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Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.

Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P - Elife (2015)

Bottom Line: We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte.Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3'UTR length and sequence conservation from unlocalized mRNAs.Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

ABSTRACT
mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3'UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT, http://tomancak-srv1.mpi-cbg.de/DOT/main.html) enables the transition from mechanistic dissection of singular mRNA localization events towards global understanding of how mRNAs transcribed in the nucleus distribute in cells.

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mRNA localizations change across time-points.(A) Schematic of changing mRNA distributions in germline cells (nurse cells, oocyte) in stage 4–7 and stage 9–10 egg-chambers. (A′) Exemplary mRNAs that show diverging combinations of mRNA localizations over the course of oogenesis: After initially being oocyte enriched at stage 2–7, Dok mRNA becomes detectable at the anterior pole, ZnT35C mRNA at the posterior pole and exu mRNA becomes ubiquitously distributed at stage 9/10. aret mRNA being ubiquitously distributed at stage 2–7 becomes weakly detectable at the posterior pole. (B) Schematic of mRNA distributions in ovary and embryonic cell types. (B′) mRNA expressions in ovarian and embryonic cells. All embryo data are from http://fly-fish.ccbr.utoronto.ca/. Sdc mRNA is localized where microtubules minus ends are enriched (Callaini and Anselmi, 1988; Clark et al., 1997; Delanoue and Davis, 2005) in the syncytial egg-chamber, in epithelial cells of the ovary and of the stage 4–5 embryo. Bsg25D mRNA is oocyte enriched, then localizes at the anterior pole in the oocyte but enriches at the posterior pole in the early embryo. Similarly, ssp2 mRNA enriches in the oocyte during oogenesis and localizes towards the posterior pole in early embryos but during late oogenesis undergoes a ubiquitous phase. CG14814 mRNA is initially ubiquitous, then shows perinuclear localization and in early embryos is enriched at the posterior pole. (A′–B′): FISH showing the RNA in green and DNA (labelled with DAPI) in magenta. Scale bar 30 μm. Embryo data are from http://fly-fish.ccbr.utoronto.ca/ (Lecuyer et al., 2007).DOI:http://dx.doi.org/10.7554/eLife.05003.014
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fig4: mRNA localizations change across time-points.(A) Schematic of changing mRNA distributions in germline cells (nurse cells, oocyte) in stage 4–7 and stage 9–10 egg-chambers. (A′) Exemplary mRNAs that show diverging combinations of mRNA localizations over the course of oogenesis: After initially being oocyte enriched at stage 2–7, Dok mRNA becomes detectable at the anterior pole, ZnT35C mRNA at the posterior pole and exu mRNA becomes ubiquitously distributed at stage 9/10. aret mRNA being ubiquitously distributed at stage 2–7 becomes weakly detectable at the posterior pole. (B) Schematic of mRNA distributions in ovary and embryonic cell types. (B′) mRNA expressions in ovarian and embryonic cells. All embryo data are from http://fly-fish.ccbr.utoronto.ca/. Sdc mRNA is localized where microtubules minus ends are enriched (Callaini and Anselmi, 1988; Clark et al., 1997; Delanoue and Davis, 2005) in the syncytial egg-chamber, in epithelial cells of the ovary and of the stage 4–5 embryo. Bsg25D mRNA is oocyte enriched, then localizes at the anterior pole in the oocyte but enriches at the posterior pole in the early embryo. Similarly, ssp2 mRNA enriches in the oocyte during oogenesis and localizes towards the posterior pole in early embryos but during late oogenesis undergoes a ubiquitous phase. CG14814 mRNA is initially ubiquitous, then shows perinuclear localization and in early embryos is enriched at the posterior pole. (A′–B′): FISH showing the RNA in green and DNA (labelled with DAPI) in magenta. Scale bar 30 μm. Embryo data are from http://fly-fish.ccbr.utoronto.ca/ (Lecuyer et al., 2007).DOI:http://dx.doi.org/10.7554/eLife.05003.014

Mentions: Our findings revealed that co-localized mRNAs share global features and have similar cytoplasmic requirements for their localization. However, as seen with zpg, mRNAs within gene sets differ in the precise timing and consequently regulation of their localization. We therefore investigated the time-course of mRNA localizations in detail. In the oocyte, mRNAs can be oocyte-enriched, anterior or posterior localized (Figure 4A). By comparing exemplary mRNAs across oogenesis time points (Figure 4A'), we observed that after being oocyte-enriched mRNAs could enrich at either anterior (Dok) or posterior pole (ZnT35C), but also de-localize and show ubiquitous distribution (exu). Conversely, mRNAs that showed ubiquitous distribution during early oogenesis could adopt posterior localization at later stages (aret). These examples show that multiple combinations of mRNA distributions from early to late oogenesis are possible and mRNAs that belong to the same gene set early are not necessarily grouped together at other time points.10.7554/eLife.05003.014Figure 4.mRNA localizations change across time-points.


Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.

