floridae (Kusakabe, R., Kusakabe, T., Satoh, N., Holland, N.D., Holland, L.Z., 1997. Differential gene expression and intracellular mRNA localization of amphioxus actin isoforms throughout development: implications for conserved mechanisms of chordate development. Dev. Genes Evol. 207, 203-215). In the present paper, we report the characterization of cDNA clones for actin genes from a closely related species, Branchiostoma belcheri, and the exon-intron organization of B. floridae actin genes. Each of these two amphioxus species has two types of actin genes, muscle and cytoplasmic. The coding and non-coding regions of each type are well-conserved between the two species. A comparison of nucleotide sequences of muscle actin genes between the two species suggests that a gene conversion may have occurred between two B. floridae muscle actin genes BfMA1 and BfMA2. From the conserved positions of introns between actin genes of amphioxus and those of other deuterostomes, the evolution of deuterostome actin genes can be inferred. Thus, the presence of an intron at codon 328/329 in vertebrate muscle and cytoplasmic actin genes but not in any known actin gene in other deuterostomes suggests that a gene conversion may have occurred between muscle and cytoplasmic actin genes during the early evolution of the vertebrates after separation from other deuterostomes. A Southern blot analysis of genomic DNA revealed that the amphioxus genome contains multiple muscle and cytoplasmic actin genes. Some of these actin genes seem to have arisen from recent duplication and gene conversion. Our findings suggest that the multiple genes encoding muscle and cytoplasmic actin isoforms arose independently in each of the three chordate lineages, and gene duplications and gene conversions established the extant actin multigene family during the evolution of chordates.

Intracellular mRNA localization plays an important role in post transcriptional gene regulation by targeting protein synthesis to a specific cellular compartment. mRNA localization has been extensively investigated with fluorescence in situ hybridization and live cell imaging in various model organisms. However, quantitative measurement of the translation of localizing mRNA with high spatiotemporal precision remains challenging. β-actin mRNA has been shown to localize to the leading edge of primary fibroblasts and provides an excellent model system to address this problem. The localization involves a cis-acting zipcode sequence and a trans-acting zipcode binding protein (ZBP1). Here we employ fluorescence fluctuation spectroscopy (FFS) to investigate the localization of β-actin mRNA and its association with ribosome subunits in live cell. Two technical advances make this experiment possible. First, we have developed a mouse model in which the β-actin gene has 24XMS2 sequences inserted. Furthermore, this mouse has been crossed with a ZBP1 knock out mouse. We generate primary mouse embryonic fibroblasts from these mice. By expressing GFP-MS2 capsid protein in the cell, all endogenous β-actin mRNA are fluorescently labeled. In addition, mCherry labeled ZBP1 or ribosome subunit are introduced into the cells to visualize their interaction with the β-actin mRNA by FFS. Second, we have developed a dual-color brightness analysis tool, specifically hetero-species partition analysis, to measure the interaction between the GFP-MS2 labeled mRNA and another mCherry labeled factor. We systematically measured the interaction between the β-actin mRNA and the ZBP1/ribosome in the perinuclear region and leading edge. Our data shows that β-actin mRNA binds more ZBP1 but less ribosome in the perinuclear region than in the leading edge, which supports the model that ZBP1 represses β-actin mRNA association with ribosome in the nuclear periphery until it reaches the leading edge.