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Table 3 The expression of Brn3a target genes: ISH and RNASeq results comparison

From: Postnatal developmental dynamics of cell type specification genes in Brn3a/Pou4f1 Retinal Ganglion Cells

Gene Known function GCL P3 GCL P0-P22 Brn3a target P3 Brn3a target any age Postnatal GCL Expression GCL Sparse Brn3a-independ. Transcripts Brn3a-regulation Gene level
Onset Peak Offset
Transcriptional and translational regulators
 Foxp2 TF yes no no yes P0 P7 no no no yes
 Tshz2 TF yes yes yes yes P3 P7 no no no yes
 Rbfox1 Splicing of neuronal genes yes no no no P0 P14 no no yes no
Intracellular signaling and cytoskeleton-associated genes
 Eml1 Microtubule-binding protein yes no no no P0 P7 no no yes no
 Hpca Calcium sensor yes yes no yes P0 P7-P14 no no yes no
 Plppr3 Neurite growth and regeneration yes yes no yes P0 P0 no no no no
 Mapk10 Axonal growth and neuronal survival yes yes no yes P0 P7-P14 no yes yes no
 Pip5kl1 Cell morphology and adhesion no no no no P3 P7 no no no no
 Pak6 Signaling kinase no no no no no no no no no na
Vesicle-associated proteins
 Ankrd13b Caveolin- mediated endosomal traffick yes yes no no P0 P7 no no no no
 Pick1 Glutamate receptor trafficking yes no no no P0 no no no yes no
 Snap91 Clathrin-mediated endocytosis yes yes yes yes P0 P7-P14 no yes yes no
 Tusc5 Insulin-stimulated glucose transport yes yes yes yes P3 P14 no yes no yes
Synapse-associated proteins
 Elfn1 Synaptic adhesion protein yes no no yes P3 P7 no yes no yes
 Gabra1 GABA receptor alpha1 subunit no no no yes P3 no no yes no yes
 Grm4 Metabotropic glutamate receptor yes no no no P0 P7 no no no yes
 Ntrk1 Neurotrophin receptor yes no no no P0 P14-P22 no no no yes
 Pnkd Synaptic vesicle release no yes no no P0 P7-P14 no yes yes no
 Rims1 Synaptic vesicle release & recycling yes yes no yes P0 P0-P3 no yes no no
Secreted proteins
 Fam19a4 Unknown no no no no P3 P3-P7 P7 no no yes
 Nptx1 Trans-synaptic, excitatory synapse yes yes no yes P0 P14 no yes no yes
 Nptx2 Trans-synaptic, excitatory synapse yes no no no P3 P7-P14 no yes no yes
 Sez6l2 Synapse formation yes yes no yes P3 P7 no no yes no
Adhesion molecules and other transmembrane proteins
 Cdh4 Cell adhesion molecule yes no yes yes P0 no no yes no yes
 Pcdh20 Cell adhesion molecule no no no yes P14 no no no no yes
 Rtn4rl2 Axon guidance molecule yes yes no yes P0 no P22 no no no
 Tmem25 Unknown no no no no P0 P7-P14 no no no no
 Tmem91 Unknown no no no yes P0 P7-P14 no no yes no
  1. Column 1 represents gene name, column 2 – known function of the gene, column 3 – GCL enrichment at P3, column 4 – consistent GCL enrichment (at least at 4 out of 5 ages) from P0-P22. Fifth column shows whether the gene is regulated by Brn3a at P3, 6th – regulated by Brn3a at any of 5 studied ages. Columns 7, 8 and 9 represent the onset, the peak and the offset respectively of postnatal gene expression in the GCL. Column 10 shows whether the gene is highly and sparsely expressed in the GCL at any of studied ages. Columns 11 and 12 identify the genes that had unregulated transcripts or exhibited gene level regulation by RNASeq