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.