Jambor H, Surendranath V, Kalinka AT, Mejstrik P, Saalfeld S, Tomancak P - Elife (2015)

mRNA localizations change across time-points.(A) Schematic of changing mRNA distributions in germline cells (nurse cells, oocyte) in stage 4–7 and stage 9–10 egg-chambers. (A′) Exemplary mRNAs that show diverging combinations of mRNA localizations over the course of oogenesis: After initially being oocyte enriched at stage 2–7, Dok mRNA becomes detectable at the anterior pole, ZnT35C mRNA at the posterior pole and exu mRNA becomes ubiquitously distributed at stage 9/10. aret mRNA being ubiquitously distributed at stage 2–7 becomes weakly detectable at the posterior pole. (B) Schematic of mRNA distributions in ovary and embryonic cell types. (B′) mRNA expressions in ovarian and embryonic cells. All embryo data are from http://fly-fish.ccbr.utoronto.ca/. Sdc mRNA is localized where microtubules minus ends are enriched (Callaini and Anselmi, 1988; Clark et al., 1997; Delanoue and Davis, 2005) in the syncytial egg-chamber, in epithelial cells of the ovary and of the stage 4–5 embryo. Bsg25D mRNA is oocyte enriched, then localizes at the anterior pole in the oocyte but enriches at the posterior pole in the early embryo. Similarly, ssp2 mRNA enriches in the oocyte during oogenesis and localizes towards the posterior pole in early embryos but during late oogenesis undergoes a ubiquitous phase. CG14814 mRNA is initially ubiquitous, then shows perinuclear localization and in early embryos is enriched at the posterior pole. (A′–B′): FISH showing the RNA in green and DNA (labelled with DAPI) in magenta. Scale bar 30 μm. Embryo data are from http://fly-fish.ccbr.utoronto.ca/ (Lecuyer et al., 2007).DOI:http://dx.doi.org/10.7554/eLife.05003.014
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fig4: mRNA localizations change across time-points.(A) Schematic of changing mRNA distributions in germline cells (nurse cells, oocyte) in stage 4–7 and stage 9–10 egg-chambers. (A′) Exemplary mRNAs that show diverging combinations of mRNA localizations over the course of oogenesis: After initially being oocyte enriched at stage 2–7, Dok mRNA becomes detectable at the anterior pole, ZnT35C mRNA at the posterior pole and exu mRNA becomes ubiquitously distributed at stage 9/10. aret mRNA being ubiquitously distributed at stage 2–7 becomes weakly detectable at the posterior pole. (B) Schematic of mRNA distributions in ovary and embryonic cell types. (B′) mRNA expressions in ovarian and embryonic cells. All embryo data are from http://fly-fish.ccbr.utoronto.ca/. Sdc mRNA is localized where microtubules minus ends are enriched (Callaini and Anselmi, 1988; Clark et al., 1997; Delanoue and Davis, 2005) in the syncytial egg-chamber, in epithelial cells of the ovary and of the stage 4–5 embryo. Bsg25D mRNA is oocyte enriched, then localizes at the anterior pole in the oocyte but enriches at the posterior pole in the early embryo. Similarly, ssp2 mRNA enriches in the oocyte during oogenesis and localizes towards the posterior pole in early embryos but during late oogenesis undergoes a ubiquitous phase. CG14814 mRNA is initially ubiquitous, then shows perinuclear localization and in early embryos is enriched at the posterior pole. (A′–B′): FISH showing the RNA in green and DNA (labelled with DAPI) in magenta. Scale bar 30 μm. Embryo data are from http://fly-fish.ccbr.utoronto.ca/ (Lecuyer et al., 2007).DOI:http://dx.doi.org/10.7554/eLife.05003.014
Mentions: Our findings revealed that co-localized mRNAs share global features and have similar cytoplasmic requirements for their localization. However, as seen with zpg, mRNAs within gene sets differ in the precise timing and consequently regulation of their localization. We therefore investigated the time-course of mRNA localizations in detail. In the oocyte, mRNAs can be oocyte-enriched, anterior or posterior localized (Figure 4A). By comparing exemplary mRNAs across oogenesis time points (Figure 4A'), we observed that after being oocyte-enriched mRNAs could enrich at either anterior (Dok) or posterior pole (ZnT35C), but also de-localize and show ubiquitous distribution (exu). Conversely, mRNAs that showed ubiquitous distribution during early oogenesis could adopt posterior localization at later stages (aret). These examples show that multiple combinations of mRNA distributions from early to late oogenesis are possible and mRNAs that belong to the same gene set early are not necessarily grouped together at other time points.10.7554/eLife.05003.014Figure 4.mRNA localizations change across time-points.

Bottom Line: We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte.Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3'UTR length and sequence conservation from unlocalized mRNAs.Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types.

View Article: PubMed Central - PubMed

Affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

ABSTRACT
mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3'UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT, http://tomancak-srv1.mpi-cbg.de/DOT/main.html) enables the transition from mechanistic dissection of singular mRNA localization events towards global understanding of how mRNAs transcribed in the nucleus distribute in cells.

Show MeSH
Related in: MedlinePlus