Selective dendritic localization of mRNA in Drosophila mushroom body output neurons

Memory-relevant neuronal plasticity is believed to require local translation of new proteins at synapses. Understanding this process requires the visualization of the relevant mRNAs within these neuronal compartments. Here, we used single-molecule fluorescence in situ hybridization to localize mRNAs at subcellular resolution in the adult Drosophila brain. mRNAs for subunits of nicotinic acetylcholine receptors and kinases could be detected within the dendrites of co-labeled mushroom body output neurons (MBONs) and their relative abundance showed cell specificity. Moreover, aversive olfactory learning produced a transient increase in the level of CaMKII mRNA within the dendritic compartments of the γ5β'2a MBONs. Localization of specific mRNAs in MBONs before and after learning represents a critical step towards deciphering the role of dendritic translation in the neuronal plasticity underlying behavioral change in Drosophila.


Introduction
Memories are believed to be encoded as changes in the efficacy of specific synaptic connections. Dendritic localization of mRNA facilitates specificity of synaptic plasticity by enabling postsynaptic synthesis of new proteins where and when they are required (Holt et al., 2019). Visualizing individual dendritically localized mRNAs in memory-relevant neurons is therefore crucial to understanding this process of neuronal plasticity.
Single-molecule fluorescence in situ hybridization (smFISH) enables cellular mRNAs to be imaged at single-molecule resolution through the hybridization of a set of complementary oligonucleotide probes, each labeled with a fluorescent dye. Recent improvements in smFISH permit mRNA transcripts to be visualized in the dense heterogenous tissue of intact Drosophila brains (Long et al., 2017;Yang et al., 2017). Combining whole fly brain smFISH with neuron-specific co-labeling makes Drosophila an ideal model to investigate cell-specific mRNA localization and whether it is regulated in response to experience.
Results and discussion mRNA localization in the intact adult Drosophila brain Mammalian CaMKII mRNA is transported to neuronal dendrites, where it is locally translated in response to neuronal activity (Bagni et al., 2000;Miller et al., 2002;Ouyang et al., 1999). Drosophila CAMKII is critical for behavioral plasticity (Griffith, 1997;Malik et al., 2013) and is also thought to be locally translated (Ashraf et al., 2006). However, fly CAMKII mRNAs have not been directly visualized within individual neurons. We therefore first hybridized CaMKII smFISH probes to whole-mount brains and imaged the mushroom body (MB) calyx ( Figure 1A, B), a recognizable neuropil containing the densely packed dendrites of~2000 KCs and their presynaptic inputs from~350 cholinergic olfactory projection neurons (Bates et al., 2020a) using a standard spinning disk confocal microscope. To detect and quantify mRNA within the 3D volume of the brain, we developed a FIJIcompatible custom-built image analysis tool that segments smFISH image data and identifies spots within the 3D volume using a probability-based hypothesis test. This enabled detection of mRNAs with a false discovery rate of 0.05. CaMKII smFISH probes labeled 56 ± 5 discrete puncta within each calyx ( Figure 1B, C). In comparison, smFISH probes directed to the a1 nicotinic acetylcholine receptor (nAChR) subunit labeled 33 ± 2 puncta in the calyx ( Figure 1B, C). Puncta were diffraction limited and the signal intensity distribution was unimodal ( Figure 1D-D'), indicating that they represent single mRNA molecules.

