Abstract
Messenger RNA localization is a conserved mechanism for spatial control of protein synthesis, with key roles in generating cellular and developmental asymmetry. Whereas different transcripts may be targeted to the same subcellular domain, the extent to which their localization is coordinated is unclear. Using quantitative single-molecule imaging, we analysed the assembly of Drosophila germ plasm mRNA granules inherited by nascent germ cells. We find that the germ-cell-destined transcripts nanos, cyclin B and polar granule component travel within the oocyte as ribonucleoprotein particles containing single mRNA molecules but co-assemble into multi-copy heterogeneous granules selectively at the posterior of the oocyte. The stoichiometry and dynamics of assembly indicate a defined stepwise sequence. Our data suggest that co-packaging of these transcripts ensures their effective segregation to germ cells. In contrast, compartmentalization of the germline determinant oskar mRNA into different granules limits its entry into germ cells. This exclusion is required for proper germline development.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Change history
01 February 2016
In the version of this Article originally published, the sentence ‘13% of GFP–Vas granules contain nos mRNAs and 11% contain cycB’ in the caption of Fig. 4h–j was incorrect; it should have read ‘69% of GFP–Vas granules contain nos and 51% contain cycB’. This has been corrected in all online versions of the Article.
References
Pratt, C. A. & Mowry, K. L. Taking a cellular road-trip: mRNA transport and anchoring. Curr. Opin. Cell Biol. 25, 99–106 (2013).
Marchand, V., Gaspar, I. & Ephrussi, A. An intracellular transmission control protocol: assembly and transport of ribonucleoprotein complexes. Curr. Opin. Cell Biol. 24, 202–210 (2012).
Lange, S. et al. Simultaneous transport of different localized mRNA species revealed by live-cell imaging. Traffic 9, 1256–1267 (2008).
Amrute-Nayak, M. & Bullock, S. L. Single-molecule assays reveal that RNA localization signals regulate dynein–dynactin copy number on individual transcript cargoes. Nat. Cell Biol. 14, 416–423 (2012).
Tubing, F. et al. Dendritically localized transcripts are sorted into distinct ribonucleoprotein particles that display fast directional motility along dendrites of hippocampal neurons. J. Neurosci. 30, 4160–4170 (2010).
Mikl, M., Vendra, G., Doyle, M. & Kiebler, M. A. RNA localization in neurite morphogenesis and synaptic regulation: current evidence and novel approaches. J. Comp. Physiol. 196, 321–334 (2010).
Batish, M., van den Bogaard, P., Kramer, F. R. & Tyagi, S. Neuronal mRNAs travel singly into dendrites. Proc. Natl Acad. Sci. USA 109, 4645–4650 (2012).
Jambor, H., Brunel, C. & Ephrussi, A. Dimerization of oskar 3′ UTRs promotes hitchhiking for RNA localization in the Drosophila oocyte. RNA 17, 2049–2057 (2011).
Mahowald, A. P. Assembly of the Drosophila germ plasm. Int. Rev. Cytol. 203, 187–213 (2001).
Rangan, P. et al. Temporal and spatial control of germ-plasm RNAs. Curr. Biol. 19, 72–77 (2009).
Lecuyer, E. et al. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131, 174–187 (2007).
Cinalli, R. M., Rangan, P. & Lehmann, R. Germ cells are forever. Cell 132, 559–562 (2008).
Nakamura, A. & Seydoux, G. Less is more: specification of the germline by transcriptional repression. Development 135, 3817–3827 (2008).
Becalska, A. N. & Gavis, E. R. Lighting up mRNA localization in Drosophila oogenesis. Development 136, 2493–2503 (2009).
Sinsimer, K. S., Jain, R. A., Chatterjee, S. & Gavis, E. R. A late phase of germ plasm accumulation during Drosophila oogenesis requires Lost and Rumpelstiltskin. Development 138, 3431–3440 (2011).
