3.3 │ Functions of histone H1 subtypes interacting proteins
The four main functional categories of H1 partner proteins indicated in the SIFTER database include enzymatic activity and binding of the proteins, DNA and RNA (Figure 4). Although proportions of proteins assigned to a given functional category were detected as statistically insignificant between histone H1 subtypes (F = 0, p = 1), a distribution of proteins representing various activities is non-uniform. This suggest that H1 subtypes are differently engaged in the protein and nucleic acids-dependent events. Histone H1.2, H1.3 and H1.5, having more than 50% interacting proteins responsible of protein binding, might more frequently realize its function via protein-protein interaction than through the interaction with nucleic acids, due to that their partner proteins are able to bind them in at most 10%. A binding of proteins is attributed to the chromatin builders, e.g. histone H2A-Bbd type 2/3 and histone H3.3, and regulators, e.g. PHD finger protein 6 and protein-lysine 6-oxidase, but also to the factors involved in the protein degradation by ubiquitination, e.g. cullin 4B and cullin 5. The other proteins are engaged in cell adhesion and signaling, e.g. intercellular adhesion molecule 1 and integrin alpha-4, as well as in the control of cell cycle, e.g. G1/S-specific cyclin-E1 and G2/mitotic-specific cyclin-B1. Whereas proteins which bind to the DNA are poorly represented among the partners of H1 histones, in an amount not exceed 10%, the RNA binding proteins are more abundant. Histones H1.1 and H1.4 are an examples of H1 subtypes displaying 21% and 34% interactions, respectively, with RNA binding partners. They include proteins that bind to the mRNA, e.g. UAP56-interacting factor, tRNA, e.g. lupus LA protein, and rRNA, eg. RNA-binding motif protein 19, thus, they might be directly involved in the biogenesis of the RNA. Moreover a group of these RNA-binding proteins, alike 60 ribosomal protein L37 and cellular nucleic acid-binding protein, are the components of translation machinery. Also, among the partners of H1 histones are proteins displaying the enzymatic activity, mainly such that modify histones, e.g. N-methyltransferase, H3 lysine-79 specific and histone acetyltransferase KAT2B, as well as the DNA, e.g. DNA (cytosine-5)-methyltransferase 3B, and RNA, e.g. ribosomal RNA-processing protein 8. Among the miscellaneous functions assigned to histone H1 interacting proteins, mostly represented is protein homodimerization activity, characteristic for the partners of all H1 subtypes. Likewise a zinc ion binding is represented by proteins interacting with four H1 subtypes. Besides functions assigned to the proteins interacting with several H1 histones, there are also functions characteristic of a given subtype only. For example, chromatin binding is attributable for proteins partnering subtype H1.3 and transmembrane signaling receptor for the partners of subtype H1.5. However, a highest number of partners having various functions possess subtype H1.2. Among them are nucleosome binding, protein heterodimerization activity and magnesium ion binding that are not represented by partners of other H1 subtypes. In this context, histone H1.2 can be perceived as peculiar subtype, participating in the processes specific only for them. A selective function that regard histone H1.2 is related, for instance, to its ability of gene silencing by forming compacted chromatin structure together with repressive transcription complex PRC2.28
Functional characterization of analyzed proteins as per the GO terms was done with CELLO2GO (Table 1). Among the molecular function corresponding to the proteins interacting with all of H1 subtypes is ion binding (GO:0043167), DNA binding (GO:0003677), RNA binding (GO:0003723) and kinase activity (GO:0016301). A rest of top molecular functions was assigned to the proteins that are partners for particular H1 subtypes only. For partner proteins of four (H1.1, H1.3, H1.4 and H1.5) and three (H1.1, H1.2 and H1.4) histone H1 subtypes, a hydrolase activity (GO:0016787) and structural constituent of ribosome (GO:0003735), respectively, is attributed. A transferase activity (GO:0016740) is characteristic for proteins interacting with subtype H1.3 and H1.5 while protein binding (GO:0005515) correspond to the partners of subtype H1.2. However, the differences in the abundance of proteins with a given GO term that interact with particular H1 subtype may suggest its weaker and/or stronger preferences to fulfill a specific function. Thus, in contrast to other H1 histones, the subtype H1.1 and H1.4 should be more effective in the binding RNA and forming structure of the ribosome. Likewise, binding of DNA can be mostly attributed to the subtype H1.2. Only two biological processes, i.e. biosynthetic (GO:0009058) and cellular nitrogen compound metabolic (GO:0034641), were indicated in the comparable proportions as related to the proteins partnering all of histone H1 subtypes. The interacting proteins of four histone H1 subtypes (H1.2, H1.3, H1.4 and H1.5) take part in the cellular protein modifications (GO:0036211), similarly to the proteins interacting with the subtype H1.1, H1.3, H1.4 and H1.5 that are involved in the signal transduction (GO:0007165). Both biological processes were detected as comparably abundant among histone H1 interacting proteins. A less frequently represented are biological processes characteristic of proteins interacting with a lower number of H1 subtypes. Besides translation (GO:0006412) assigned to the proteins interacting with subtype H1.1, H1.2 and H1.4, there are also processes characteristic of proteins partnering a single H1 subtype. Based on this, some of H1 subtypes might individually participate in the characteristic biological processes, i.e. H1.3 in the cell adhesion (GO:0007155) and a response to stress (GO:0006950) as well as H1.5 in the cell division (GO:0051301). A cell, nucleus and organelle was selected as main cellular component for all histone H1 interacting proteins. However, unlike the others H1 subtypes, subtype H1.4 possess partner proteins designated as a component of the ribosome. This may confirm a participation of this H1 subtype in the biological processes linked to the ribosome, i.e. ribosome biogenesis and translation, which were found as associated with its partnering proteins. A similar molecular functions and biological processes of proteins partnering the subtype H1.4 were recorded as enrichment by g:GOSt algorithm (Table 2). They include mainly molecular functions and biological processes coupled to the RNA binding and metabolism. The same analysis revealed a shared molecular functions of proteins interacting with histone H1.1 and H1.4, suggesting a functional closeness of both subtypes. Such a proximity may be also attributed to the subtype H1.1 and H1.2 due to an engagement of its partners in the chromosome organization (GO:0051276) and chromatin organization (GO:0006325). Interestingly, histone H1.2 as the only H1 subtype interact with proteins displaying enriched molecular function and biological process referring to the ubiquitin-dependent events, i.e. ubiquitin protein ligase binding (GO:0031625), ubiquitin-like protein ligase binding (GO:0044389) and protein modification by small protein conjugation (GO:0032446). The above findings that concern biological process and molecular function of proteins partnering histone H1 subtypes are closely associated with the pathways indicated in the Reactome database (Table 3).