Literature DB >> 18632762

Phosphorylation of the carboxy-terminal domain of histone H1: effects on secondary structure and DNA condensation.

Alicia Roque1, Inma Ponte, José Luis R Arrondo, Pedro Suau.   

Abstract

Linker histone H1 plays an important role in chromatin folding. Phosphorylation by cyclin-dependent kinases is the main post-translational modification of histone H1. We studied the effects of phosphorylation on the secondary structure of the DNA-bound H1 carboxy-terminal domain (CTD), which contains most of the phosphorylation sites of the molecule. The effects of phosphorylation on the secondary structure of the DNA-bound CTD were site-specific and depended on the number of phosphate groups. Full phosphorylation significantly increased the proportion of beta-structure and decreased that of alpha-helix. Partial phosphorylation increased the amount of undefined structure and decreased that of alpha-helix without a significant increase in beta-structure. Phosphorylation had a moderate effect on the affinity of the CTD for the DNA, which was proportional to the number of phosphate groups. Partial phosphorylation drastically reduced the aggregation of DNA fragments by the CTD, but full phosphorylation restored to a large extent the aggregation capacity of the unphosphorylated domain. These results support the involvement of H1 hyperphosphorylation in metaphase chromatin condensation and of H1 partial phosphorylation in interphase chromatin relaxation. More generally, our results suggest that the effects of phosphorylation are mediated by specific structural changes and are not simply a consequence of the net charge.

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Year:  2008        PMID: 18632762      PMCID: PMC2504289          DOI: 10.1093/nar/gkn440

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


INTRODUCTION

H1 linker histones are involved in chromatin structure and gene regulation (1). Histone H1 contains three distinct domains: a short amino-terminal domain (20−35 amino acids), a central globular domain (∼70 amino acids) and a long carboxy-terminal domain (CTD) (∼100 amino acids) (2). Several studies indicate that the ability of linker histones to stabilize chromatin folding resides in the CTD of the molecule (3). The CTD displays a high degree of conformational flexibility. In aqueous solution, the CTD is dominated by the random coil and turn-like conformations in rapid equilibrium with the unfolded state, but when it interacts with DNA it folds cooperatively. The DNA-bound structure is extremely stable and includes α-helix, β-sheet, turns and open loops (flexible regions) (4). The H1 CTD thus appears to belong to the so-called intrinsically disordered proteins undergoing coupled binding and folding (5–7). In addition, in the presence of macromolecular crowding agents the unbound CTD acquires the properties of a molten globule with native-like secondary structure and compaction (8). The phenotypic roles of histone H1 may be determined by complementary and overlapping effects of stoichiometry, subtype composition and post-translational modifications. Phosphorylation of the consensus sequences of cyclin-dependent kinases (CDKs), (S/T)-P-X-(K/R), is the main post-translational modification affecting histone H1 (9). In mammalian subtypes these sequences are localized mostly in the CTD. The maximum number of phosphate groups often corresponds to the number of CDK sites in the molecule. Histone H1 is phosphorylated in a cell cycle-dependent manner. The levels of phosphorylation are lowest in G1 and rise during S and G2 (10,11). During interphase, H1 subtypes are present as a mixture of unphosphorylated and low-phosphorylated species with a proportion of 35–75% of unphosphorylated forms, according to the particular subtype and cell line and the moment of the cell cycle. The highest number of phosphorylated sites is found in mitosis, when chromatin is maximally condensed. Phosphorylation of H1 variants may occur site-specifically during the phases of the cell cycle (12). It is not clear how H1 phosphorylation affects chromatin condensation during interphase and mitosis. A number of studies indicate that interphase phosphorylation is involved in chromatin relaxation (13–15); however, in metaphase chromosomes, H1 is hyperphosphorylated, and it has been shown that H1 hyperphosphorylation is required to maintain metaphase chromosomes in their condensed state (16). Here we report the effects of partial and full phosphorylation on the secondary structure of the CTD of histone H1 using IR spectroscopy. We have also estimated the relative affinities for the DNA and the DNA condensing capacity of the different phosphorylated species of the CTD. The results, showing site-specific effects depending on the number and position of phosphate groups may contribute to reconcile the roles of H1 phosphorylation in interphase and mitosis.