Forrest, K. M. & Gavis, E. R. Live imaging of endogenous mRNA reveals a diffusion and entrapment mechanism for nanos mRNA localization in Drosophila. Curr. Biol. 13, 1159–1168 (2003).
Dalby, B. & Glover, D. M. 3′ non-translated sequences in Drosophila cyclin B transcripts direct posterior pole accumulation late in oogenesis and peri-nuclear association in syncytial embryos. Development 115, 989–997 (1992).
Nakamura, A., Amikura, R., Mukai, M., Kobayashi, S. & Lasko, P. Requirement for a noncoding RNA in Drosophila polar granules for germ cell establishment. Science 274, 2075–2079 (1996).
Lerit, D. A. & Gavis, E. R. Transport of germ plasm on astral microtubules directs germ cell development in Drosophila. Curr. Biol. 21, 439–448 (2011).
Little, S. C., Tikhonov, M. & Gregor, T. Precise developmental gene expression arises from globally stochastic transcriptional activity. Cell 154, 789–800 (2013).
Petkova, M. D., Little, S. C., Liu, F. & Gregor, T. Maternal origins of developmental reproducibility. Curr. Biol. 24, 1283–1288 (2014).
Bergsten, S. E. & Gavis, E. R. Role for mRNA localization in translational activation but not spatial restriction of nanos RNA. Development 126, 659–669 (1999).
Sinsimer, K. S., Lee, J. J., Thiberge, S. Y. & Gavis, E. R. Germ plasm anchoring is a dynamic state that requires persistent trafficking. Cell Rep. 5, 1169–1177 (2013).
Zimyanin, V. L. et al. In vivo imaging of oskar mRNA transport reveals the mechanism of posterior localization. Cell 134, 843–853 (2008).
Micklem, D. R., Adams, J., Grunert, S. & St Johnston, D. Distinct roles of two conserved Staufen domains in oskar mRNA localization and translation. EMBO J. 19, 1366–1277 (2000).
Rongo, C., Gavis, E. R. & Lehmann, R. Localization of oskar RNA regulates oskar translation and requires Oskar protein. Development 121, 2737–2746 (1995).
Chekulaeva, M., Hentze, M. W. & Ephrussi, A. Bruno acts as a dual repressor of oskar translation, promoting mRNA oligomerization and formation of silencing particles. Cell 124, 521–533 (2006).
Besse, F., Lopez de Quinto, S., Marchand, V., Trucco, A. & Ephrussi, A. Drosophila PTB promotes formation of high-order RNP particles and represses oskar translation. Genes Dev. 23, 195–207 (2009).
Glotzer, J. B., Saffrich, R., Glotzer, M. & Ephrussi, A. Cytoplasmic flows localize injected oskar RNA in Drosophila oocytes. Curr. Biol. 7, 326–337 (1997).
Ephrussi, A. & Lehmann, R. Induction of germ cell formation by oskar. Nature 358, 387–392 (1992).
Ghosh, S., Marchand, V., Gaspar, I. & Ephrussi, A. Control of RNP motility and localization by a splicing-dependent structure in oskar mRNA. Nat. Struct. Mol. Biol. 19, 441–449 (2012).
Gavis, E. R., Curtis, D. & Lehmann, R. Identification of cis-acting sequences that control nanos RNA localization. Dev. Biol. 176, 36–50 (1996).
Smith, J. L., Wilson, J. E. & Macdonald, P. M. Overexpression of oskar directs ectopic activation of nanos and presumptive pole cell formation in Drosophila embryos. Cell 70, 849–859 (1992).
Koch, A. L. The logarithm in biology. 1. Mechanisms generating the log-normal distribution exactly. J. Theor. Biol. 12, 276–290 (1966).
Limpert, E., Stahel, W. A. & Abbt, M. Log-normal distributions across the sciences: keys and clues. Bioscience 51, 341–352 (2001).
Brangwynne, C. P. et al. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science 324, 1729–1732 (2009).