mRNA localization within MBON dendrites
Drosophila learning is considered to be implemented as plasticity of cholinergic KC-MBON synapses. To visualize and quantify mRNA specifically within the dendritic field of the g5b'2a and g1pedc>a/b MBONs, we expressed a membrane-tethered UAS-myr::SNAP reporter transgene using MBON-specific GAL4 drivers. This permitted simultaneous fluorescent labeling of mRNA with smFISH probes and the MBON using the SNAP Tag ( Figure 1E). To correct for chromatic misalignment (Matsuda et al., 2018) that results from imaging heterogenous tissue at depth, we also costained brains with the dsDNA-binding dye Vybrant DyeCycle Violet (VDV). VDV dye has a broad emission spectrum so labeled nuclei can be imaged in both the SNAP MBON and smFISH mRNA channels. This triple-labeling approach allowed quantification and correction of any spatial mismatch between MBON and smFISH channels in x, y, and z planes, which ensures that smFISH puncta are accurately assigned within the 3D volume of the MBON dendritic field ( Figure 1F).
Using this smFISH approach, we detected an average of 32 ± 2 CaMKII mRNAs ( Figure 1G, G') within the dendrites of g5b'2a MBONs. However, in contrast to the calyx, we did not detect nAChRa1 in g5b'2a MBON dendrites ( Figure 1H, H'). This differential localization of the CaMKII and nAChRa1 mRNAs within neurons of the mushroom body is indicative of cell specificity. To probe mRNA localization in MBONs more broadly, we used a single YFP smFISH probe set and a collection of fly strains harboring YFP insertions in endogenous genes (Lowe et al., 2014). We selected YFP insertions in the CaMKII, PKA-R2, and Ten-m genes as test cases and compared the localization of their YFP-tagged mRNAs between g5b'2a MBON and g1pedc>a/b MBON dendrites.
The CaMKII::YFP allele is heterozygous in flies also expressing myr::SNAP in MBONs. Therefore, YFP smFISH probes detected half the number of CaMKII mRNAs in g5b'2a MBON dendrites compared to CaMKII-specific probes ( Figure 2A, A', C). Importantly, YFP probes hybridized to YFP-negative control brains produced background signal ( Figure 2B, B') that was statistically distinguishable in brightness from genuine smFISH puncta ( Figure 2D). Comparing data from YFP-negative and YFP-positive samples allowed us to define the false discovery rate to be 14% when using YFPdirected probes ( Figure 2D, Figure 2-figure supplement 1). These results indicate that the YFP probes are specific and that the YFP insertion does not impede localization of CaMKII mRNA. We detected a similar abundance of CaMKII::YFP in the dendritic field of g5b'2a ( Figure 2E) and the g1 dendritic region of g1pedc>a/b ( Figure 2F) MBONs ( Figure 2G). In contrast, more PKA-R2 mRNAs were detected in the dendrites of g5b'2a MBONs compared to g1pedc>a/b MBONs ( Figure 2G). Importantly, the relative abundance of dendritically localized CaMKII and PKA-R2 mRNAs did not simply reflect the levels of these transcripts detected in the MBON somata ( Figure 2H). In addition, we did not detect Ten-m mRNAs in either g5b'2a or g1pedc>a/b MBON dendrites ( Figure 2G, I), although they were visible in neighboring neuropil and at low levels in the MBON somata ( Figure 2H). These results suggest that CaMKII and PKA-R2 mRNAs are selectively localized to MBON dendrites.
Although we did not detect nAChRa1 mRNA within g5b'2a MBON dendrites, prior work has shown that nAChR subunits, including nAChRa1, are required in g5b'2a MBON postsynapses to register odor-evoked responses and direct odor-driven behaviors . Since the YFP insertion collection does not include nAChR subunits, we designed nAChRa5 and nAChRa6specific smFISH probes. These probes detected nAchRa5 and nAchRa6 mRNAs within g5b'2a and g1pedc>a/b MBON dendrites, with nAchRa6 being most abundant ( Figure 2G). Importantly, we detected nAchRa1, nAchRa5, and nAchRa6 at roughly equivalent levels in the g5b'2a and g1pedc>a/b MBON somata ( Figure 2H). Therefore, the selective localization of nAchRa5 and nAchRa6a6 mRNA to MBON dendrites indicates that these receptor subunits may be locally translated to modify the subunit composition of postsynaptic nAChR receptors.
Localized mRNAs were on average 2.8Â more abundant in g5b'2a relative to the g1 region of g1pedc>a/b MBON dendrites ( Figure 2G). We therefore tested whether this apparent differential localization correlated with dendritic volume and/or the number of postsynapses between these MBONs. Using the recently published electron microscope volume of the Drosophila 'hemibrain'  Figure 2E, F), we calculated the dendritic volume of the g5b'2a MBON to be 1515.36 nm 3 and the g1 region of the g1pedc>a/b MBON to be 614.20 nm 3 . In addition, the g5b'2a regions of the g5b'2a MBON dendrite contain 30,625 postsynapses, whereas there are only 17,020 postsynapses in the g1 region of the g1pedc>a/b MBON. Larger dendritic field volume and synapse number is therefore correlated with an increased number of localized nAchRa5, nAchRa6, and PKA-R2 mRNAs. The correlation, however, does not hold for CaMKII mRNA abundance. Selective localization of mRNAs to MBON dendrites therefore appears to be more nuanced than simply reflecting the size of the dendritic arbor, the number of synapses, or the level of transcripts detected throughout the cell.
Learning transiently changes CAMKII mRNA abundance in g5b'2a

