<p dir="ltr">RNA localization to neuronal axons and dendrites provides spatiotemporal control over gene expression to support synapse function. Neuronal messenger RNAs (mRNAs) localize as ribonucleoprotein particles (RNPs), commonly known as RNA granules, the composition of which influences when and where proteins are made. High-throughput sequencing has revealed thousands of mRNAs that localize to the hippocampal neuropil. Whether these mRNAs are spatially organized into common RNA granules or distributed as independent mRNAs for proper delivery to synapses is debated. Here, using highly multiplexed single molecule fluorescence in situ hybridization (HiPlex smFISH) and colocalization analyses, we investigate the subcellular spatial distribution of 15 synaptic neuropil localized mRNAs in the male and female rodent hippocampus. We observed that these mRNAs are present in the neuropil as heterogeneously sized fluorescent puncta with spatial colocalization patterns that generally scale by neuropil mRNA abundance. Indeed, differentially expressed mRNAs across cell types displayed colocalization patterns that scaled by abundance, as did simulations that reproduce cell-specific differences in abundance. Thus, the probability of these mRNAs colocalizing in the neuropil is best explained by stochastic interactions based on abundance, which places constraints on the mechanisms mediating efficient transport to synapses. </p>
Funding
Cell-Type Specific Regulation of Dendritic mRNA in the Hippocampus
National Institute of Mental Health
Find out more...2021 NARSAD Young Investigator Grant
R01NS12333
History
Publisher
University Libraries, Virginia TechCorresponding Author Name
Shannon FarrisFiles/Folders in Dataset and Description
Folder 1:
This folder has 4 raw maximum projection multichannel TIFF images from CA2 region of the hippocampus of N=4 mice. Each images has 4 channels. Channel Order is DAPI, Rgs14, Adcy1, Ppp1r9b.
Image names are:
1) MCC 412_CA2_Raw_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
2) MCC 420_CA2_Raw_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
3) MCC 453_CA2_Raw_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
4) TD 171_CA2_Raw_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
This folder also has 4 processed maximum projection multichannel TIFF images of the corresponding raw images from CA2 region of the hippocampus of N=4 mice. Each images has 4 channels. Channel Order is DAPI, Rgs14, Adcy1, Ppp1r9b.
Image names are:
1) MCC 412_CA2_Processed_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
2) MCC 420_CA2_Processed_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
3) MCC 453_CA2_Processed_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
4) TD 171_CA2_Processed_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
This folder also has 4 excel files that contain the coordinates of RNA puncta detected as binary objects from the corresponding processed images. Each excel file has two sheets named as “adcy1_coords” and “ppp1r9b cords” for corresponding RNA channel.
Each excel sheet has following columns:
Entity: Name of the RNA channel
ObjectId: Binary object ID for each detected RNA puncta
ObjectArea[µm²]: 2D area of each binary object (RNA puncta)
CentroidX[µm]: Centroid X coordinate of each binary object (RNA puncta)
CentroidY[µm]: Centroid Y coordinate of each binary object (RNA puncta)
MaxFeret[µm]: Feret’s diameter of each binary object
SumObjIntensity: Total intensity per puncta for each binary object
Excel File names are:
1) mcc412_ca2_coords_adcy1 ppp1r9b
2) mcc420_ca2_coords_adcy1 ppp1r9b
3) mcc453_ca2_coords_adcy1 ppp1r9b
4) td171_ca2_coords_adcy1 ppp1r9b
Folder 2:
This folder has 4 raw maximum projection multichannel TIFF images from Dentate (DG) region of the hippocampus of N=4 mice. Each images has 4 channels. Channel Order is DAPI, Rgs14, Adcy1, Ppp1r9b. Image names are started with MouseIDs.
Image names are:
1) MCC 412_DG_Raw_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
2) MCC 420_DG_Raw_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
3) MCC 453_DG_Raw_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
4) TD 171_DG_Raw_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
This folder also has 4 processed maximum projection multichannel TIFF images of the corresponding raw images from DG region of the hippocampus of N=4 mice. Each images has 4 channels. Channel Order is DAPI, Rgs14, Adcy1, Ppp1r9b.
Image names are:
1) MCC 412_DG_Processed_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
2) MCC 420_DG_Processed_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
3) MCC 453_DG_Processed_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
4) TD 171_DG_Processed_MaxIP_DAPI Rgs14 Adcy1 Ppp1r9b
This folder also has 4 excel files that contain the coordinates of RNA puncta detected as binary objects from the corresponding processed images. Each excel file has two sheets named as “adcy1_coords” and “ppp1r9b cords” for corresponding RNA channel.
Each excel sheet has following columns:
Entity: Name of the RNA channel
ObjectId: Binary object ID for each detected RNA puncta
ObjectArea[µm²]: 2D area of each binary object (RNA puncta)
CentroidX[µm]: Centroid X coordinate of each binary object (RNA puncta)
CentroidY[µm]: Centroid Y coordinate of each binary object (RNA puncta)
MaxFeret[µm]: Feret’s diameter of each binary object
SumObjIntensity: Total intensity per puncta for each binary object
Excel File names are:
1) mcc412_DG_coords_adcy1 ppp1r9b
2) mcc420_DG_coords_adcy1 ppp1r9b
3) mcc453_DG_coords_adcy1 ppp1r9b
4) td171_DG_coords_adcy1 ppp1r9b