MATERIALS AND METHODS

Cloning, expression and purification of the CTD

The CTD of histones H1° and H1e were obtained from recombinant Escherichia coli (M15) as described previously (4). The sequence encoding the CTD of histone H1e was amplified from mouse genomic DNA by PCR. The primers used for the amplification reaction were 5′AAACTCCATATGAAGGCGGCTTCCGGTGAG3′ and 5′GAACTCGAGCTTTTTCTTGGCTGCTTT3′. The amplification products were cloned in the pET21 vector (Novagen; Darmstadt, Germany) using the NdeI and XhoI restriction sites to yield the expression vector pCTH1e. The recombinant protein was expressed in Escherichia coli BL21 and purified as described for the CTD of histone H1° (CH1°).

Construction of mutants of the CDK2 sites

The mutant clones for the CDK2 phosphorylation sites of the CH1° were obtained by PCR using the QuickChange Site-directed Mutagenesis Kit (Strategene; Amsterdam, Netherlands) following the manufacturer's instructions. The primers used for each phosphorylation site were mutated so that the threonine residue was changed to alanine. For threonine at position 118 the primers were 5′TCAAGAAAGTGGCAGCTCCAAAGAAGGCA3′ and 5′TGCCTTCTTTGGAGCTGCCACTTTCTTGA3′. For position T140 the primers were 5′AGAAACCCAAAGCCGCCCCTGTCAAGAAG3′ and 5′CTTCTTGACAGGGGCGGCTTTGGGTTTGGGTTTCT3′. For position T152 the primers were 5′GCTGCCGCGCCCAAGAAAGCAAAAAGCC3′ and 5′GGCTTTTTGGCTTTCTTGGGCGCGGCAGC3′. Double and triple mutants were obtained in successive rounds of PCR. The introduction of the correct mutation was evaluated by DNA sequencing of the recombinant clones. The recombinant plasmids were named according to the position mutated in each case. Clones were expressed and purified as described for the wild-type CTD.

In vitro phosphorylation assay

The CTD of histone H1 subtypes were phosphorylated in vitro with CDK2-cyclin A kinase (New England Biolabs; Ipswich, MA, USA). Phosphorylation reactions were carried out in 50 mM Tris.HCl, 10 mM MgCl2, 1 mM EGTA, 20mM dithiotreitol, pH 7.5, plus 200 µM ATP and 1 U of CDK2-cyclin A per 5 µg of CTD. The mixture was incubated at 30°C for 1 h and the reaction buffer was eliminated by gel filtration on a HiTrap desalting column (GE Healthcare; München, Germany). The extent of phosphorylation was evaluated by MALDI-TOF mass spectrometry.

IR spectroscopy

The CTD of histone H1 were measured at 50mg/ml in 10 mM HEPES, pH 7.0 plus 140 mM NaCl. DNA–protein complexes contained the appropriate amount of DNA for each protein/DNA ratio (w/w): Measurements were performed on a Nicolet Magna II 5770 spectrometer equipped with a MCT detector, using a demountable liquid cell with calcium fluorine windows and 50 μm spacers for D2O medium and 6 μm spacers for H2O medium measurements. Typically, 1000 scans for each background and sample were collected and the spectra were obtained with a nominal resolution of 2 cm−1, at 22°C. The protein concentration for the D2O measurements was 5 mg/ml, while for the H2O measurements it was 20 mg/ml. The spectra of the complexes were recorded both in H2O and D2O to facilitate the assignment of the amide I components (4). Data treatment and band decomposition were as previously described (17). The DNA contribution to the spectra of the complexes with the C-terminus was subtracted using a DNA sample of the same concentration; the DNA spectrum was weighted so as to cancel the symmetric component of the phosphate vibration at 1087 cm−1 in the difference spectra as described in (18).

Affinity measurements

The apparent relative affinities of the unphosphorylated and the different phosphorylated species of CH1° were estimated in competition experiments as previously described (19). The different forms of CH1° were made to compete with an approximately equal amount of the CTD of histone H1t (CH1t). A total of 3.0 μg of CTD was mixed with 0.5 μg of DNA in a final volume of 25 μl in 0.14 M NaCl, 0.01 M phosphate buffer, pH 7.0, 5% glycerol. The complexes were recovered by centrifugation at 14 000 g for 10 min. The protein composition of the complexes and of the free protein left in the supernatant was analyzed by SDS-PAGE and visualized by staining with Amido Black. The relative affinities were obtained with the expression: where the concentration of complexes, [iDNA] and [jDNA], was obtained from the band intensities in the pellets and the concentration of free protein, [i]free and [j]free, from the band intensities of the supernatants.

