4 Discussion
Applicating chromosome conformation capture-based high-throughput
approaches has greatly promoted the presentation of spatial chromatin
interaction architecture in mammals (Beagrie et al., 2017; Tjong et al.,
2016). In poultry, a few studies have also attempted to discover
higher-order chromatin structure using Hi-C technique (Veniamin et al.,
2018). Here, we advanced a high-resolution genome-wide analysis of
chromatin interactions in chicken liver cells. Our results revealed that
the spatial genome organization observed in chicken cells displayed a
typical paid-pattern without sharp transition between A- and B-
compartments, which appeared to be similar in several previously
mammalian species (Battulin et al., 2015; Dixon et al., 2012; Rao et
al., 2014). In chicken, we provided the concrete evidence of genome
partitioning of A/B compartments in both LDC and WCC, which was in
accord with findings in chicken
erythrocytes and
fibroblasts (Veniamin et al., 2018).
At the TAD scale, we found that LDC hepatocyte genomes contain
similar numbers of TADs and average
TAD size with WCC hepatocyte. This finding was inconsistent with an
earlier study between chicken erythrocytes and fibroblasts (Veniamin et
al., 2018), which might attribute to their markedly different cellular
properties. In support of this idea, heterogeneity of cancer cells could
contribute to more diverse 3D genomes and increase the detected TAD
numbers when compared with normal cells (Franke et al., 2016). We also
characterized the TAD boundaries, and obtained most of the same TAD
boundaries between two cells, which further confirmed accumulated tiny
but not sharp genomic genetic variations that contributed to extreme
environment adaption (Elbeltagy et al., 2017; Fleming et al., 2017;
Zhang et al., 2018b). More studies of 3D chicken genomes will further
elucidate the relationship between genome alterations and 3D genome
organization.
During cell biological process, such as cell differentiation, cancer
development, or stimulation response, the 3D architecture of the genome
is reorganized, which is connected with changes in gene expression and
epigenetic variations (Barutcu et al., 2015; Dixon et al., 2015; Rafique
et al., 2015; Taberlay et al., 2016). We found that about 5% of genome
regions switched between the A compartment and B compartment as making
comparative analysis between LDC and WCC 3D genome, which was associated
with changes in gene expression. Pathway enrichment analysis likewise
illustrated that some genes located in the switched compartments were
strongly associated with cell proliferation and differentiation, a
common adaptive response to extreme environment (Lindsey and Tropepe,
2014; Luger et al., 2003). Not surprisingly, Tight junction and
RIG-I-like receptor signaling pathway had been verified having a close
relationship with heat tolerance, with an integration between metabolic
and immune responses to ensure energy balance and permit growth and
defense (Bethany et al., 2018; Liu et al., 2017). Interestingly, Notch
signaling pathway was found not only involving in high temperature
response (Liu et al., 2017), but also had a strong correlation with cold
challenge (Kim et al., 2019; Wang et al., 2012), and played an extremely
important role in the adaption to hypoxic environment (Ishida et al.,
2013). Vascular smooth muscle contraction that includes vasoconstriction
and vasodilation is a process involved in cold acclimatization (Cardona
et al., 2014). Here we presented a list of cold adaption candidate genes
in vascular smooth muscle contraction, among which, ROCK2 and MYLK were
identified exaggerating vasoconstriction by directly phosphorylating
myosin light chains (Takashima, 2009; Walsh, 1994), under these
conditions, the validated interactions between ROCK2 and MYLK further
demonstrated their role in environment adaption (Pasha et al., 2015).
These genes in our selected pathways could be major targets for tropical
and frigid environment tolerance, and many of which can be understood
with further function analysis. Nonetheless, mechanisms allowing
adaption to the extreme environment are expected to be complex, and our
study partly provides insight into the extreme environment adaption.