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• W2809650930 abstract "There is renewed interest in linker histone (LH)—nucleosome binding and how LHs influence eukaryotic DNA compaction. For a long time, the goal was to uncover “the structure of the chromatosome,” but recent studies of LH-nucleosome complexes have revealed an ensemble of structures. Notably, the reconstituted LH-nucleosome complexes used in experiments rarely correspond to the sequence combinations present in organisms. For a full understanding of the determinants of the distribution of the chromatosome structural ensemble, studies must include a complete description of the sequences and experimental conditions used, and be designed to enable systematic evaluation of sequence and environmental effects. There is renewed interest in linker histone (LH)—nucleosome binding and how LHs influence eukaryotic DNA compaction. For a long time, the goal was to uncover “the structure of the chromatosome,” but recent studies of LH-nucleosome complexes have revealed an ensemble of structures. Notably, the reconstituted LH-nucleosome complexes used in experiments rarely correspond to the sequence combinations present in organisms. For a full understanding of the determinants of the distribution of the chromatosome structural ensemble, studies must include a complete description of the sequences and experimental conditions used, and be designed to enable systematic evaluation of sequence and environmental effects. In eukaryotes, DNA is wrapped around core histone protein oligomers to form chromatin (Kornberg, 1974Kornberg R.D. Chromatin structure: a repeating unit of histones and DNA.Science. 1974; 184: 868-871Crossref PubMed Scopus (1634) Google Scholar). For cell function, it is crucial to dynamically compact the genetic material—which is about 2 m long in humans—in such a way that specific genes for transcription can be accessed when required (Taube and Barton, 2006Taube J.H. Barton M.C. Chromatin and regulation of gene expression.in: Ma J. Gene Expression and Regulation. Springer, 2006: 95-109Crossref Google Scholar). Despite more than 30 years of research, the mechanism of higher-order chromatin compaction is not fully resolved (van Holde and Zlatanova, 2007van Holde K. Zlatanova J. Chromatin fiber structure: where is the problem now?.Semin. Cell Dev. Biol. 2007; 18: 651-658Crossref PubMed Scopus (85) Google Scholar, Grigoryev and Woodcock, 2012Grigoryev S.A. Woodcock C.L. Chromatin organization — the 30nm fiber.Exp. Cell Res. 2012; 318: 1448-1455Crossref PubMed Scopus (98) Google Scholar). The repeating unit of chromatin, the nucleosome, is composed of a nucleosome core flanked by two linker DNA (L-DNA) arms. The nucleosome core consists of 145–147 bp of nucleosomal DNA (N-DNA) wrapped around a histone octamer composed of two copies of each of the core histone proteins H2A, H2B, H3, and H4 (Klug et al., 1980Klug A. Rhodes D. Smith J. Finch J.T. Thomas J.O. A low resolution structure for the histone core of the nucleosome.Nature. 1980; 287: 509-516Crossref PubMed Scopus (224) Google Scholar, Luger et al., 1997Luger K. Mäder A.W. Richmond R.K. Sargent D.F. Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 A resolution.Nature. 1997; 389: 251-260Crossref PubMed Scopus (6884) Google Scholar). In addition to the core histones, a linker histone (LH) protein, H1 or H5, can bind to the nucleosome between the two L-DNA arms to form a chromatosome (Pruss et al., 1996Pruss D. Bartholomew B. Persinger J. Hayes J. Arents G. Moudrianakis E.N. Wolffe A.P. An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres.Science. 1996; 274: 614-617Crossref PubMed Scopus (164) Google Scholar, Zhou et al., 2013Zhou B.-R. Feng H. Kato H. Dai L. Yang Y. Zhou Y. Bai Y. Structural insights into the histone H1-nucleosome complex.Proc. Natl. Acad. Sci. USA. 2013; 110: 19390-19395Crossref PubMed Scopus (147) Google Scholar, Zhou et al., 2015Zhou B.