Midbrain is located between forebrain and hindbrain and is commonly segmented into tectum, aqueduct, tegmentum, basis pedunculi. The major part of tectum constitutes superior and interior colliculi (processing visual and auditory information, respectively). The cerebral aqueduct, which is the smallest ventricle in the brain linking 3rd and 4th ventricle, accommodates periaqueductal grey, dorsal raphe nucleus and several nuclei related to visual system. Tegmentum facilitates homeostasis and reflexes. The crucial tegmental nuclei include median raphe-, red nuclei (involved in motor coordination) and ventral tegmental area, the biggest dopamine production site. The basis pedunculi provides path to major nerve tracts, eg. corticospinal tract, internal capsule. It also contains affected in Parkinson disease substantia nigra, the dopamine production center. Developmentally, midbrain emerges from the second vesicle of neural tube and does not sub-divide further, in comparison to other brain regions.

The transcriptome analysis shows that 83% (n=16240) of all human protein-coding genes (n=19670) are expressed in the human midbrain (represented by RNA expression in substantia nigra). Human one-to-one orthologues were investigated in pig and mouse brain, suggesting that 11762 of all mouse one-to-one orthologues (n=15160) are expressed in the mouse midbrain and that 12635 of all pig orthologues (n=14656) are expressed in the pig midbrain.

Figure 1. Schematic drawing of the human brain, indicating the location of midbrain from a sagittal view.

Raphe nucleus

Raphe nuclei are clusters of nuclei in the brain stem, containing
serotonergic neurons. The more posterior nuclei reside in pons and medulla and project to spinal cord and cortical areas. The parts residing in the midbrain, dorsal and median raphe nucleus (MRN) are considered to be implicated in the depression. The MRN outputs target the Hippocampus and are involved in the long-term memory formation. The dorsal raphe nucleus projects to amygdala, cerebral cortex, caudate, putamen and olfactory bulb.

TPH2 - Dorsal raphe
TPH2 - Caudate nucleus

SLC6A4 - Dorsal raphe
SLC6A4 - Caudate nucleus

SNCG - Median raphe
PAK1 - Dorsal raphe

Ventral tegmental area

Ventral tegmental area (VTA) is the largest center for production of dopamine, and together with Substantia Nigra, origin of the major dopamine pathways: 1) mesolimbic (projecting to nucleus accumbens and olfactory tubercle); 2) mesocortical (delivering dopamine to the prefrontal cortex). VTA outputs are also targeting Hippocampal formation, Amygdala and Olfactory bulb. Most of the neuronal connections are reciprocal. The VTA is implicated in the reward system (addiction), cognition and psychiatric disorders.

TH - Ventral tegmental area

Substantia Nigra

Substantia Nigra is divided into two parts: 1) pars compacta (SNc) projects to the caudate and putamen (dopaminergic niagrostratal pathway); 2) pars reticulata (SNpr) receives inputs from basal ganglia (direct and indirect pathway) and conveys to other brain areas, including thalamus and superior colliculus. SN is involved in the reward system and motor control. The name substantia nigra (latin for black substance) comes from the darker color of the residing dopaminergic cells, containing pigment neuromelanin. Loss of dopaminergic neurons is implicated in Parkinson's Disease.

SNCG - Substantia nigra
DRD2 - Substantia nigra

SLC6A3 - Substantia nigra

The transcriptome analysis shows that 83% (n=16240) of all human proteins (n=19670) are expressed in the midbrain. 56 genes show an elevated expression level in midbrain compared to other regions of the brain.

• 14 regionally enriched genes
• 56 regionally elevated genes in total
• 34 of the midbrain elevated genes are elevated in other tissues than the brain.
• 22 of the midbrain elevated genes are elevated in the brain.

Table 1: Schematic drawing of the human brain, indicating the location of midbrain from a coronal perspective or sagittal view.

The whole of mouse midbrain was dissected and used for this analysis, mean value of the 2 male and 2 female mice is used as representative of the midbrain.

The transcriptome analysis shows that 60% (n=11762) of all mouse one-to-one human orthologue genes (n=15160) are expressed in the midbrain and 44 genes show an elevated expression in midbrain compared to other regions of the brain.

Table 3: Number of genes within the different categories of regionally elevated expression, in mouse midbrain

Figure 2. Schematic drawing of the mouse brain, indicating the location of midbrain from a sagittal view.

Figure 3. Schematic drawing of the pig brain, indicating the location of midbrain from a sagittal view.

Elevated expression in midbrain compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in midbrain compared to all other regions), group enriched (at least four-fold higher mRNA levels in a group of 2-5 regions) and regionally enhanced (at least four-fold higher mRNA levels in midbrain compared to the average of all regions).

The substantia nigra, superior colliculus and periaqueductal gray were dissected out as separate areas of the midbrain and analyzed separated from the remaining midbrain area. The highest expression value of the 4 midbrain samples were used as representative as midbrain in the regional expression comparison.

The transcriptome analysis shows that 64% (n=12635) of all pig one-to-one human orthologue genes (n=14656) are expressed in the midbrain. 93 genes show an elevated expression in midbrain compared to other regions of the brain.

Table 5: Number of genes within the different categories of regionally elevated expression, in pig midbrain