MBON dendrites
We tested whether CaMKII::YFP mRNA abundance in g5b'2a and g1pedc>a/b MBONs was altered following aversive learning ( Figure 3A, B). We also quantified mRNA in the somata and nuclei of these MBONs ( Figure 3A, B'). Transcriptional activity is indicated by a bright nuclear transcription focus ( Figure 3C, Figure 3-figure supplement 1). We initially subjected flies to four conditions ( Figure 3D): (1) an 'untrained' group that was loaded and removed from the T-maze but not exposed to odors or shock; (2) an 'odor only' group, exposed to the two odors as in training but without shock; (3) a 'shock only' group that was handled as in training and received the shock delivery but no odor exposure; and (4) a 'trained' group that was aversively conditioned by pairing one  MBON (black) showing the dendritic field (blue) and MB (light gray). The projection to the contralateral MB is truncated. (F) Alignment of dendrite and smFISH imaging channels using co-labeling with dsDNA Vybrant DyeCycle Violet (VDV) dye. VDV is excited with 405 nm and emission is collected in the dendritic and smFISH imaging channels, which were then aligned in x, y, and z planes. (G, G') CaMKII smFISH within the g5b'2a MBON dendrite co-labeled with R66C08-GAL4-driven UAS-myr::SNAP and visualized with JF547SNAP dye. Images are maximum intensity projections of ten 0.2 mm z-sections. (H, H') nAchRa1 smFISH in g5b'2aMBONs. Images are maximum intensity projections of ten 0. of the two odors with shock. Fly brains were extracted 10 min, 1 hr, or 2 hr after training and processed for smFISH.
CaMKII mRNA increased significantly in g5b'2a MBON dendrites 10 min after training ( Figure 3E) compared to all control groups. Including an additional 'unpaired' experiment, where odor and shock presentation was staggered, confirmed that the increase at 10 min after training requires coincident pairing of odor and shock (Figure 3-figure supplement 2). Moreover, levels returned to baseline by 1 hr and remained at that level 2 hr after training ( Figure 3E). CaMKII mRNAs in g5b'2a MBON somata showed a different temporal dynamic, with transcripts peaking 1 hr after training, albeit only relative to untrained and odor only controls ( Figure 3E). The proportion of g5b'2a nuclei containing a CaMKII transcription focus did not differ between treatments ( Figure 3E), suggesting that the transcript increase in the somata is not correlated with the number of actively transcribing g5b'2a nuclei, at least at the timepoints measured. In addition, the mean brightness of g5b'2a transcription foci did not change across treatments ( Figure 3G), although the variation was substantial. An increase of dendritically localized CaMKII mRNAs could result from enhanced trafficking or through the release of transcripts from protein bound states, which would increase smFISH probe accessibility and hence spot brightness (Buxbaum et al., 2014). Since the brightness of CaMKII mRNA spots detected in the dendrites of g5b'2a MBONs did not change with treatment ( Figure 3H), we conclude that the increased abundance likely results from altered traffic.
Assessing CaMKII mRNA abundance in g1pedc>a/b MBONs after learning did not reveal a change in mRNA abundance in the dendrites or somata between trained flies and all control groups at all timepoints measured ( Figure 3F). These results indicate specificity to the response observed in the g5b'2a MBONs.
Since CaMKII protein is also labeled with YFP in CaMKII::YFP flies, we assessed protein expression by measuring YFP fluorescence intensity specifically within the MBON dendrites. This analysis did not reveal a significant difference in fluorescence intensity across treatments (Figure 3-figure supplement 2). However, since smFISH provides single-molecule estimates of mRNA abundance, a similar level of single-molecule sensitivity may be required to detect subcellular resolution changes in protein copy number. Moreover, new synthesis and replacement of specific isoforms of CaMKII could radically change local kinase activity (Kuklin et al., 2017;Zalcman et al., 2018), even without an observable change in overall abundance.
