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).