Band shift gel electrophoresis

Complexes were formed in 0.14 M NaCl, 10 mM phosphate buffer, pH 7.0 and incubated at room temperature for 30 min before separation on 1% agarose gels. The electrophoresis buffer was 36 mM Tris, 30 mM NaH2PO4, 1 mM EDTA, pH 7.7 (20). Gels were stained with ethidium bromide. The dsDNA fragment of 50 bp used in complex formation was obtained by annealing the oligonucleotide 5′CTATGATATATAGATAGTTAATGTAATATGATATAGATATAGGGATCC3′ with its complementary sequence. The dsDNA fragment of 108 bp was obtained from pUC19 by PCR using the primers 5′GCGGTTAGCTCCTTCGGTCCTC3′ and 5′GGATGGCATGACAGTAAGAGAA3′.

RESULTS

Conformational changes associated to full phosphorylation of the DNA-bound CTD of histone H1

The apparently conflicting roles of H1 phosphorylation suggest the existence of specific effects that depend on the number and position of phosphate groups. This led us to examine the secondary structure of the different phosphorylated forms of the DNA-bound CTD using IR spectroscopy. The CH1° contains three CDK sites. Phosphorylation of CH1° at all three sites brought about a large structural rearrangement characterized by a decrease in the proportion of α-helix and an increase in that of β-sheet (Figure 1; Table 1). The extent of the structural change appeared to be dependent on the protein to DNA ratio (, w/w). At = 0.25 or lower the α-helix decreased from 24% in the unphosphorylated CTD to 8% and the β-sheet increased from ∼24% to ∼36%. At = 0.5 the α-helix further decreased down to 6% and the β-sheet increased up to ∼46%. At = 0.7, which was approximately the saturation ratio, the CTD eventually became an all β protein, with no α-helix, ∼16% flexible regions, ∼20% turns and ∼74% β-sheet.
Figure 1.

Amide I decomposition of DNA-bound triphosphorylated CH1° at different protein/DNA ratio () (w/w). The spectra were measured in D2O. The buffer was 10 mM HEPES plus 140 mM NaCl, pH 7.0, at 20°C. The protein concentration was 5 mg/ml. The β-structure components are highlighted in blue.

Table 1.

Percentages of secondary structure of the DNA-bound triphosphorylated (3p) CH1°

Assignment3p
0p
r = 0.25
r = 0.5
r = 0.7
r = 0.7
D2O
H2O
D2O
H2O
D2O
H2O
D2O
H2O
Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%
Turns168111677616828
Turns168121679616701016808167141671916681316739
Turns166320166114166013166319165914166113165915166316
α-helix1654816536165024
α-helix/random coil16552116547165224
Flexible regions16412216462116466164018
Random coil/flexible regions16443516452316466163918
Random coila13200
Random coilb13100
β-sheet163024163228163331163326163652163745163016163016
Low frequency β-sheet161811161691620161619191623241624271617816189

The values corresponding to the unphosphorylated (0p) domain are included for comparison and were taken from Roque et al. (3). Band position (cm−1) and percentage area (%) and assignment of the components were obtained after curve fitting of the amide I band in D2O and H2O and in 140 mM NaCl. The values were rounded off to the nearest integer.

aThe value corresponds to the difference between the components at 1641–46 cm−1in D2O and H2O.

bThe value corresponds to the difference between the components at 1650–55 cm−1 in H2O and D2O.