Hachet, O. & Ephrussi, A. Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization. Nature 428, 959–963 (2004).
Herpers, B., Xanthakis, D. & Rabouille, C. ISH-IEM: a sensitive method to detect endogenous mRNAs at the ultrastructural level. Nat. Protoc. 5, 678–687 (2010).
Lindsley, D. L. & Zimm, G. G. The Genome of Drosophila Melanogaster (Academic Press, 1992).
Vanzo, N. F. & Ephrussi, A. Oskar anchoring restricts pole plasm formation to the posterior of the Drosophila oocyte. Development 129, 3705–3714 (2002).
Lehmann, R. & Nusslein-Volhard, C. The maternal gene nanos has a central role in posterior pattern formation of the Drosophila embryo. Development 112, 679–691 (1991).
Schüpbach, T. & Wieschaus, E. Maternal-effect mutations altering the anterior-posterior pattern of the Drosophila embryo. Roux Arch. Dev. Biol. 195, 302–317 (1986).
Wang, C., Dickinson, L. K. & Lehmann, R. Genetics of nanos localization in Drosophila. Dev. Dyn. 199, 103–115 (1994).
Brechbiel, J. L. & Gavis, E. R. Spatial regulation of nanos is required for its function in dendrite morphogenesis. Curr. Biol. 18, 745–750 (2008).
Lin, M. D., Fan, S. J., Hsu, W. S. & Chou, T. B. Drosophila decapping protein 1, dDcp1, is a component of the oskar mRNP complex and directs its posterior localization in the oocyte. Dev. Cell 10, 601–613 (2006).
Martin, S. G., Leclerc, V., Smith-Litiere, K. & St Johnston, D. The identification of novel genes required for Drosophila anteroposterior axis formation in a germline clone screen using GFP-Staufen. Development 130, 4201–4215 (2003).
Johnstone, O. & Lasko, P. Interaction with eIF5B is essential for Vasa function during development. Development 131, 4167–4178 (2004).
Snee, M. J., Harrison, D., Yan, N. & Macdonald, P. M. A late phase of Oskar accumulation is crucial for posterior patterning of the Drosophila embryo, and is blocked by ectopic expression of Bruno. Differentiation 75, 246–255 (2007).
Spradling, A. C. in Drosophila: A Practical Approach (ed Roberts, D. B.) 175–197 (IRL Press, 1986).
Petrella, L. N., Smith-Leiker, T. & Cooley, L. The Ovhts polyprotein is cleaved to produce fusome and ring canal proteins required for Drosophila oogenesis. Development 134, 703–712 (2007).
Raj, A., van den Bogaard, P., Rifkin, S. A., van Oudenaarden, A. & Tyagi, S. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5, 877–879 (2008).
Little, S. C., Tkacik, G., Kneeland, T. B., Wieschaus, E. F. & Gregor, T. The formation of the Bicoid morphogen gradient requires protein movement from anteriorly localized mRNA. PLoS Biol. 9, e1000596 (2011).
Duchow, H. K., Brechbiel, J. L., Chatterjee, S. & Gavis, E. R. The nanos translational control element represses translation in somatic cells by a Bearded box-like motif. Dev. Biol. 282, 207–217 (2005).
Wang, C. & Lehmann, R. Nanos is the localized posterior determinant in Drosophila. Cell 66, 637–647 (1991).
Ephrussi, A., Dickinson, L. K. & Lehmann, R. Oskar organizes the germ plasm and directs localization of the posterior determinant nanos. Cell 66, 37–50 (1991).
Acknowledgements
We thank W. Eagle (Princeton University, USA), P. Lasko (McGill University, Canada), P. Macdonald (University of Texas, Austin, USA) and D. St Johnston (Gurdon Institute, UK) for fly stocks and reagents, S. Chatterjee and S. Kyin for technical assistance, and E. Abbaszadeh, S. Blythe and B. He for comments on the manuscript. This work was financially supported by National Institute of Health grant R01GM067758 (E.R.G.) and the Howard Hughes Medical Institute (E.F.W.).
