Real-time visualization of ZBP1 association with beta-actin mRNA during transcription and localization

Abstract

Background: mRNA localization in somatic cells is an important mechanism for gene expression regulation. In fibroblasts, the protein ZBP1 associates with the sequence that localizes beta-actin mRNA to the leading edge of fibroblasts, augmenting motility. beta-actin mRNA localizes in a cytoskeleton-dependent manner, depending on intact actin and myosin ATP-hydrolysis, and is largely bound to the actin cytoskeleton. The ZBP1 protein contains four KH RNA binding domains and a classic RBD RNA binding domain. It also contains a putative nuclear import and export sequence, suggesting a nuclear phase in this protein's function.

Results: Using high-speed imaging, we show here the targeting of this RNA binding protein to beta-actin pre-mRNA transcripts in the nuclei of living cells and measure the residence time of the RNA-protein complex before it leaves the transcription site. Then, the RNA-protein particle is exported to the cytoplasm, where it localizes at velocities of 0.6 microm/s by using actin filaments and/or microtubules. This RNA-ZBP1 complex is required for cytoplasmic localization in fibroblasts; mislocalizing the protein also mislocalizes the RNA, and expressing the protein in a ZBP1-deficient cell line induces beta-actin mRNA localization.

Conclusions: This work demonstrates that the RNA-protein association, essential for cytoplasmic localization, begins as soon as the RNA is transcribed. The ZBP1 then forms a ribonucleoprotein particle and moves in a myosin-dependent fashion by using the cytoskeleton for directional transport.

Figure 1. Cytoplasmic Distribution and Relocalization of ZBP1

(A) Cells were fixed and stained with anti-ZBP1 antiserum (red), which was digitally superimposed on the Nomarski image and nuclear staining (DAPI, blue). (B) Cells extracted with Triton X-100 for 30 s before treatment described in (A). (C) Colocalization of endogenous (left) and GFP-fused (right) ZBP1 (green) and β-actin mRNA (red) in chicken embryo fibroblasts. Left: cells were stained with anti-ZBP1 serum and were subsequently hybridized with β-actin mRNA fluorescent oligonucleotide probes. Right: cells were transfected with the ZBP1-GFP fusion, and green cells were visualized by deconvolution microscopy after fixation and in situ hybridization. The yellow staining in the protrusions demonstrates RNA and protein colocalization. The scale bar represents 10 µm. (D) ZBP1-GFP particles moving in living cells and localizing to a dynamic, moving lamella. Panels are shown at approximately 100-s intervals. The scale bar represents 10 µm. See Movies 1–11 in the Supplementary Material.

Figure 2. ZBP1 Associates with the Cytoskeleton

(A) Immunofluorescence staining of ZBP1 (red), actin (green), and tubulin (blue). Arrows indicate localization of ZBP1 along microtubules. (B) Immunofluorescence staining of ZBP1 (red) and actin (green). Arrows indicate ZBP1 along filament bundles. (C) ZBP1 distribution in cytochalasin-treated cells. (D) ZBP1 distribution in colchicine-treated cells. (E) ZBP1 distribution in BDM-treated cells. See Movie 12 in the Supplementary Material. (F) Electron microscopy of ZBP1 in CEFs. Thin-sectioned cells were stained with anti-ZBP1 antibody and secondary gold-conjugated antibody. MT, microtubule; MF, actin. The scale bar in (B) represents 2 µm in (A) and (B), the scale bar in (C) represents 10 µm in (C)–(E), and the scale bar in (F) represents 200 nm.

Figure 3. ZBP1 and β-actin mRNA Association Are Required for Localization

(A and B) Antisense to the zipcode inhibits localization of ZBP1 and β-actin mRNA. CEFs were incubated with (A) antisense oligonucleotides to the zipcode or (B) reverse control ODN for 12 hr, fixed, and stained for ZBP1 (green) and β-actin mRNA (red). The scale bar represents 10 µm. (C) Number of cells localizing mRNA and ZBP1 after antisense or control treatment (n = 115 in each group).

