The landscape of regulatory genes in brain-wide neuronal phenotypes of a vertebrate brain

Abstract

Multidimensional landscapes of regulatory genes in neuronal phenotypes at whole-brain levels in the vertebrate remain elusive. We generated single-cell transcriptomes of ~67,000 region- and glutamatergic/neuromodulator-identifiable cells from larval zebrafish brains. Hierarchical clustering based on effector gene profiles ('terminal features') distinguished major brain cell types. Sister clusters at hierarchical termini displayed similar terminal features. It was further verified by a population-level statistical method. Intriguingly, glutamatergic/GABAergic sister clusters mostly expressed distinct transcriptional factor (TF) profiles ('convergent pattern'), whereas neuromodulator-type sister clusters predominantly expressed the same TF profiles ('matched pattern'). Interestingly, glutamatergic/GABAergic clusters with similar TF profiles could also display different terminal features ('divergent pattern'). It led us to identify a library of RNA-binding proteins that differentially marked divergent pair clusters, suggesting the post-transcriptional regulation of neuron diversification. Thus, our findings reveal multidimensional landscapes of transcriptional and post-transcriptional regulators in whole-brain neuronal phenotypes in the zebrafish brain.

Jag2b‐Notch3/1b‐mediated neuron‐to‐glia crosstalk controls retinal gliogenesis

“…To prepare pTol2‐Tp1:mNeonGreenCAAX , pTol2‐Tp1:gal4 plasmids, we used the vector from pTol2‐Tp1bglob:EGFP (Addgene plasmid #73586), then recombination with gal4 or mNeonGreenCAAX using ClonExpressMultiS One Step Cloning Kit (Vazyme, C113‐02). And to prepare pTol2‐uas:dla‐P2A‐H2B‐ECFP‐vmhc:mCherry，pTol2‐uas:dlb‐P2A‐H2B‐ECFP‐vmhc:mCherry , pTol2‐uas:dlc‐P2A‐H2B‐ECFP‐vmhc:mCherry , pTol2‐uas:dld‐P2A‐H2B‐ECFP‐vmhc:mCherry , pTol2‐uas:notch1b NICD‐P2A‐H2B‐ECFP‐vmhc:mCherry , pTol2‐uas:notch3 NICD‐P2A‐H2B‐ECFP‐vmhc:mCherry , 10× uas backbone was amplified from plasmid Tol2‐10× uas:loxp‐stop‐loxp‐tdtomato (Zhang et al , 2021), and dla/dlb/dlc/dld/notch3‐NICD codon were cloned with zebrafish cDNA.…”

Specific biomarkers and neurons distribution of different brain regions in largemouth bass (Micropterus salmoides)

“…To determine the distribution of neurons synthesizing different neurotransmitters across various brain regions, the marker genes of seven neurotransmitter-type neurons, specifically glutamatergic neuron ( slc17a6 ), GABAergic neuron ( gad ), glycinergic neuron ( slc6a5 ), dopaminergic neuron ( th ), serotonergic neuron ( tph2 ), noradrenergic neuron ( dbh ), and cholinergic neuron ( chata ) were screened from the transcriptomes of six brain regions, referencing data from the model zebrafish ( 20 ). In all brain regions, the expression levels of glutamatergic ( slc17a6a , slc17a6b ) and GABAergic ( gad1 , gad2 ) marker genes were significantly higher compared to other neurotransmitter types.…”

“…The distributions of neurons and non-neuronal cells in different brain regions were predicted based on the expression levels of related marker genes. The marker genes for various types of neurons and non-neuronal cells were identified using data from model species zebrafish ( 20 ). Seven types of neurons were distinguished by specific marker genes: glutamatergic neurons by slc17a6 , GABAergic neurons by gad , glycinergic neurons by slc6a5 , dopaminergic neurons by th , serotonergic neurons by tph2 , noradrenergic neurons by dbh , and cholinergic neurons by chata .…”

“…Additionally, potential receptors for these seven neurotransmitters were screened based on the genome annotation of largemouth bass, and total expressions of each type receptor in six brain regions were also calculated and analyzed. The marker genes for five types of non-neuronal cells, including olig2 , sox10 (oligodendrocytes), apoeb , mpeg1 (microglia), rbp4 (endothelial cells), cx43 (radial astrocytes), and pcna (neuroprogenitors) ( 20 ), were also identified in the transcriptomes of the largemouth bass brain. By comparing the expression levels of these marker genes across the six brain regions, predictions were made regarding the distribution of neurons and non-neuronal cells in different brain regions.…”

“…As a model organism for studying complex brain disorders, zebrafish has been studied more deeply, and functions of its brain sub-regions are beginning to become clearer ( 19 ). Recently, cell types and gene expression characteristics of four brain regions (forebrain, optic tectum, hindbrain and the region underneath the optic tectum) have been revealed in zebrafish using single-cell transcriptome sequencing ( 20 ). However, compared with the study of zebrafish, the research progress on the function of different brain regions in farmed fish is still in its infancy.…”