Author information
Authors and Affiliations
Contributions
S.C.L., K.S.S. and E.R.G. designed the experiments. S.C.L., K.S.S., J.J.L. and E.R.G. performed the experiments S.C.L. and E.R.G. analysed the data. S.C.L., E.R.G. and E.F.W. wrote the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Integrated supplementary information
Supplementary Figure 1 Unlocalized nos mRNAs are found as individual molecules, whereas localized granules contain many mRNAs.
(a) Imaged particles are diffraction-limited objects. Normalized intensities of 50 nm fluorescent beads (black dashed line), unlocalized nos (green), and polar granules (blue) are plotted. Red: fitted Gaussian distribution. (b) nos particle density decreases upon localization. Blue: normalized fluorescence signal density at n.c. 3. Vertical line: border of the localization domain where fluorescence exceeds that found in the anterior. Red: particles/μm3. (c) Histogram of intensities (arbitrary units, log scale) of all particles found in the left half, posterior third of an embryo. Vertical line separates dim and bright peaks. (d) Fraction of objects >164 A.U. at given distance from the posterior pole. Vertical line demarcates the localization domain, where the majority of bright objects are found. (e) Absolute RT-qPCR yields 2.5 +/− 0.8∗106 nos molecules per embryo. Blue: dilution series of plasmid DNA template. Red: dilution series of in vitro transcribed mRNA. Inset: dilution of single embryos (n = 6 embryos). (f) Poisson model of random co-localization: probability that imaging volumes contain n = (0,1,2… ) mRNAs when particles occupy 0.35 μm3. Inset: probabilities of particles containing n ≥ 1 mRNA. (g) Non-uniform distribution of nos throughout interior of embryo. Pixels lacking signal (red) cover 52% of the image. (h) In two colour labelling, rotation of one image stack by 90o yields a 10% co-localization frequency. (i) Poisson model as in (f) with 0.2 μm3 imaging volumes and particles occupying 60% of available volume. (j) Pair-correlation functions showing density of nos (blue) or pgc (red) particles as a function of distance from 594 reference nos particles. Error bars: standard deviations (SD). Mean densities and SD were calculated within bins of 2 pixel width at intervals of 2 pixels. Inset: P-values from paired sample t-test comparing density in first bin to densities at all other distances. Densities are not significantly different (dashed line: P-value of 0.1). (k) Histogram of intensities of cortical objects after normalization to the most commonly observed intensity. Granules have >4 mRNAs. Inset: in dual-colour labelling, normalized data fall on a line of slope = 1, indicating 4% measurement error. (l) Cumulative probability distribution of nos mRNA in granules containing >4 nos mRNAs as a function of distance from the posterior pole. Inset: number of localized granules as a function of distance. (m) Histogram of nos mRNA content in oskA87/+ oocytes (stage 10b). (n) Histogram of nos mRNA content in vas PD/vas D1 oocytes (stage 11–12). (o) Mean nos mRNA content of granules with >4 mRNAs as a function of distance from the posterior pole. Upper inset: variance divided by mean (Fano factor). For a process of random arrival of mRNAs at assembly sites, predicted Fano factor is 1 (red line). Lower inset: fractional SD of mRNA content (SD/mean) as a function of distance.
Supplementary Figure 2 Localization results from the formation of granules that maintain nos content during rapid transit.
(a) Upper: Normalized nos fluorescence density as a function of position during late oogenesis. Vertical lines indicate position at which density exceeds that found in the oocyte anterior. Lower: Plot showing fraction of all objects containing >4 mRNAs as a function of position. Nearly all bright granules are found within the localization domain. (bd) Calibrated mRNA content (red) of four selected highly motile nos particles during rapid displacement (blue). Selected frames for each particle from Supplementary Video 2 are shown. Red arrowheads indicate motile particles.
