Murine Retina Outer Plexiform Layer Development and Transcriptome Analysis of Pre-Synapses in Photoreceptors
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals
2.2. DNA Construction
2.3. In Vivo Electroporation
2.4. Immunohistochemistry
2.5. Image Analysis
2.6. Gene Profile Analyses
3. Results
3.1. Wild-Type Outer Plexiform Layer Development in Murine Retina
3.2. Characterization of Individual Spherules and Pedicles
3.3. Characterization of Pre-Synapses in Nrl-/- Photoreceptors
3.4. Nrl-/- Retina Outer Plexiform Layer Development
3.5. Comparison of Gene Expression in Spherules vs. Pedicles
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
3D | three-dimensional |
adj. p | adjusted p-value |
ARVO | Association for Research in Vision and Ophthalmology |
BPM | bins per million mapped reads |
CAR | cone arrestin |
Clm | clomeleon |
Cplx | complexin |
CrxpNrl | Crx promoter |
DAPI | 4′,6-diamidino-2-phenylindole |
DEGs | differentially expressed genes |
Dlg4 | discs large MAGUK scaffold protein 4 |
Dmd | dystrophin muscular dystrophy |
downSCL | down-regulated genes in developing S-cone-like photoreceptors |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
GEO | Gene Expression Omnibus |
GFP | green fluorescent protein |
Gnb | G protein subunit beta |
GO | Gene Ontology |
Goα | guanine nucleotide-binding protein alpha subunit |
Nr2E3 | nuclear receptor subfamily 2 group E member 3 |
NRL | neural retina leucine zipper |
Nrlp-EGFP | Nrl promoter-driven enhanced GFP |
Nrlp-GFP | Nrl promoter-driven GFP |
OCT | optimal cutting temperature |
OPL | outer plexiform layer |
P | postnatal day |
PFA | paraformaldehyde |
PKCα | Protein Kinase C alpha |
PNA | peanut agglutin lectin |
PSD-95 | postsynaptic density protein 95 |
pUB | Ubiquitin C promoter |
S-opsinp-tdT | S opsin promoter-driven tdTomato |
SCL | S-cone like |
shRNA | short hairpin ribonucleic acid |
Sv | Synaptic vesicle glycoprotein |
SynGO | Synaptic Gene Ontologies and annotations |
TPM | transcript per million |
upRod-NRL | upregulated NRL binding genes in developing WT rods |
upSCL-NRL | upregulated NRL binding genes in developing S-cone-like photoreceptors |
vs. | versus |
WT | Wild-type |
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GOterm | Go ID | Genes |
---|---|---|
myelin sheath | 0043209 | NSF, NAPB, HSP90AA1, ENO1B, ATP1A3, THY1, ENO1, COX6A1, NFASC, PKM, GNB1, GNB5, SLC25A12, ALDOA, SLC25A5 |
synapse | 0045202 | RAB3A, NRN1, RPLP1, CABP4, CLSTN1, CAMK2A, ATP1A3, TULP1, YBX3, ZDHHC2, LY6C1, EPS8, GABRR2, GABRR1, SYNGR1, SV2B, TMEM108, RABAC1, SH3GL2, SNTA1, CACNG5, PTPRN2, WHRN, CARTPT, MYRIP, USH2A, CDH10, SPARCL1, RPS21, VAMP2, SNTB2 |
neuron projection | 0043005 | HSP90AA1, PACRG, WHRN, CAMK2A, RTN4RL2, LSM4, EPS8, GABRR2, GABRR1, PCP4, NFASC, RIT2, SV2B, BBS7, STX3, VAMP2, CDK5R2, RGS6 |
dendrite | 0030425 | GNAZ, RCVRN, KCNJ12, KCNIP2, CAMK2A, ZDHHC5, RTN4RL2, THY1, TRAK1, TXN2, SLC6A6, PEX5L, NFASC, GNB1, TMEM108, STX3 |
Calcium ion binding | 0005509 | CRB1, SYT3, RCVRN, KCNIP2, CABP4, CLSTN1, GUCA1A, RHOT2, PCP4, EHD4, VSNL1, PITPNM1, CDH10, CDHR1, SPARCL1, PLCH2, SLC25A12, GAS6, NUCB2, SLC25A25, TGM3 |
vesicle-mediated transport | 0016192 | NSF, NAPB, RAB4A, SYT3, TULP1, AP2A2, ARL4D, SPIRE2, STX3, VAMP2, HSPA1B, VTI1B, HSPA1A |