Early studies in Drosophila demonstrated that broad disruption of CAMKII function impaired courtship learning (Broughton et al., 2003;Griffith et al., 1994;Griffith et al., 1993;Joiner and Griffith, 1997). In contrast, later studies that manipulated activity more specifically in olfactory projection neurons or particular classes of KCs reported a preferential loss of middle-term or long-term allele is heterozygous, resulting in detection of half as many CaMKII mRNAs in g5b'2a MBONs using YFP probes relative to that detected with CaMKII gene-specific probes. (D) Signal/background intensity distribution of YFP probe signals in CaMKII::YFP brains relative to control brains with no threshold on signal detection. The signal/background intensity threshold for quantitative analyses (dotted red line) resulted in a false discovery rate of 14% (indicated by the overlap of the histograms on the right side of the dotted red line) (see also  dendrites with YFP smFISH probes and gene-specific nicotinic acetylcholine receptor (nAChR) subunit smFISH probes. More PKA-R2 transcripts localize within the dendrites of g5b'2a MBONs relative to g1pedc>a/b MBONs (unpaired t-test: p=0.004, t = 5.069, df = 11). Ten-m mRNAs did not localize to either MBON dendritic field. CaMKII mRNAs were detected in equal abundance. nAchRa1 mRNAs did not localize to the dendrites of either g5b'2a or g1pedc>a/b MBONs. More nAchRa5 (unpaired t-test: p=0.004, t = 3.368, df = 15) and nAchRa6 (unpaired t-test: p=0.046, t = 2.274, df = 10) mRNAs localized to g5b'2a MBON dendrites relative to g1pedc>a/b MBON dendrites. (H) Quantification of mRNA in g5b'2a and g1pedc>a/b MBON somata with YFP smFISH probes and gene-specific nAChR subunit smFISH probes. More CaMKII transcripts were present within g5b'2a MBON somata relative to g1pedc>a/b MBON somata (unpaired t-test: p=0.0061, t = 3.103, df = 18). More Ten-m (Mann-Whitney test: p=0.0093, Mann-Whitney U = 120) and nAchRa1 (unpaired t-test: olfactory memory (Akalal et al., 2010;Ashraf et al., 2006;Malik et al., 2013). Here, we focused our analyses on two subtypes of MBONs, which are known to exhibit changes in odor-evoked activity after a single trial of aversive olfactory conditioning. Whereas g1pedc>a/b MBON responses to the previously shock-paired odor are depressed immediately after aversive learning (Hige et al., 2015;Perisse et al., 2016), prior studies observed a learning-related increase of the conditioned odor response of g5b'2a MBONs (Bouzaiane et al., 2015;Owald et al., 2015), likely resulting from a release of feedforward inhibition from g1pedc>a/b MBONs (Felsenberg et al., 2018;Perisse et al., 2016). We therefore speculate that the specific change in CaMKII mRNA abundance in the g5b'2a MBONs after aversive learning might be a consequence of network-level potentiation of their activity, such as that that would result from a release from inhibition. Since CAMKII local translation-dependent plasticity is expected to underlie more extended forms of memory (Giese and Mizuno, 2013;Miller et al., 2002), it will be interesting to investigate whether the training-evoked change in CaMKII mRNA abundance in the g5b'2a MBON dendrites contributes to later aversive memory formation and maintenance. This may be possible with MBON-specific targeting of CAMKII mRNAs that contain the long 3'UTR, which is essential for dendritic localization and activitydependent local translation (Aakalu et al., 2001;Kuklin et al., 2017;Mayford et al., 1996;Rook et al., 2000).