Amide I decomposition of DNA-bound triphosphorylated CH1° at different protein/DNA ratio () (w/w). The spectra were measured in D2O. The buffer was 10 mM HEPES plus 140 mM NaCl, pH 7.0, at 20°C. The protein concentration was 5 mg/ml. The β-structure components are highlighted in blue. Percentages of secondary structure of the DNA-bound triphosphorylated (3p) CH1° The values corresponding to the unphosphorylated (0p) domain are included for comparison and were taken from Roque et al. (3). Band position (cm−1) and percentage area (%) and assignment of the components were obtained after curve fitting of the amide I band in D2O and H2O and in 140 mM NaCl. The values were rounded off to the nearest integer. aThe value corresponds to the difference between the components at 1641–46 cm−1in D2O and H2O. bThe value corresponds to the difference between the components at 1650–55 cm−1 in H2O and D2O. We also examined the secondary structure of the CTD of mouse H1e (CH1e), which shares only a 44% of sequence identity with CH1°. Like CH1°, it has three CDK sites. The unphosphorylated CH1e had a significantly higher starting proportion of α-helix (34%) and less β-structure (18%) than CH1° (Supplementary Figure 1, Table 1). Upon full phosphorylation, the amount of α-helix decreased and that of β-structure increased in function of , as in CH1°, but in contrast to the latter, the fully phosphorylated CH1e conserved a significant proportion of α-helix (17%) and the increase in β-structure was less pronounced (55%). Phosphorylation did not affect the overall conformation of the CTD free in solution. In physiological salt the conformation of both phosphorylated and unphosphorylated CTD was dominated by the random coil and turn conformations (Supplementary Table 2). Phosphorylation did not alter the proportions of secondary structure motifs in crowded conditions either (Supplementary Table 2). The specific structural changes promoted by phosphorylation appeared thus to be dependent on DNA interaction.

Site-specific effects of partial phosphorylation on the secondary structure of the DNA-bound CTD

In order to examine the effects of phosphorylation of one or two of the three TPXK sites present in CH1°, we prepared a series of single and double T→A mutants of the TPXK sites; so that, three monophosphorylated species, CH1°(p118), CH1°(p140) and CH1°(p152), and three diphosphorylated species, CH1°(p118p140), CH1°(p118p152) and CH1°(p140p152), were obtained. None of these T/A substitutions significantly altered the structure of the DNA-bound domains, as judged by the similarity of their spectra to that of the wild-type domain (Supplementary Table 3). Of the three CDK sites, phosphorylation of T118 affected the structure the most, leading to a decrease in the α-helix content from 24% to 10% and to the appearance of 18−20% of random coil, which was absent in the unphosphorylated domain (Figure 2, Table 2). This amount of random coil together with a ∼17% of flexible regions gave a significant 35% of undefined structure. The region upstream to the first phosphorylation site is known to be in a helical conformation in the unphosphorylated domain and is thus a clear candidate for destabilization by phosphorylation at this site (21). The amount of undefined structure in CH1°(p140) was also very high (36%), but in this case the flexible regions (27%) predominated over the random coil (9%) and the α-helix decreased only slightly (down to 19%). The structure of CH1°(p152) was the closest to that of the unphosporylated domain as the changes in the proportions of secondary structure motifs did not exceed 6%. Doubly phosphorylated domains had increased amounts of random coil/flexible regions (Figure 2, Table 3). Those containing pT118, i.e. CH1°(p118p140) and CH1°(p118p152), had a low proportion of α-helix (9−10%), while in CH1°(p140p152) it decreased only slightly (17%), which also suggests that pT118 has a central role in α-helix destabilization. All mono- and diphosphorylated species had similar amounts of β-structure (∼27%), which were only slightly higher than those of the unphosphorylated domain (∼24%). The secondary structure of the mono- and diphosphorylated species was not dependent on the protein to DNA ratio (Supplementary Table 4). The dependence of the conformation on thus appears as a specific property of the hyperphosphorylated species.
Figure 2.

Amide I decomposition of the DNA-bound CH1° phosphorylated at one or two positions. The numbers in parenthesis indicate the phosphorylated position. The spectra were measured in D2O. The buffer was 10 mM HEPES plus 140 mM NaCl, pH 7.0 at 20°C. The protein concentration was 5 mg/ml. The protein/DNA ratio (w/w) was 0.5. The α-helix component is highlighted in red and the random coil/flexible regions component is highlighted in orange.

Table 2.

Percentages of secondary structure of the DNA-bound monophosphorylated species (1p) of the CH1° at r = 0.5

Assignment1p(118)
1p(140)
1p(152)
D2O
H2O
D2O
H2O
D2O
H2O
Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%
Turns16822168321680116814
Turns167241675161672141674716711516727
Turns16612716651316626166111166113166014
α-helix165410165319165021
α-helix/random coil165630165529165622
Flexible regions164317164127164422
Random coil/flexible regions164335164036164020
Random coila1892
Random coilb20101
β-sheet16321716351816308162915163216163417
Low frequency β-sheet1624716221016223162211162212
Low frequency β-sheet1623716145161451614316142

Band position (cm−1) and percentage area (%) and assignment of the components were obtained after curve fitting of the amide I band in D2O and H2O and in 140 mM NaCl. The values were rounded off to the nearest integer.