ion transport | 0006811 | KCNG1, KCNJ5, KCNE2, KCNK9, KCNJ12, KCNIP2, SLC6A15, ATP1A3, SLC5A2, SLC4A5, GABRR2, GABRR1, NIPAL1, CNGA1, SCN4A |
growth cone | 0030426 | EPS8, WHRN, ENO1B, RASGRF1, STX3, THY1, ENO1, CDK5R2 |
calmodulin binding | 0005516 | PCP4, RIT2, CAMK2A, VAMP2, MYLK, SNTA1, SNTB2 |
GABA-ergic synapse | 0030425 | SLC6A6, GABRR2, GABRR1, CDH10, CLSTN1, ZDHHC5 |
postsynaptic membrane | 0045211 | SLC6A6, GABRR2, GABRR1, CLSTN1, CACNG5, SNTA1, SYNE1 |
chemical synaptic transmission | 0007268 | GABRR2, GABRR1, SV2B, CLSTN1, CARTPT |
extracellular matrix | 0031012 | ADAMTSL1, COL26A1, COL3A1, ADAMTS3, COL4A3, RTN4RL2, MMP9 |
transmembrane transport | 005508 | KCNG1, SLC25A29, SV2B, CNGA1, SCN4A, SLC5A2, SLC25A5, SLC25A12, SLC25A25, SLC4A5 |
cell adhesion | 0007155 | NFASC, PRPH2, CDHR1, CDH10, CLSTN1, ROM1, COL4A3, ADAM9, SPG7, THY1, CD34 |
extracellular region | 0005576 | CRB1, CCDC126, CDNF, PRCD, CLSTN1, LOXL4, TULP1, PLA2G7, GLB1L2, CST3, ADAMTSL1, FTH1, NRTN, FAM3C, CD34, ST3GAL1, CTSB, CHGA, COL26A1, CARTPT, MMEL1, USH2A, MMP9, POMC, COL3A1, RBP3, QPCT, COL4A3, SPARCL1, GAS6, NUCB2, HSPA1A |
GOterm | Go ID | Genes |
---|---|---|
actin binding | 0003779 | DIAPH3, PARVG, WIPF1, EPB41L1, MYO7A, CAP2 |
dendrite | 0030425 | ACHE, OPN4, NEGR1, NR1D1, IGSF9, CNNM4 |
actin cytoskeleton | 0015629 | RINL, PARVG, WIPF1, MYO7A |
cell morphogenesis | 0000902 | GREM1, GNAT2, CAP2 |
ATP-dependent microtubule motor activity, minus-end-directed | 0008569 | KIFC1, DNAH7C |
axon | 0030424 | ACHE, OPN4, MAP4, IGSF9, DCLK1 |
amino acid transmembrane transport | 0003333 | SLC7A8, SLC38A3 |
microtubule | 0005874 | KIFC1, MAP4, DNAH7C |
calcium ion binding | 0005509 | HEG1, CALU, SPOCK1, AMY1, DNAH7C |
extracellular region | 0005576 | GREM1, ACHE, ORM1, CALU, SPOCK1, AMY1 |
GOterm | Go ID | Genes |
---|---|---|
synapse | 0045202 | SYNPR, RNF112, GRM5, CDH10, PDYN, SHISA9, CDH9, INSYN2A |
cell-cell junction assembly | 0007043 | CDH10, NR1H4, CDH9 |
neuronal dense core vesicle lumen | 0099013 | IGF1, PDYN |
postsynaptic membrane | 0045211 | GRM5, GRM6, SHISA9, CDH9 |
glutamatergic synapse | 0098978 | GRM5, CDH10, IGF1, SHISA9, CDH9 |
postsynaptic density | 0014069 | RNF112, GRM5, SHISA9, INSYN2A |
calcium-mediated signaling using intracellular calcium source | 0035584 | GRM5, VCAM1 |
myotube differentiation | 0014902 | IGF1, ANKRD2 |
response to zinc ion | 0010043 | VCAM1, ABCC8 |
regulation of long-term neuronal synaptic plasticity | 0048169 | GRM5, AGT |
dendrite | 0030425 | GRM6, GNB1, PDYN, CDH9 |
extracellular region | 0005576 | TAFA4, VCAM1, FRZB, IGF1, PDYN, BMP7 |
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Kim, S.-Y.; Park, C.H.; Moon, B.-H.; Seabold, G.K. Murine Retina Outer Plexiform Layer Development and Transcriptome Analysis of Pre-Synapses in Photoreceptors. Life 2024, 14, 1103. https://doi.org/10.3390/life14091103
Kim S-Y, Park CH, Moon B-H, Seabold GK. Murine Retina Outer Plexiform Layer Development and Transcriptome Analysis of Pre-Synapses in Photoreceptors. Life. 2024; 14(9):1103. https://doi.org/10.3390/life14091103
Chicago/Turabian StyleKim, Soo-Young, Christine Haewon Park, Bo-Hyun Moon, and Gail K. Seabold. 2024. "Murine Retina Outer Plexiform Layer Development and Transcriptome Analysis of Pre-Synapses in Photoreceptors" Life 14, no. 9: 1103. https://doi.org/10.3390/life14091103