Pons and Medulla oblongata Neurotransmitter systems in pons and medulla oblongata Regionally elevated expression in human Regionally elevated expression in mouse Regionally elevated expression in pig

Pons and Medulla oblongata

Pons and medulla oblongata together with midbrain and thalamus are part of the brainstem, which is located in the posterior part of the brain. It is a region of transition between central and peripheral nervous system, containing cell nuclei of majority of cranial nerves from which they are emerging to the spinal cord. The pons and medulla developmentally originate from the third vesicle of neural tube (rhombencephalon). Hox genes orchestrate the segmented organization of spinal cord, pons and medulla and are not expressed in other parts of the brain. Pons facilitates connections between medulla and cerebellum, as well as into the thalamus. Medulla receives inputs from pyramidal tracts originating from the cerebral cortex. These nerves are involved in control of the motoric functions. An important function of pons and medulla is the autonomous control of the body's vital functions. For example the cardiovascular (medulla) centers receive sensory inputs from the heart and blood vessels (mechano-, baro- and chemoreceptors) via the vagus nerve and modulates heart rate and blood pressure. A complex network between antagonistic respiratory (pons & medulla) centers regulates the pattern and rate of the respiratory cycle of inhalation and exhalation.

Figure 1. Schematic drawing of the human brain, indicating the location of pons and medulla from a coronal perspective or sagittal view.

EMX2 - NTS
FEV - NTS

CALCA - n. ambiguus
ADCYAP1 - parabrachial n.

The transcriptome analysis shows that 85% (n=16774) of all human protein-coding genes (n=19670) are expressed in the human pons and medulla. Human one-to-one orthologues were investigated in pig and mouse brain, suggesting that 11777 of all mouse one-to-one orthologues (n=15160) are expressed in the mouse pons and medulla and that 12452 of all pig orthologues (n=14656) are expressed in the pig pons and medulla.

Gene classification based on regional RNA expression in human, pig and mouse pons and medulla defines 200 genes as pons and medulla enriched in either of the three species, and 34 out of those genes show highest expression levels in pons and medulla in all three species.

Neurotransmitter systems in pons and medulla oblongata

Noradrenalin

Noradrenalin belongs to the monoamine family of neurotransmitters. It is a hormone and neurotransmitter that increases body arousal and reaches high levels during stress (sympathetic system). The locus coeruleus (LC) located near the 4th ventricle, is the major site of Noradrenalin synthesis in the brain. The LC neurons have projections to all regions of the brain, modulating the arousal state of the brain. Example enzymes involved in noradrenalin synthesis and noradrenalin transport can be found below.

TH - LC
SLC6A2 - LC
SLC6A2 - projections

Glycine

Glycine is the simplest amino acid, with the hydrogen atom as a side chain.
In the brain. Glycine acts as an inhibitory neurotransmitter predominantly in the brain stem, spinal cord and retina, where activation of glycine receptors causes influx of chloride ions.

GLRA1

Acetylcholine

Acetylcholine is an excitatory neurotransmitter that in the brain has a role in the arousal, plasticity and reward. The pons and medulla oblongata contain several populations of cholinergic neurons. These include groups of motor neurons that regulate facial expression and eye movements. In addition, the pons contains populations of cholinergic projection neurons that innervate other parts of the brain including thalamus, hypothalamus and midbrain.

SLC18A3
SLC18A3

Regionally elevated expression in human

The transcriptome analysis shows that 85% (n=16774) of all human proteins (n=19670) are expressed in the Pons and medulla. 393 genes show an elevated expression level in cerebellum compared to other regions of the brain.

174 regionally enriched genes
393 regionally elevated genes in total
224 of the pons and medulla elevated genes are elevated in other tissues than the brain.
169 of the pons and medulla elevated genes are elevated in the brain.

Table 1: Number of genes within the different categories of regionally elevated expression, in human pons and medulla.

Specificity	Number of Human elevated genes
Region enriched	174
Group enriched	133
Region enhanced	86
Elevated	393

Elevated expression in pons and medulla compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in pons and medulla 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 pons and medulla compared to the average of all regions), The number of genes in the individual category is shown in Table 1. In Table 2, the 12 genes with the highest level of regional specificity among the 174 enriched genes are listed.