Supplementary Figure 3 Co-localization of nos, cycB, and pgc.
(a–d) nos, cycB, and pgc do not co-localize in nurse cells at stage 8. 2D histograms show fluorescence intensities of cycB channel at positions where nos particles are found (a), nos at cycB positions (b), pgc at nos positions (c), and nos at pgc positions (d). Vertical green and horizontal red lines indicate thresholds separating signal from imaging noise. (e) Time course of cycB and nos localization. Scale bars: 5 μm (upper, middle); 10 μm (lower). (f) 2D histograms of nos and cycB content at stages 10a, 12, and 13. cycB begins assembling into large granules slightly earlier than nos, likely because of high levels of cycB expression at earlier times compared to nos. In contrast to the cycB mRNA that accumulates at late stages of oogenesis, this initial population of localized cycB mRNA shows only weak co-localization with nos. Color indicates relative density of data points, with red showing highest density. Red and green lines indicate thresholds separating localized and unlocalized particles. For all particles surpassing the localized threshold in one channel, the fraction surpassing the localization threshold in the second channel is shown in the upper right quadrant (green: cycB, red: nos). The fraction of localized particles containing 0 mRNAs in the second channel is shown in the upper left (for localized nos) or lower right (for localized cycB) quadrants. Very little nos surpasses the localized threshold at early time points.
Supplementary Figure 4 Assembly by random selection does not explain co-localization.
(a) Data fit to a model where nos and cycB mRNAs compete for integration into granules. Plot shows the fraction of localized granules containing 0 nos or cycB as a function of the sum of nos and cycB mRNA content. Total mRNA content for each localized granule was determined by summing nos and cycB. For granules with a given total content, the fraction containing 0 nos (blue) or 0 cycB (red) was calculated and plotted as a function of the total. Due to measurement uncertainty, granules can possess apparent non-integer mRNA numbers. Therefore, x-axis values were generated in increments of 0.25 mRNA, using bins of total content spanning ± 0.5 mRNAs. Lines indicate best fit curves (1 − p) n where n is total mRNA content (that is, fitting observations to binomial distribution). Fitting yields probabilities of P = 0.17 for incorporation of nos mRNA and P = 0.08 for incorporation of cycB mRNA into a forming granule. Actual total granule content is likely larger, given the enrichment of many genes in the germ plasm. Thus, these probabilities represent upper bounds. (b–e) Probabilities obtained in (a) were used to predict the distribution of nos and cycB content as a function of total content (b,d). Predictions were compared to measurements (c,e). Heat maps indicate relative densities. Magenta arrows: discrepancy between model and observation, namely, where data points predicted by model are absent in observations despite the presence of many granules completely lacking one of the two mRNAs. Because the actual total content is likely larger, the apparent relationship between observed content and total content (that is, the slope of a line fitted to the data clouds in c and e) is likely to be lower. However, the change in slope does not account for the absence of data points (arrows) in the observations. Data falling on the line of slope = 1 are those granules that contain only nos (c) or only cycB (e); in actuality these granules co-localize with other mRNAs (for example, pgc), and therefore have a higher total content than suggested by these plots.
Supplementary Figure 5 Quantification of osk mRNA in localized granules.