Materials and methods
Key resources Continued on next page

Fly strains
Flies were raised on standard cornmeal agar food in plastic vials at 25˚C and 40-50% relative humidity on a 12 hr:12 hr light:dark cycle. Details of fly strains are listed in the Key Resources Table. smFISH probes Oligonucleotide probe sets were designed using the web-based probe design software https:// www.biosearchtech.com/stellaris-designer. The YFP smFISH probe set was purchased from LGC Bio-Search Technologies (CA, USA) prelabeled with Quasar-670 dye. CaMKII, nAChRa1, nAChRa5, and nAChRa6 DNA oligonucleotide sets were synthesized by Sigma-Aldrich (Merck) and enzymatically labeled with ATTO-633 according to Gaspar et al., 2017. DNA oligonucleotide sequences for each smFISH probe set are provided in Supplementary file 1.

Whole Drosophila brain smFISH
Whole adult brain smFISH was performed essentially as described (Yang et al., 2017). The 2-4-dayold adult Drosophila brains were dissected in 1Â phosphate buffered saline (PBS) and fixed in 4% v/ v paraformaldehyde for 20 min at room temperature. Brains were washed 2Â with PBS, followed by 20 min in 0.3% v/v Triton X-100 in PBS (PBTX) to permeabilize the tissue, then 15 min in PBTX with 500 nM JF549-SNAPTag (Grimm et al., 2015) for neuronal labeling. Then, 3 Â 10 min washes in PBTX removed excess dye. Samples were then incubated in wash buffer (2Â RNase-free SSC + 10% v/v deionized formamide) for 10 min at 37˚C, wash buffer was replaced with hybridization buffer (2Â RNase-free SSC, 10% v/v deionized formamide, 5% w/v dextran sulphate, 250 nM smFISH probes), and samples incubated overnight at 37˚C. Hybridization buffer was removed before samples were washed 2Â in freshly prepared wash buffer and incubated 40 min in wash buffer containing Vybrant DyeCycle Violet Stain (1:1000) to label nuclei. Samples were then washed 3Â times in wash buffer, mounted on a glass slide covered with Vectashield anti-fade mounting medium (refractive index 1.45), and immediately imaged.

Olfactory conditioning
Aversive olfactory conditioning was performed essentially as described by Tully and Quinn, 1985. 3-Octanol (OCT) was used as the shock-paired odor. 4-Methylcyclohexanol (MCH) was used as the unpaired odor. Odors were prepared at concentrations of 9 ml OCT in 8 ml mineral oil, and 8 ml MCH in 8 ml mineral oil. Groups of~100 flies were aliquoted into plastic vials containing standard cornmeal agar food and a 2 Â 6 cm piece of filter paper. Flies were conditioned as follows: 1 min OCT paired with 12 Â 90 V shocks at 5 s interstimulus interval; 45 s clean air; 1 min MCH. Control groups were handled in the same way except for the differing presentation of either odors or shock. Untrained flies experienced no odor or shock, the odor only group experienced the two odor presentations without shock, and the shock only group received the shock presentations but no odors. Aversive olfactory conditioning was performed at 23˚C and 70% relative humidity. Following training, flies were returned to food vials and brains were dissected either 10 min, 1 hr, or 2 hr later, and smFISH analyses performed. For the 'unpaired' experiment, the interval between presentations was extended from 45 to 180 s to avoid trace conditioning of the unpaired odor. In the trained group, flies were presented with 1 min OCT paired with 12 Â 90 V shocks at 5 s interstimulus interval, 180 s clean air, and then 1 min MCH. In the unpaired group, flies received 12 Â 90 V shocks at 5 s interstimulus interval (no odor pairing), 180 s clean air, and then 1 min MCH. Other control groups were handled in the same way except that the odor only group experienced the two odor presentations without shock and the shock only group received the shock presentations but no odors. Following training, flies were returned to food vials and brains were dissected 10 min later for smFISH analyses.