The numbers in parenthesis indicate the phosphorylated positions.

aThe value corresponds to the difference between the components at 1640–44 cm−1 in D2O and H2O.

bThe value corresponds to the difference between the components at 1650–56 cm−1 in H2O and D2O.

Table 3.

Percentages of secondary structure of the DNA-bound diphosphorylated species (2p) of the CH1° at r = 0.5

Assignment2p(118/140)
2p(118/152)
2p(140/152)
D2O
H2O
D2O
H2O
D2O
H2O
Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%Band (cm−1)%
Turns168281681316822
Turns16721016726167213168051671916808
Turns16611916602516611316671816601316688
α-helix16501016539165017
α-helix/random coil165611165617165720
Flexible regions164426164331164427
Random coil/flexible regions164224164137164029
Random coila262
Random coilb183
β-sheet163018163317163011163312163116163219
Low frequency β-sheet16225162111162310162410162211162213
Low frequency β-sheet161561616116145161671615516155

Band position (cm−1) and percentage area (%) and assignment of the components were obtained after curve fitting of the amide I band in D2O and H2O and in 140 mM NaCl. The values were rounded off to the nearest integer. The numbers in parenthesis indicate the phosphorylated positions.

aThe value corresponds to the difference between the components at 1640–44 cm−1 in D2O and H2O.

bThe value corresponds to the difference between the components at 1650–57 cm−1 in H2O and D2O.

Amide I decomposition of the DNA-bound CH1° phosphorylated at one or two positions. The numbers in parenthesis indicate the phosphorylated position. The spectra were measured in D2O. The buffer was 10 mM HEPES plus 140 mM NaCl, pH 7.0 at 20°C. The protein concentration was 5 mg/ml. The protein/DNA ratio (w/w) was 0.5. The α-helix component is highlighted in red and the random coil/flexible regions component is highlighted in orange. Percentages of secondary structure of the DNA-bound monophosphorylated species (1p) of the CH1° at r = 0.5 Band position (cm−1) and percentage area (%) and assignment of the components were obtained after curve fitting of the amide I band in D2O and H2O and in 140 mM NaCl. The values were rounded off to the nearest integer. The numbers in parenthesis indicate the phosphorylated positions. aThe value corresponds to the difference between the components at 1640–44 cm−1 in D2O and H2O. bThe value corresponds to the difference between the components at 1650–56 cm−1 in H2O and D2O. Percentages of secondary structure of the DNA-bound diphosphorylated species (2p) of the CH1° at r = 0.5 Band position (cm−1) and percentage area (%) and assignment of the components were obtained after curve fitting of the amide I band in D2O and H2O and in 140 mM NaCl. The values were rounded off to the nearest integer. The numbers in parenthesis indicate the phosphorylated positions. aThe value corresponds to the difference between the components at 1640–44 cm−1 in D2O and H2O. bThe value corresponds to the difference between the components at 1650–57 cm−1 in H2O and D2O.

Phosphorylation had a small effect on the affinity of the CTD for the DNA

We examined the relative affinities of unphosphorylated CTD (0p), one monophosphorylated species (1p), CH1°(p118), one diphosphorylated species (2p), CH1°(p118p140) and the triphosphorylated species (3p). Relative affinities were estimated by competition of the different phosphorylated species of CH1° with an equivalent amount of the CH1t for a limited amount of DNA as previously described (Figure 3) (19). Phosphorylation caused a small decrease of the affinity of the CTD for the DNA, which was proportional to the number of phosphate groups. The apparent relative affinities were 1 (0p): 0.9 (1p): 0.7 (2p): 0.3 (3p). A higher effect was not expected on a purely electrostatic basis given the small proportion of the CH1° positive charge (40 lysine residues) represented by the incorporated phosphate groups (a maximum of three). In contrast, sea-urchin testis-specific H1 and H2B have most basic amino acids residues in their N-terminal regions in multiple SPKK sites; in this case, general Ser phosphorylation could effectively abolish the net charge of the entire N-terminal region and thus greatly weaken its interaction with DNA (22).
Figure 3.