-R. Jiang J. Feng H. Ghirlando R. Xiao T.S. Bai Y. Structural mechanisms of nucleosome recognition by linker histones.Mol. Cell. 2015; 59: 628-638Abstract Full Text Full Text PDF PubMed Scopus (151) Google Scholar, Flanagan et al., 2016Flanagan T.W. Files J.K. Casano K.R. George E.M. Brown D.T. Photobleaching studies reveal that a single amino acid polymorphism is responsible for the differential binding affinities of linker histone subtypes H1.1 and H1.5.Biol. Open. 2016; 5: 016733Crossref Scopus (17) Google Scholar). Chromatosomes were first revealed by digestion of chromatin by a non-specific nuclease to consist of the nucleosome core, about 20 bp of L-DNA and one LH (Simpson, 1978Simpson R.T. Structure of the chromatosome, a chromatin particle containing 160 base pairs of DNA and all the histones.Biochemistry. 1978; 17: 5524-5531Crossref PubMed Scopus (443) Google Scholar). The chromatosome can therefore be considered as a fundamental unit of the chromatin structure (Widom, 1998Widom J. Chromatin structure: linking structure to function with histone H1.Curr. Biol. 1998; 8: R788-R791Abstract Full Text Full Text PDF PubMed Google Scholar), and the determination of the three-dimensional structure of this subnucleosomal particle has been a longstanding goal. LHs are composed of about 200 amino acid residues, and contain three distinct domains, a short (∼40 residues) unstructured N-terminal tail, a relatively conserved globular domain (GD) (∼80 residues), and a basic disordered C-terminal tail (∼100 residues) (Roque et al., 2016Roque A. Ponte I. Suau P. Interplay between histone H1 structure and function.Biochim. Biophys. Acta. 2016; 1859: 444-454Crossref PubMed Scopus (31) Google Scholar). Previous studies have shown that, even though the N- and C-terminal tails can affect the affinity and geometry of LH-nucleosome binding (Hutchinson et al., 2015Hutchinson J.B. Cheema M.S. Wang J. Missiaen K. Finn R. Gonzalez Romero R. Th’ng J.P.H. Hendzel M. Ausió J. Interaction of chromatin with a histone H1 containing swapped N- and C-terminal domains.Biosci. Rep. 2015; 35: e00209Crossref PubMed Scopus (10) Google Scholar), they do not appear to affect the position of the LH GD (Syed et al., 2010Syed S.H. Goutte-Gattat D. Becker N. Meyer S. Shukla M.S. Hayes J.J. Everaers R. Angelov D. Bednar J. Dimitrov S. Single-base resolution mapping of H1-nucleosome interactions and 3D organization of the nucleosome.Proc. Natl. Acad. Sci. USA. 2010; 107: 9620-9625Crossref PubMed Scopus (157) Google Scholar, Zhou et al., 2016Zhou B.-R. Feng H. Ghirlando R. Li S. Schwieters C.D. Bai Y. A small number of residues can determine if linker histones are bound on or off dyad in the chromatosome.J. Mol. Biol. 2016; 428: 3948-3959Crossref PubMed Scopus (36) Google Scholar). Furthermore, both the GD and the full-length LH protect the same L-DNA from micrococcal nuclease digestion (Puigdomènech et al., 1983Puigdomènech P. José M. Ruiz-Carrillo A. Crane-Robinson C. Isolation of a 167 basepair chromatosome containing a partially digested histone H5.FEBS Lett. 1983; 154: 151-155Crossref PubMed Scopus (16) Google Scholar). Thus, the position of the LH on the chromatosome is mainly governed by the LH GD. For this reason, and because of the difficulties of studying disordered regions of proteins, most in vitro studies aimed at revealing the structure of the chromatosome have been focused on LH GD-nucleosome complexes. Recent research has shown that LH proteins have a range of functions, including roles in DNA replication, epigenetic regulation, genome stability, and DNA repair (for a recent review see Fyodorov et al., 2017Fyodorov D.V. Zhou B.-R. Skoultchi A.I. Bai Y. Emerging roles of linker histones in regulating chromatin structure and function.Nat. Rev. Mol. Cell Biol. 2017; 19: 192-206Crossref PubMed Scopus (222) Google Scholar). Higher eukaryotes have a family of LH proteins consisting of a number of variants, also referred to as subtypes, which have a relatively conserved GD and more variable N and C termini (Kowalski and Pałyga, 2016Kowalski A. Pałyga J. Modulation of chromatin function through linker histone H1 variants.Biol. Cell. 2016; 108: 339-356Crossref PubMed Scopus (17) Google Scholar). It has been shown that LH variants can have different functions, tissue expression levels, and DNA binding affinities (Millán-Ariño et al., 2016Millán-Ariño L. Izquierdo-Bouldstridge A. Jordan A. Specificities and genomic distribution of somatic mammalian histone H1 subtypes.Biochim. Biophys. Acta. 2016; 1859: 510-519Crossref PubMed Scopus (43) Google Scholar, Parseghian, 2015Parseghian M.H. What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery.Biophys. 