3.4 │ Networks of histone H1 subtypes-partner proteins interactions
Networks of histone H1 subtypes-partner proteins interactions were extracted from STRING database (v11.0) and introduced to the Cytoscape software (v3.8.0) for further analysis. A comparison of several topological parameters obtained by MCM function of Network Analyzer plugin indicate on an overall similarity of the networks (F = 0.613, p = 0.654) (Table 4). Although that some of analyzed topological parameters, such as characteristic path length, clustering coefficient, centralization and heterogeneity, possess the roughly similar numeric values, the differences are noticeable among the others. Because the networks sizes are defined ambiguously, e.g. small sized contain less than 10 – 20 nodes 29, small- and medium sized contain 50 – 500 nodes 30 and small to large sized contain 100 – 1000 nodes 31, a concrete determination of H1 networks scales is rather intuitive because they differ three to four times on average. The subtype H1.1, H1.2 and H1.4 (126, 86 and 92 nodes) belong to greater networks compared to small scale networks of subtype H1.3 and H1.5 (30 and 47 nodes). Likewise, a network connectivity expressed by the average number of neighbors also differentiate the histone H1 subtype-interacting protein networks. The average connectivity of node, strongly related to the network resilience32, is about two and three times higher in the network of subtype H1.1 (13.872) and H1.4 (11.525) than in the network of subtype H1.5 (6.718) and H1.3 (3.6). These values characteristic of subtype H1.3 and H1.5 interaction network are also lower that of the subtype H1.2 (9.02). This indicate that the networks created by histone H1 subtypes differ in their compaction. Because highly connected nodes do not have a higher density 33, the networks of subtype H1.1, H1.2 and H1.4 are more sparse than that of more dense of subtype H1.3 and H1.5. Another parameter, i.e. connected components indicating a connectivity of the network, is comparable for the networks of subtype H1.2, H1.3, H1.4 and H1.5 (in the range from 8 to 12), but its value is much lower (amounting 3) for the network created by histone H1.1. This pointing to a stronger connectivity of H1.1 subtype network compared to the networks of subtypes H1.2 – H1.5 34and simultaneously reflecting their tendency to an increased fragmentation to the separated clusters. 35 Most relevant neighborhood of histone H1 in the networks were identified by construction the active subnetworks using Diffusion algorithm of Cytoscape. In the vast majority, they contain proteins which GO terms that were predicted by CELLO2GO as associated with processes involved in the metabolism of DNA and regulation of its activity. It seems that in the DNA-dependent processes histone H1 subtypes displays a similar activity realized, however, by interactions with different proteins. The only one protein, i.e. DNA fragmentation factor subunit beta, turned out to be a component of subnetworks formed by subtypes H1.1, H1.3 and H1.5 (Table 5).
To find a highly connected nodes (hub proteins) with essential biological properties in the histone H1 subtypes-protein interaction networks, the MCM method of cytoHubba plugin was adopted. With the help of this tool, a top hub proteins of the networks were ranked (Table 6). An overview of the functions of selected proteins allow to designate the cell processes in which histone H1 subtypes might operate in common with their partnering proteins. Based on a similarity of molecular function and biological process of identified hubs, the histone H1 subtypes may be divided into three categories. First class includes subtypes H1.1 and H1.4 having five common proteins which, just like other top hubs, are involved in the RNA binding and biogenesis of ribosome. Second class contain subtypes H1.3 and H1.5 possessing three same proteins engaged in the control and regulation of cell cycle as well as in the cell division, similarly to the rest of the hubs. Third class encompass a single subtype H1.2 interacting with proteins responsible of protein ubiquitination and degradation. It should be noticed that among five histone H1 subtypes, the only subtype H1.3 was designated as a hub in the network. This suggest its critical role in the maintenance of the network structure. 36 Thus, according to the centrality-lethality rule 37, histone H1.3 may be recognized as functionally significant since its lack may disturb a pathway function. 38 Moreover, a comparison of topological parameters values presented in the Table 6, indicated a disparity between the network constructed with subtype H1.1 and the networks created with subtype H1.3 and H1.5. A statistically significant difference was determined for a closeness centrality (H1.1 – H1.3 p < 0.05 and H1.1 – H1.5 p < 0.01), clustering coefficient (H1.1 – H1.3 p < 0.05 and H1.1 – H1.5 p < 0.05) and a neighborhood connectivity (H1.1 – H1.3 p < 0.001 and H1.1 – H1.5 p < 0.001). Such a distinctions between the networks hubs suggest functional dissimilarity between histone H1.1 and histone H1.3 and H1.5.