Deconvolution
Deconvolution was carried out using commercially available software (Huygens Professional v19.10.0p1, SVI Delft, The Netherlands). Raw image data generated in .mvd2 file format were converted to OME.tiff format using FIJI (Schindelin et al., 2012) (convert_mvd2_to_tif.ijm). Spherical aberration was estimated from the microscope parameters (see Microscopy). Z-dependent momentum preserving deconvolution (CLME algorithm, theoretical high-NA PSF, iteration optimized with quality change threshold 0.1% and iterations 40 maximum, signal-to-noise ratio 20, area radius of background estimation is 700 nm, a brick mode is 1 PSF per brick, single array detector with reduction mode SuperXY) was then applied to compensate for the depth-dependent distortion in point spread function, thereby reducing artifacts and increasing image sharpness.

Multi-channel alignment
Misalignment between channels was corrected for using Chromagnon (v. 0.81) (Matsuda et al., 2018). To estimate channel misalignment, nuclei were labeled with the broad emission spectrum dye (Vybrant DyeCycle Violet Stain, Thermo Fisher) (Smith et al., 2015). The dye was excited at 405 nm, and emission was recorded using the appropriate filters for each imaging channel. Chromatic shift was estimated by finding the affine transformation that delivers a minimum mean square error between the nuclear stain in the various channels. Nuclear calibration channels for chromatic shift correction were separated using ImageJ (see macro Split_ometiff_channels_for_chromcorrect.ijm). The affine transformation was estimated and alignment was performed by calling Chromagnon from Python (see script chromagnon_bash.py). The resulting aligned and deconvolved images were saved in .dv format for further downstream analysis.
Calculating postsynaptic abundance and volume of g5b'2a and g1pedc>a/b MBON dendrites Neuromorphological calculations were performed with NAVis 0.2.0 library functions in Python (https://pypi.org/project/navis/) (Bates et al., 2020a) using data obtained from the Drosophila hemibrain dataset (v.1.1) (https://neuprint.janelia.org) . To calculate the dendritic volume and postsynaptic abundance of g5b'2a and g1pedc>a/b MBONs, neuron skeletons, neuropil meshes, and synapse data were first imported. Neural skeletons were then used to generate 3D neuron reconstructions. Dendritic processes of the g5b'2a MBON were determined by intersecting neuronal skeletons with the MB mesh containing the g5 and b'2a compartments. Dendritic processes of the g1pedc>a/b MBON were determined by intersecting the skeleton within the g1 MB compartment mesh. The available g1 MB compartment mesh did not encompass the entirety of the g1pedc>a/b MBON dendrites in the g1 MB compartment, so the volume of the mesh was scaled up 1.35Â. This intersects with almost all g1pedc>a/b MBON dendrites in the g1 MB compartment, but not any other substantial part of the neuron. Dendritic volume (nm 3 ) was calculated as the sum of the neurite voxels multiplied by 8 3 since the resolution of each voxel is 8 nm 3 . The number of postsynapses within these compartments was also determined using the synapse data that accompany the neuron skeletons .
Data visualization smFISH data were visualized in FIJI (Schindelin et al., 2012). Maximum intensity projections representing 2 mm sections are presented for visualization purposes. Figure 1I and J are single z-sections (representing a 0.2 mm section). The 3D reconstructions of g5b'2a and g1pedc>a/b MBONs were created in Blender v.2.8.2 with NAVis 0.2.0 plug-in and using data obtained from http://www.neuprint.janelia.org.

mRNA detection
An smFISH spot detection MATLAB script based on Smith et al., 2015 was written to quantify localized mRNA transcripts in Drosophila brains. Software for processing smFISH datasets is available as Supplementary Software. The smFISH channel was extracted and stored as a 3D grayscale image. mRNA signal was detected using 3D generalized likelihood ratio test (Smith et al., 2015). The false detection rate is 0.05, and the spot width is s x,y = 1.39 and s z = 3.48. After 3D detection, the intensity, background, width, and subpixel position of the detected mRNA spots are estimated using maximum likelihood estimation (MLE) (Smith et al., 2010).To reduce the impact of overlapping spots in 3D, only a 2D cross section is used from the z-plane where the spot is detected. To filter out spurious detections, all spots with a width >5 pixels are discarded.