Effect of phosphorylation of CH1° on relative affinity. Competitions of pairs of CTDs for a limited amount of DNA. (A) The unphosphorylated CH1° (0p), the fully phosphorylated species (3p), a diphosphorylated species, CH1°/p118p144 (2p) and a monophosphorylated species, CH1°/p118 (1p), were made to compete with the unphosphorylated CH1t. p, pellet; s, supernatant. (B) The relative affinities of CH1° species (in bold numbers) were obtained from their relative affinities for CH1t (in italics). The values are the average of three independent determinations.

Effect of phosphorylation of CH1° on relative affinity. Competitions of pairs of CTDs for a limited amount of DNA. (A) The unphosphorylated CH1° (0p), the fully phosphorylated species (3p), a diphosphorylated species, CH1°/p118p144 (2p) and a monophosphorylated species, CH1°/p118 (1p), were made to compete with the unphosphorylated CH1t. p, pellet; s, supernatant. (B) The relative affinities of CH1° species (in bold numbers) were obtained from their relative affinities for CH1t (in italics). The values are the average of three independent determinations.

Differential aggregation of DNA fragments by fully and partially phosphorylated CTD

The capacity of unphosphorylated CTD and its different phosphorylated species to aggregate DNA fragments was investigated by band-shift-gel-electrophoresis. With DNA fragments of 100 bp and = 0.5, the unphosphorylated CTD and all phosphorylated species formed large complexes that could not enter the gel (Figure 4A). Decreasing either the size of the DNA or the value revealed different aggregation capacities for the different CTD forms. Figure 4B and C shows bandshift assays with DNA fragments of 100 bp at = 0.25 and with DNA fragments of 50 bp at = 0.5. In both conditions, the unphosphorylated C-terminus aggregated the totality of the DNA fragments. Phosphorylation of either one or two sites decreased the aggregation capacity of the C-terminus significantly. Surprisingly, the hyperphosphorylated C-terminus regained to a large extent the aggregation capacity of the unphosphorylated C-terminus, displaying a strong aggregation band and little free DNA.
Figure 4.

Electrophoretic mobility shift assay of DNA fragments with CH1° and its phosphorylated species. Binding was carried out in physiological salt (0.14 M NaCl). (A) DNA of 100 bp and = 0.5; (B) DNA of 100 bp and = 0.25; (C) DNA of 50 bp and = 0.5. The arrow indicates the aggregates that do not enter the gel.

Electrophoretic mobility shift assay of DNA fragments with CH1° and its phosphorylated species. Binding was carried out in physiological salt (0.14 M NaCl). (A) DNA of 100 bp and = 0.5; (B) DNA of 100 bp and = 0.25; (C) DNA of 50 bp and = 0.5. The arrow indicates the aggregates that do not enter the gel. Electron microscopy of the DNA complexes confirmed the bandshift results. The complexes had varied morphologies, but the aggregates formed with either unphosphorylated or fully phosphorylated CTD were consistently larger and denser than those with partially phosphorylated species (Supplementary Figure 2).

