3.5.4 Neural wiring
A range of genes and functional categories involved in neural wiring,
including cell migration and adhesion, and neurite growth and synapse
formation were affected by CO2 treatment, also mostly
exhibiting an upregulation in the CNS (Table 3). There was small,
coordinated upregulation of genes involved in cell migration functional
categories, including ‘motor activity’, ‘actin binding’, ‘cell adhesion’
and ‘integrin complex’. Those genes positively correlated with
CO2 treatment and all three activity traits in the CNS
were enriched for similar functional categories: ‘actin filament
binding’, ‘myosin complex’, ‘myofibril’, ‘motor activity’ and ‘ruffle
membrane’. Genes with a role specifically in neuron migration and
adhesion, and the related processes of dendrite and axon outgrowth and
branching, dendritic spine formation, and synapse formation were also
positively correlated with CO2 treatment and activity
(rac1, ptpr, adgrb3, apbb1). One gene involved in neurite
growth and branching (futsch) was negatively correlated with
CO2 treatment and activity traits.
3.5.5
Transcription, RNA processing, and protein processing
There was generally an upregulation of genes and functional categories
involved in transcription, RNA processing and protein processing in the
CNS, and to a smaller extent in the eyes (Table 4). In the CNS, there
was small, coordinated upregulation of genes belonging to functional
categories involved in transcription, including ‘DNA duplex unwinding’,
and its’ daughter term ‘3’-5’ DNA helicase activity’ was enriched in
those genes positively correlated with CO2 treatment and
all three activity traits (Figure 5). There was small, coordinated
upregulation in the CNS of genes belonging to the functional category
‘nuclear pore’, and ‘nuclear pore’ was also enriched for those genes
positively correlated with CO2 treatment and all three
activity traits in the CNS (Figure 5). Genes involved in transcription
were also DE; nme6, chrac1 and znf271 were upregulated in
the CNS, and gtf2e2 downregulated in the eyes. There was small,
coordinated upregulation of genes involved in ‘RNA processing’, ‘mRNA
processing’ and ‘rRNA processing’, as well as functional categories
involved in the processes and components of the spliceosome, which
excises introns to produce mature mRNA (Figure 3). Components of the
spliceosome (snrpa, snrnp200) were also identified as
correlated with CO2 treatment and behaviours (Table 4).
A range of genes and functional categories involved in protein
synthesis, folding and degradation/turnover were significantly
upregulated in the CNS, and some were also upregulated in the eyes.
Small, coordinated upregulation of genes involved in the initiation and
process of translation as well as in functional categories for ribosomal
components occurred in both tissues (Figure 3). Genes with similar
functions were also positively correlated with CO2 treatment and activity traits in the CNS, including translation
initiation factors (eif3b, eif3d), an elongation factor
(eef1g), and ribosomal components (rpl23a, rpl4, rpl7l, rps27a). Genes involved in protein translocation
(stt3a, rpn1, rpn2, tmed2), and protein folding and quality
control (pdia3, pdia4, pdia5, hspa5) were correlated with
CO2 treatment and behaviours in the CNS. The endoplasmic
reticulum associated degradation (ERAD) pathway involves protein
ubiquitination followed by proteasomal degradation and we found a range
of genes involved in this process to be affected by CO2 treatment. There was small, coordinated upregulation of genes in the
‘endoplasmic reticulum’ and five ubiquitin-related functional categories
in the CNS, of ‘proteasome complex’ in both tissues, and of ‘peptide
metabolic process’ in the eyes. Genes positively correlated with
CO2 treatment and all three activity traits were
enriched for ‘endoplasmic reticulum lumen’ and included genes coding for
E3 ubiquitin ligases (cblb, ttc3) and a subunit for the 26S
proteasome (rpn1). A gene coding for an E3 ubiquitin ligase
(syvn1- b) was also upregulated in the CNS. Lysosomal degradation
is another method for protein turnover, and a gene essential for
lysosomal function (ykt6) was upregulated in both the CNS and
eyes.