mRNA-dendrite co-localization
To quantify calyx and dendritic localized smFISH puncta, the calyx and dendritic area were first segmented manually. The contour of the calyx and dendritic area is converted to a mask (M 1 ) using the MATLAB R2019b function roipoly. To quantify smFISH puncta co-localizing with dendrite label, a mask of the dendrite label is created by enhancing the image using a difference of Gaussians filter (width of 1 and 5 pixels) and then thresholding the product between the enhanced image (A) and masked area (M 1 ) to obtain a mask (M 2 ): where mean() and std() are the sample mean and sample standard deviation of the image intensity values, and A B is the Hadamard product between A and B. The sample standard deviation is calculated as where N is the number of data points. smFISH signal within g5b'2a MBON dendrites innervating the g5 and b'2a MB compartments was analyzed. smFISH signal within the g1pedc>a/b dendrites innervating the g1 MB compartment was analyzed. Sections of 10 Â 0.2 mm individual z-slices of MB calyx, g5b'2a MBON dendrites, or g1pedc>a/b MBON dendrites were analyzed. smFISH puncta overlapping with the calyx or dendrite mask were considered co-localizing and therefore localized within that neuronal compartment.

Spot brightness and full width half maximum (FWHM) analysis
For each detection, a region of interest (ROI) is extracted as a 2D box in the x-y plane with a size of 2Â(3s x,y +1). For each ROI, the MLE of the x and y position, the number of photons, the number of background photons, and the width of the 2D Gaussian, s x,y, is computed. The FWHM of the spots is calculated as FWHM ¼ 2 ffiffiffiffiffiffiffiffiffiffiffiffi ffi 2ln 2 ð Þ p s x;y .

Verification of transcription foci
Soma containing bright nuclear transcription foci were selected to quantify the difference in intensity relative to diffraction-limited smFISH puncta. The nuclear localization of the smFISH puncta with the highest photon count was validated by visual inspection and considered to correspond to the transcription site. The width (s x,y ) of the transcription foci significantly differs from the sparse smFISH signal and is estimated by fitting a 2D Gaussian to the transcription site using the MATLAB 2019b nonlinear least-squares routine lsqcurvefit. Transcription foci brightness and background were computed using the same MLE protocol as for diffraction-limited spots, but with the estimated s x,y .

YFP fluorescence intensity
To quantify YFP fluorescence intensity within co-labeled neurons, we developed a FIJI-compatible macro plug-in. Depth-dependent bleaching was first corrected for over the z-stack using an exponential fit. Background signal was then subtracted in each z-section using a rolling ball filter with a width of 60 pixels. Five z-sections above and below the center of the image were cropped for analysis. YFP fluorescence intensity was recorded within the dendrites or soma of the co-labeled neuron using the mask described above (mRNA-dendrite co-localization). Fluorescence intensity was calculated as analog digital units (adu)/volume (dendrites or soma) to give adu/voxel. Software for analyzing fluorescent protein expression in single neurons is available as Supplementary Software.

Statistical analyses
Data were visualized and analyzed statistically using GraphPad Prism version 8.3.1 (332). The distribution of a dataset was assessed with a Shapiro-Wilk test. Gaussian distributed smFISH abundance was compared between two groups using an unpaired t-test. Gaussian distributed smFISH abundance between multiple groups was compared using a one-way ANOVA followed by Tukey's post hoc test. Non-Gaussian distributed smFISH abundance was compared between two groups using a Mann-Whitney U test. Proportions of transcriptionally active soma were compared to transcriptionally inactive soma using a chi-square test. YFP-positive and -negative smFISH intensity distributions were compared with a two-sided Wilcoxon rank-sum test. YFP fluorescence intensity across treatments was compared using a one-way ANOVA for Gaussian distributed data and a Kruskal-Wallis test for non-Gaussian distributed data. Statistical significance is defined as p<0.05.