(a,b) Confocal section taken near the cortical surface (a) or near the mid-sagittal plane (b) of an early (n.c. 3) embryo (anterior left, dorsal up) labeled with osk probes. Green boxed region in inset of (a) shows area displayed in main panel. Middle and right panels show magnified views of red (upper panels) and yellow (lower panel) boxes. Two contrast levels are used to display the extreme brightness of localized granules compared to unlocalized mRNAs. Scale bars: 20 μm (left panels); 2 μm (magnified views). (c) Absolute RT-qPCR for osk using DNA standard (blue) or in vitro transcribed mRNA standard (red) compared to a dilution series of single embryos (inset). (d) In embryos, unlocalized particles display a heavy bias toward 2-4 mRNA, similar to that seen in oocytes. (e–h) Estimates of osk mRNA content in four motile granules. (e′–h′) Selected frames from time-lapse movies of granules analysed in (e–h). Red arrowheads indicate granule traced and displayed in e–h. In h′, three granules (arrowheads) converge to the same point, resulting in (h) in apparent increased mRNA content at around 30 s (when particles denoted by green and red arrowheads merge) and 50 s (merging of particle denoted by yellow arrowhead). (i) osk mRNAs are often found on track-like structures along with nos in nurse cells during mid-oogenesis. (j) Log normal distribution of localized granule content. (k) osk content of localized granules in an early embryo. (l) Estimated total accumulated osk in the posterior localization domain shows a marked increase during late oogenesis. Time points are estimated from ref. 1 and correspond to stages 7, 8, 9, 10b, 12, and 13.
Supplementary Figure 6 Localization of gfp-nos3’UTR mRNA to polar granules does not affect pole cell formation.
(a,b) FISH analysis of gfp-nos3’UTR (GN) embryos with nos and gfp probes. Z-series projections of the posterior cortex at n.c. 3 (a) and n.c. 11 (b) show colocalization of GN and nos. Individual channels are shown at right. Scale bars: 10 μm (a); 5 μm (b). (c) Anti-Vas immunofluorescence in wild-type (upper) and GN (lower) embryos. (d) Box plot showing mean (red line), 25th and 75th quartiles (blue boxes), and range (black lines) of Vas-positive pole cell number (WT, n = 29; GN, n = 30). Supplementary Video 1 : Subsection of a confocal stack of an early (n.c. 3) embryo posterior labeled with nos probes. First section is adjacent to the lateral cortex. Stack is shown twice, followed by magnified views of unlocalized and localized regions. To facilitate visualization of unlocalized punctae, the stack is displayed at high contrast such that localized granules appear saturated. However, no saturated pixels are present in raw images, as illustrated with a single cortical image slice displayed at alternating high and low contrast settings. Z-sections are separated by 340 nm. Supplementary Video 2 : Time lapse movie of germ plasm RNP particles containing nos∗GFP at the oocyte posterior. Maximum projection of 5 z-sections spanning a total of 6 μm and a total time of 5 min. Supplementary Table 1: Oligonucleotide sequences used to design probes for this study.
Supplementary information
Supplementary Information
Supplementary Information (PDF 2631 kb)
Subsection of a confocal stack of an early (n.c. 3) embryo posterior labeled with nos probes.
First section is adjacent to the lateral cortex. Stack is shown twice, followed by magnified views of unlocalized and localized regions. To facilitate visualization of unlocalized punctae, the stack is displayed at high contrast such that localized granules appear saturated. However, no saturated pixels are present in raw images, as illustrated with a single cortical image slice displayed at alternating high and low contrast settings. Z-sections are separated by 340 nm. (AVI 26019 kb)
Time lapse movie of germ plasm RNP particles containing nos*GFP at the oocyte posterior.
Maximum projection of 5 z-sections spanning a total of 6 μm and a total time of 5 min. (AVI 797 kb)
Rights and permissions
About this article
Cite this article
Little, S., Sinsimer, K., Lee, J. et al. Independent and coordinate trafficking of single Drosophila germ plasm mRNAs. Nat Cell Biol 17, 558–568 (2015). https://doi.org/10.1038/ncb3143
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ncb3143
This article is cited by
-
smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods
Communications Biology (2021)
-
Comparative Proteomics Reveal Me31B’s Interactome Dynamics, Expression Regulation, and Assembly Mechanism into Germ Granules during Drosophila Germline Development
Scientific Reports (2020)
-
Glial granules contain germline proteins in the Drosophila brain, which regulate brain transcriptome
Communications Biology (2020)
-
The PIWI protein Aubergine recruits eIF3 to activate translation in the germ plasm
Cell Research (2020)
-
Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains
Nature Communications (2019)