Table 2. The 12 genes with the highest level of enriched expression in human cerebellum. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.

Gene	Description	Predicted location	RS-score
PHOX2B	Paired like homeobox 2b	Intracellular	99
PHOX2A	Paired like homeobox 2a	Intracellular	96
HOXB8	Homeobox B8	Intracellular	82
UPK3B	Uroplakin 3B	Intracellular,Membrane	58
CALCA	Calcitonin related polypeptide alpha	Secreted	48
HOXA5	Homeobox A5	Intracellular	46
DBH	Dopamine beta-hydroxylase	Intracellular	45
HOXA2	Homeobox A2	Intracellular	44
FBP2	Fructose-bisphosphatase 2	Intracellular	36
SLC6A4	Solute carrier family 6 member 4	Membrane	36
HOXB5	Homeobox B5	Intracellular	33
HPD	4-hydroxyphenylpyruvate dioxygenase	Intracellular	29

Regionally elevated expression in mouse

Figure 2. Schematic drawing of the mouse brain, indicating the location of pons and medulla from a coronal perspective or sagittal view.

The transcriptome analysis shows that 60% (n=11777) of all mouse one-to-one human orthologue genes (n=15160) are expressed in the pons and medulla and 103 genes show an elevated expression in pons and medulla compared to other regions of the brain.

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

Specificity	Number of Mouse elevated genes
Region enriched	39
Group enriched	46
Region enhanced	18
Elevated	103

Elevated expression in pons and medulla compared to other brain regions is divided into three different categories; regionally enriched (at least four-fold higher mRNA levels in pons and medulla 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 pons and medulla compared to the average of all regions), The number of genes in the individual category is shown in Table 3. In Table 4, the 12 genes with the highest level of regional specificity among the 39 enriched genes are listed.

Table 4: The 12 genes with the highest level of enriched expression in mouse pons and medulla. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.

Gene	Description	Predicted location	RS-score
HOXB5	Homeobox B5	Intracellular	90
HOXA5	Homeobox A5	Intracellular	88
HOXB6	Homeobox B6	Intracellular	60
HOXB8	Homeobox B8	Intracellular	48
HOXA4	Homeobox A4	Intracellular	47
HOXB7	Homeobox B7	Intracellular	45
HOXB3	Homeobox B3	Intracellular	40
HOXC5	Homeobox C5	Intracellular	40
HOXB4	Homeobox B4	Intracellular	36
HOXD3	Homeobox D3	Intracellular	36
HOXA2	Homeobox A2	Intracellular	35
HOXA6	Homeobox A6	Intracellular	34

PCP4L1
SLC10A4
CALCA

Regionally elevated expression in pig

The transcriptome analysis shows that 63% (n=12452) of all pig genes (n=14656) are expressed in pons and medulla and 78 genes show an elevated expression in pons and medulla compared to other regions of the brain.

Table 5: Number of genes within the different categories of regionally elevated expression, in pig pons and medulla.

Specificity	Number of Pig elevated genes
Region enriched	26
Group enriched	46
Region enhanced	6
Elevated	78

Figure 3. Schematic drawing of the pig brain, indicating the location of pons and medulla from a coronal perspective or sagittal view .

Table 6: The 12 genes with the highest level of enriched expression in pig pons and medulla. "Predicted localization" shows the classification of each gene into three main classes: Secreted, Membrane, and Intracellular, where the latter consists of genes without any predicted membrane and secreted features. RS-score (Regional Specificity score) corresponds to the score calculated as the fold change to the second highest region.

Gene	Description	Predicted location	RS-score
HOXB5	Homeobox B5	Intracellular	128
HOXA4	Homeobox A4	Intracellular	60
DBH	Dopamine beta-hydroxylase	Intracellular	38
HOXA3	Homeobox A3	Intracellular	34
HOXD3	Homeobox D3	Intracellular	32
SLC6A2	Solute carrier family 6 member 2	Intracellular,Membrane	32
HOXB2	Homeobox B2	Intracellular	29
HOXB3	Homeobox B3	Intracellular	29
HOXD4	Homeobox D4	Intracellular	28
HOXA2	Homeobox A2	Intracellular	27
PHOX2B	Paired like homeobox 2b	Intracellular	27
HOXB6	Homeobox B6	Intracellular	25