DISCUSSION

We have shown that full phosphorylation of the DNA-bound CTD brings about a large structural change consisting in a significant increase in β-structure accompanied by a decrease in α-helix. The effect is apparent at the lowest values ( = 0.15), but is favored by the saturation of the DNA lattice, suggesting that protein-protein interactions contribute to the conformational transition. Partial phosphorylation induces in general a large proportion of undefined structure (random coil and flexible regions), but, in contrast to full phosphorylation, it does not lead to a significant increase in β-structure. The increase of β-sheet content and the loss of α-helical structure in the H1 CTD following full phosphorylation is a kind of structural conversion similar to that observed in amyloidogenic proteins during fibril formation (23). In prion encephalopaties, the analogy can be pushed further as it has been shown that interaction with DNA converts the α-helical cellular isoform into a β-isoform similar to that found in the fibrilar state (24). Furthermore, H1 has been found associated to amyloid-like fibrils (25). The effects of phosphorylation on the affinity of the CTD for the DNA were moderate: a three-fold decrease for the fully phosphorylated domain and smaller effects for the mono- and diphosphorylated species. It is interesting to note that in spite of its lower affinity for DNA, the fully phosphorylated domain showed a higher aggregation capacity of DNA fragments than the partially phosphorylated species. The aggregation capacity of the fully phosphorylated species was indeed nearly as high as that of the unphosphorylated domain. The high condensing capacity of the fully phosphorylated species might have a structural basis. A general feature of the sequences of the CTD of H1 histones is the large proportion of basic residues present as doublets: about 75% in mammalian somatic subtypes. In β-sheets, consecutive side chains project alternatively above and below the sheet-like structure. It is likely that the abundance of Lys doublets together with the β-sheet structure generates a binding motif with two cationic surfaces, particularly in the hyperphosphorylated CTD. Such a structure seems well suited to the electrostatic crosslinking of two segments of DNA. The site-specificity of the effects of phosphorylation on the secondary structure and DNA condensing capacity of the CTD, together with the moderate effect of phosphorylation on the affinity for the DNA, suggest that the effects of phosphorylation are mediated by specific structural changes and are not a simple effect of the net charge. According to this, the properties of hyperphosphorylated H1 would not represent the extreme of a continuous variation in molecular properties depending on the number of phosphates, but would be determined by the specific structures associated with full phosphorylation. The reasons for general H1 hyperphosphorylation in metaphase chromosomes remain unclear. However, the specific structural features, in particular the high β-sheet content and the higher aggregation capacity of the fully phosphorylated domain suggest that hyperphosphorylation may play a role, together with other condensing factors, in metaphase chromatin condensation. Conversely, the loss of defined structure and the lower condensing capacity of some mono- and diphosphorylated species could explain the relaxing effect of partially phosphorylated H1 on chromatin structure during interphase, particularly in S phase. Some reports support the occurrence of opposite effects of moderate as opposed to full phosphorylation. SV40 minichromosomes reconstituted with either unphosphorylated or hyperphosphorylated H1 were more compact and less efficient as substrate in in vitro replication compared with minichromosomes reconstituted with moderately phosphorylated H1 (26). It has been suggested that hyperphosphorylation of histone H1 and H3 leads to inhibition of glucocorticoid receptor-mediated chromatin remodeling and inactivation of the mouse mammary tumor virus (MMTV) promoter by preventing the association of transcription factors with the promoter in vivo. In contrast, a moderate amount of H1 phosphorylation contributes significantly to the induction of transcription from the MMTV promoter (27). It has also been shown that phosphorylation of only one site within the CTD of H1b severely disrupts the interaction between H1b and the heterochromatin protein 1α (HP1α), a key component of mammalian heterochromatin (28). Chromatin condensation associated with hyperphosphorylation in metaphase chromosomes may be structurally and mechanistically distinct from other condensed chromatin states associated with unphosphorylated H1, such as those of chicken erythrocyte nuclei (29), sea urchin sperm (30), Tetrahymena macronuclei or interphase heterochromatin (31). Figure 5 shows a schematic representation of some H1 related factors that may be involved in the transition between relaxed and condensed chromatin in different systems.
Figure 5.

H1 related factors involved in the transition between relaxed and condensed chromatin.

H1 related factors involved in the transition between relaxed and condensed chromatin.

SUPPLEMENTARY DATA

Supplementary Data are available at NAR Online.
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1.  Rapid exchange of histone H1.1 on chromatin in living human cells.

Authors:  M A Lever; J P Th'ng; X Sun; M J Hendzel
Journal:  Nature       Date:  2000-12-14       Impact factor: 49.962

Review 2.  Structure and dynamics of membrane proteins as studied by infrared spectroscopy.

Authors:  J L Arrondo; F M Goñi
Journal:  Prog Biophys Mol Biol       Date:  1999       Impact factor: 3.667

Review 3.  Linker histone binding and displacement: versatile mechanism for transcriptional regulation.

Authors:  J Zlatanova; P Caiafa; K Van Holde
Journal:  FASEB J       Date:  2000-09       Impact factor: 5.191

Review 4.  Revisiting the structure and functions of the linker histone C-terminal tail domain.

Authors:  Xu Lu; Jeffrey C Hansen
Journal:  Biochem Cell Biol       Date:  2003-06       Impact factor: 3.626

5.  Induction of secondary structure in a COOH-terminal peptide of histone H1 by interaction with the DNA: an infrared spectroscopy study.