Figure 4. Distribution of ZBP1 Determines Distribution of β-actin mRNA

(A–C) Expression of ZBP1-GFP in C2C12 cells. β-actin mRNA (red); ZBP1-GFP (green). C2C12 cells were transfected with ZBP1-GFP DNA, fixed, and β-actin mRNA-stained via in situ hybridization. The expression of ZBP1-GFP in cells without endogenous ZBP1 causes the formation and polarized location of particles of β-actin mRNA. Nontransfected C2C12 cells in the same field exhibit a diffuse RNA pattern. The scale bar represents 10 µm. (D) Control, just CFP fused to the membrane signal. (E and F) Expression of ZBP1 fused to the neuromodulin membrane-targeting signal (green) accumulates at cellular membranes and mislocalizes β-actin mRNA (red). The scale bar represents 5 µm.

Figure 5. Nuclear Distribution of ZBP1 in LMB-Treated Cells

(A) ZBP1 (green) and β-actin mRNA distribution (red) in chicken embryo fibroblasts treated with LMB for 6 hr. The mid-nuclear focal plane is displayed. Retention of ZBP1 in the nuclei resulted in significant delocalization of β-actin mRNA (overlap). The scale bar represents 10 µm. (B) Percentage of β-actin mRNA and ZBP1 localized after treatment (n = 113).

Figure 6. ZBP1 Nuclear Transport and Accumulation at β-actin Transcription Sites

(A) Accumulation of endogenous ZBP1 at β-actin transcription sites in CEF nuclei. Serum was applied to chick embryo fibroblasts for 5 min after synchronization by serum starvation. The cells were immediately fixed and stained for β-actin mRNA (red) by in situ hybridizaton and ZBP1 (green) by immunofluorescence. ZBP1 and β-actin mRNA colocalize (yellow) at the transcription sites. (B) Accumulation of ZBP1-GFP fusion at β-actin transcription sites. CEFs were transfected with ZBP1-GFP fusion DNA and were imaged live after treatment as in (A). After identification and imaging of transcription sites in live cells (see [E]), they were fixed and stained by in situ hybridization for the β-actin mRNA (red). The image was subjected to deconvolution to yield the optical section shown. (C) ZBP1-GFP fusion proteins move into the nucleus and bind to nascent chains of β-actin at the transcription site shortly after serum induction. The transcription site in a ZBP1-GFP-transfected CEF was photobleached, and fluorescence recovery was monitored by confocal microscopy. Half-recovery occurred within 90 s. The panels shown are at 30-s intervals. “Before,” before photobleaching; “0,” after photobleaching for 20 s. See Movie 13 in the Supplementary Material. (D) Time plot of ZBP1-GFP fluorescence recovery at a transcription site. Relative intensity was calculated from raw imaging data and was plotted as a fraction of intensity prior to bleaching. The time in seconds after bleaching was complete is indicated on the horizontal axis. (E) The same cell as in (B) before fixation and in situ hybridization. ZBP1 particle movement between the nuclear envelope and β-actin transcription site can be seen in live cells. The time between the frames shown is 800 ms. See Movie 14 in the Supplementary Material. (F) Electron microscopy of ZBP1 at the nuclear pore (arrow). Sections of cells treated in (A) were stained with anti-ZBP1 antibody and secondary gold-conjugated antibody. N, nucleus; C, cytoplasm. The scale bars in (A)–(C) represent 5 µm, the scale bar in (E) represents 10 µm, and the scale bar in (F) represents 100 nm.

Figure 7. Proposed Model of ZBP1-mRNA Localization

The travels of ZBP1. ZBP1 shuttles into and out of the nucleus. If it encounters the nascent zipcode sequences, it binds there as the nascent RNA and finishes transcription and processing/polyadenylation before export to the cytoplasm. Once in the cytoplasm, it associates with cytoskeletal elements (actin filament bundles are shown here) and localizes to the leading edge.