Authors:  R Vila; I Ponte; M Collado; J L Arrondo; P Suau
Journal:  J Biol Chem       Date:  2001-06-18       Impact factor: 5.157

6.  Inhibition of histone phosphorylation by staurosporine leads to chromosome decondensation.

Authors:  J P Th'ng; X W Guo; R A Swank; H A Crissman; E M Bradbury
Journal:  J Biol Chem       Date:  1994-04-01       Impact factor: 5.157

7.  DNA converts cellular prion protein into the beta-sheet conformation and inhibits prion peptide aggregation.

Authors:  Y Cordeiro; F Machado; L Juliano; M A Juliano; R R Brentani; D Foguel; J L Silva
Journal:  J Biol Chem       Date:  2001-10-16       Impact factor: 5.157

8.  Extended disordered proteins: targeting function with less scaffold.

Authors:  Kannan Gunasekaran; Chung-Jung Tsai; Sandeep Kumar; David Zanuy; Ruth Nussinov
Journal:  Trends Biochem Sci       Date:  2003-02       Impact factor: 13.807

Review 9.  Mammalian prion biology: one century of evolving concepts.

Authors:  Adriano Aguzzi; Magdalini Polymenidou
Journal:  Cell       Date:  2004-01-23       Impact factor: 41.582

10.  The dynamic mobility of histone H1 is regulated by cyclin/CDK phosphorylation.

Authors:  Alejandro Contreras; Tracy K Hale; David L Stenoien; Jeffrey M Rosen; Michael A Mancini; Rafael E Herrera
Journal:  Mol Cell Biol       Date:  2003-12       Impact factor: 4.272

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  27 in total

1.  N- and C-terminal domains determine differential nucleosomal binding geometry and affinity of linker histone isotypes H1(0) and H1c.

Authors:  Payal Vyas; David T Brown
Journal:  J Biol Chem       Date:  2012-02-10       Impact factor: 5.157

Review 2.  The H1 linker histones: multifunctional proteins beyond the nucleosomal core particle.

Authors:  Sonja P Hergeth; Robert Schneider
Journal:  EMBO Rep       Date:  2015-10-15       Impact factor: 8.807

3.  Open and closed: the roles of linker histones in plants and animals.

Authors:  Ryan S Over; Scott D Michaels
Journal:  Mol Plant       Date:  2013-11-22       Impact factor: 13.164

4.  Emergence of chromatin hierarchical loops from protein disorder and nucleosome asymmetry.

Authors:  Akshay Sridhar; Stephen E Farr; Guillem Portella; Tamar Schlick; Modesto Orozco; Rosana Collepardo-Guevara
Journal:  Proc Natl Acad Sci U S A       Date:  2020-03-12       Impact factor: 11.205

5.  Nucleosome linker DNA contacts and induces specific folding of the intrinsically disordered H1 carboxyl-terminal domain.

Authors:  Tamara L Caterino; He Fang; Jeffrey J Hayes
Journal:  Mol Cell Biol       Date:  2011-04-04       Impact factor: 4.272

Review 6.  dBigH1, a second histone H1 in Drosophila, and the consequences for histone fold nomenclature.

Authors:  Rodrigo González-Romero; Juan Ausio
Journal:  Epigenetics       Date:  2014-03-12       Impact factor: 4.528

Review 7.  Post-translational modifications of the intrinsically disordered terminal domains of histone H1: effects on secondary structure and chromatin dynamics.

Authors:  A Roque; I Ponte; P Suau
Journal:  Chromosoma       Date:  2016-04-21       Impact factor: 4.316

8.  Structured States of Disordered Proteins from Genomic Sequences.

Authors:  Agnes Toth-Petroczy; Perry Palmedo; John Ingraham; Thomas A Hopf; Bonnie Berger; Chris Sander; Debora S Marks
Journal:  Cell       Date:  2016-09-22       Impact factor: 41.582

9.  Site-specifically phosphorylated forms of H1.5 and H1.2 localized at distinct regions of the nucleus are related to different processes during the cell cycle.

Authors:  Heribert Talasz; Bettina Sarg; Herbert H Lindner
Journal:  Chromosoma       Date:  2009-07-16       Impact factor: 4.316

10.  Histone H1 phosphorylation is associated with transcription by RNA polymerases I and II.

Authors:  Yupeng Zheng; Sam John; James J Pesavento; Jennifer R Schultz-Norton; R Louis Schiltz; Sonjoon Baek; Ann M Nardulli; Gordon L Hager; Neil L Kelleher; Craig A Mizzen
Journal:  J Cell Biol       Date:  2010-05-03       Impact factor: 10.539

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