2015; 2: 724-772Crossref Scopus (24) Google Scholar, Parseghian and Hamkalo, 2001Parseghian M.H. Hamkalo B.A. A compendium of the histone H1 family of somatic subtypes: an elusive cast of characters and their characteristics.Biochem. Cell Biol. 2001; 79: 289-304Crossref PubMed Scopus (106) Google Scholar). In mammals, there are seven standard H1 subtypes with varying sequence conservation, chromatin binding affinity, and genomic distribution (Kowalski and Pałyga, 2016Kowalski A. Pałyga J. Modulation of chromatin function through linker histone H1 variants.Biol. Cell. 2016; 108: 339-356Crossref PubMed Scopus (17) Google Scholar). H1 LH proteins have been shown to be essential for mouse development (Pan and Fan, 2016Pan C. Fan Y. Role of H1 linker histones in mammalian development and stem cell differentiation.Biochim. Biophys. Acta. 2016; 1859: 496-509Crossref PubMed Scopus (45) Google Scholar). For example, even though a single H1 isoform knockout did not result in any significant phenotypic change, deletion of three isoforms was shown to be embryonically lethal (Drabent et al., 2000Drabent B. Saftig P. Bode C. Doenecke D. Spermatogenesis proceeds normally in mice without linker histone H1t.Histochem. Cell Biol. 2000; 113: 433-442Crossref PubMed Scopus (83) Google Scholar, Fan et al., 2001Fan Y. Sirotkin A. Russell R.G. Ayala J. Skoultchi A.I. Individual somatic H1 subtypes are dispensable for mouse development even in mice lacking the H1(0) replacement subtype.Mol. Cell. Biol. 2001; 21: 7933-7943Crossref PubMed Scopus (141) Google Scholar, Fan et al., 2003Fan Y. Nikitina T. Morin-Kensicki E.M. Zhao J. Magnuson T.R. Woodcock C.L. Skoultchi A.I. H1 linker histones are essential for mouse development and affect nucleosome spacing in vivo.Mol. Cell. Biol. 2003; 23: 4559-4572Crossref PubMed Scopus (238) Google Scholar). On the other hand, studies in unicellular eukaryotes, such as Aspergillus nidulans and Tetrahymena thermophila, have indicated that knockout of the sole H1 isoform is not lethal but can cause some genes to be up- or downregulated (Ramón et al., 2000Ramón A. Muro-Pastor M.I. Scazzocchio C. Gonzalez R. Deletion of the unique gene encoding a typical histone H1 has no apparent phenotype in Aspergillus nidulans.Mol. Microbiol. 2000; 35: 223-233Crossref PubMed Scopus (65) Google Scholar, Shen and Gorovsky, 1996Shen X. Gorovsky M.A. Linker histone H1 regulates specific gene expression but not global transcription in vivo.Cell. 1996; 86: 475-483Abstract Full Text Full Text PDF PubMed Scopus (273) Google Scholar). Furthermore, it was previously reported that LHs behave as regulators of specific genes by affecting nucleosome spacing (Fan et al., 2003Fan Y. Nikitina T. Morin-Kensicki E.M. Zhao J. Magnuson T.R. Woodcock C.L. Skoultchi A.I. H1 linker histones are essential for mouse development and affect nucleosome spacing in vivo.Mol. Cell. Biol. 2003; 23: 4559-4572Crossref PubMed Scopus (238) Google Scholar). Even with many biological and physiological roles being associated with the LH, its function remains enigmatic. However, recent breakthroughs in the determination of LH-nucleosome structures, coupled with a growing number of epigenetic studies, open up the possibility of achieving a thorough understanding of the mechanism of formation of LH-nucleosome complexes (for a recent review see Cutter and Hayes, 2017Cutter A.R. Hayes J.J. Linker histones: novel insights into structure-specific recognition of the nucleosome.Biochem. Cell Biol. 2017; 95: 171-178Crossref PubMed Scopus (21) Google Scholar). Here, we compare the five recently determined three-dimensional structures of LH-nucleosome complexes (Bednar et al., 2017Bednar J. Garcia-Saez I. Boopathi R. Cutter A.R. Papai G. Reymer A. Syed S.H. Lone I.N. Tonchev O. Crucifix C. et al.Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1.Mol. Cell. 2017; 66: 384-397.e8Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar, Song et al., 2014Song F. Chen P. Sun D. Wang M. Dong L. Liang D. Xu R.-M. Zhu P. Li G. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.Science. 2014; 344: 376-380Crossref PubMed Scopus (394) Google Scholar, Zhou et al., 2013Zhou B.-R. Feng H. Kato H. Dai L. Yang Y. Zhou Y. Bai Y. Structural insights into the histone H1-nucleosome complex.Proc. Natl. Acad. Sci. USA. 2013; 110: 19390-19395Crossref PubMed Scopus (147) Google Scholar, Zhou et al., 2015Zhou B.-R. Jiang J. Feng H. Ghirlando R. Xiao T.S. Bai Y. Structural mechanisms of nucleosome recognition by linker histones.Mol. Cell. 2015; 59: 628-638Abstract Full Text Full Text PDF PubMed Scopus (151) Google Scholar, Zhou et al., 2016Zhou B.-R. Feng H. Ghirlando R. Li S. Schwieters C.D. Bai Y. A small number of residues can determine if linker histones are bound on or off dyad in the chromatosome.J. Mol. Biol. 2016; 428: 3948-3959Crossref PubMed Scopus (36) Google Scholar) (see Figure 1), and consider what can be learnt from these experimentally determined structures, as well as from modeling and simulation studies. Our analysis suggests that the different structures of LH-nucleosome complexes revealed in these studies can be reconciled by a paradigm shift away from the concept of “the structure of the chromatosome” toward “the structural ensemble distributions of individual chromatosomes,” in which alternative configurations of LH-nucleosome complex structures can exist. In particular, these configurations differ in the position and orientation of the LH GD with respect to the nucleosome. Our analysis also highlights the importance of comprehensive documentation of protein and DNA sequences and post-translational modifications (PTMs) in future studies of LH-nucleosome complexes. Reconstitution of nucleosomes requires certain conditions that are far from physiological conditions, such as 2 M salt concentration, as well as suitable DNA and protein sequences (Luger et al., 1999Luger K. Rechsteiner T.J. Richmond T.J. Expression and purification of recombinant histones and nucleosome reconstitution.Methods Mol. Biol. 1999; 119: 1-16PubMed Google Scholar). Obtaining chromatosomes in a form suitable for structure determination has been difficult. As can be seen in Table 1, the systems studied have a combination of DNA, core histone, and LH sequences of different origins and DNA and protein constructs of different lengths. Moreover, the LH-nucleosome complexes were reconstituted and their structures determined under a range of environmental conditions, with different LH-nucleosome ratios, with different buffers and at different pH values and temperatures. Bednar et al., 2017Bednar J. Garcia-Saez I. Boopathi R. Cutter A.R. Papai G. Reymer A. Syed S.H. Lone I.N. Tonchev O. Crucifix C. et al.Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1.Mol. Cell. 2017; 66: 384-397.e8Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar even used a chaperone, the NAP-1 histone chaperone, for reconstitution of LH-nucleosome complexes. Notably, the nucleosomes were reconstituted using salt dialysis against a gradually decreasing high salt buffer, the LH-nucleosome complexes were reconstituted by incubation at various ionic strength conditions, and the structural measurements were made at salt concentrations ranging from about 10 mM up to close to physiological ionic strength (Table 1). On the other hand, Schlick and colleagues showed that salt and LH concentration, L-DNA length, the presence of oligo-nucleosome systems, and synergistic folding of the LH C-terminal domain affect chromatin condensation and LH contacts with L-DNAs (Luque et al., 2014Luque A. Collepardo-Guevara R. Grigoryev S. Schlick T. Dynamic condensation of linker histone C-terminal domain regulates chromatin structure.Nucleic Acids Res. 2014; 42: 7553-7560Crossref PubMed Scopus (47) Google Scholar, Luque et al., 2016Luque A. Ozer G. Schlick T. Correlation among DNA linker length, linker histone concentration, and histone tails in chromatin.Biophys. J. 2016; 110: 2309-2319Abstract Full Text Full Text PDF PubMed Scopus (21) Google Scholar, Perišić and Schlick, 2017Perišić O. Schlick T. Dependence of the linker histone and chromatin condensation on the nucleosome environment.J. Phys. Chem. B. 2017; 121: 7823-7832Crossref PubMed Scopus (17) Google Scholar). Thus, the heterogeneity of the studied systems should be borne in mind in considering the relevance of results with these in vitro systems for understanding chromatosome and chromatin structure in cell nuclei.Table 1Experimentally Determined Structures of LH-Nucleosome ComplexesReferencesZhou et al., 2013Zhou B.-R. Feng H. Kato H. Dai L. Yang Y. Zhou Y. Bai Y. Structural insights into the histone H1-nucleosome complex.Proc. Natl. Acad. Sci. USA. 2013; 110: 19390-19395Crossref PubMed Scopus (147) Google ScholarSong et al., 2014Song F. Chen P. Sun D. Wang M. Dong L. Liang D. Xu R.-M. Zhu P. Li G. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units.Science. 2014; 344: 376-380Crossref PubMed Scopus (394) Google ScholarZhou et al., 2015Zhou B.-R. Jiang J. Feng H. Ghirlando R. Xiao T.S. Bai Y. Structural mechanisms of nucleosome recognition by linker histones.Mol. Cell. 2015; 59: 628-638Abstract Full Text Full Text PDF PubMed Scopus (151) Google ScholarZhou et al., 2016Zhou B.-R. Feng H. Ghirlando R. Li S. Schwieters C.D. Bai Y. A small number of residues can determine if linker histones are bound on or off dyad in the chromatosome.J. Mol. Biol. 2016; 428: 3948-3959Crossref PubMed Scopus (36) Google ScholarBednar et al., 2017Bednar J. Garcia-Saez I. Boopathi R. Cutter A.R. Papai G. Reymer A. Syed S.H. Lone I.N. Tonchev O. Crucifix C. et al.Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1.Mol. Cell. 2017; 66: 384-397.e8Abstract Full Text Full Text PDF PubMed Scopus (155) Google ScholarExperimental DetailsStructure determination methodsNMR, PREITC, HADDOCKcryo-EMultracentrifugationNMR, ITC, X-rayFRET, ultracentrifugationNMR, ITCHADDOCKultracentrifugationcryo-EM, X-rayOH footprint, CL147-bpN-DNAsynthetic DNAWidom 601synthetic DNAWidom 601synthetic DNAWidom 601synthetic DNAWidom 601synthetic DNAWidom 601Widom 601 LaThe Widom 601L N-DNA sequence is the palindrome of the left half of the Widom 601 N-DNA sequence.No. ofL-DNA bpbThe number of bp for each L-DNA arm is given, e.g., 10 + 10 denotes L-DNA1 with 10 bp and L-DNA2 with 10 bp.10 + 1030 + 3015 + 1520 + 2010 + 1010 + 1030 + 3025 + 25CorehistonesD. melanogasterX. laevisD. melanogasterD. melanogasterH. sapiensLinker histone (LH)cResidue ranges are given in parentheses.D. melanogaster H1 (WT, 37-132, 45–119, 37–211, 37–256)H. sapiens H1.4G. gallus H5 (22–98, 24–98, 22–102 and 22–142)D. melanogaster (WT and 44–118),X. laevis H1WT and mutant G. gallus H5 (24–98)D. melanogaster H1 (WT and 45–119)X. laevis H1.0H. sapiens H1.0X. laevis H1.0bH. sapiens H1.5 (1–177 and 40–112)Environmental conditions for LH-nucleosome structural measurementsdThe ionic strength is classified as low: ca. 10–20 mM, and medium: ca. 100–150 mM.low IS, pH 6.0–7.4low IS, pH 8.0NMR: low IS, X-ray, ITCFRET: medium IS, pH 3.75–8.0NMR: low ISITC: medium IS, pH 7.4–8.0Cryo-EM: low ISX-ray: medium IS, pH 6.4Resolution (Å)–11 and 253.5–5.5 (X-ray)Structure DetailsBasis for nucleosome structurenucleosome from PDB: 1ZBB and 1KX5cryo-EM map fitted with nucleosome PDB: 1AOI and 1ZBBelectron density fitted with nucleosome PDB: 4INM and 3MVDDNA from PDB: 4QLCelectron density fitted with nucleosome PDB: 3UT9N-DNAH. sapiensX chromosomeα satellite DNApalindromic 147 bpH. sapiensX chromosomeα satellite DNApalindromic 146 bpsynthetic DNAWidom 601147 bpsynthetic DNAWidom 601147 bpsynthetic DNAWidom 601 LaThe Widom 601L N-DNA sequence is the palindrome of the left half of the Widom 601 N-DNA sequence.145 bpNo. of L-DNA bpbThe number of bp for each L-DNA arm is given, e.g., 10 + 10 denotes L-DNA1 with 10 bp and L-DNA2 with 10 bp.10 + 1015 + 1520 + 2010 + 100 + 026 + 26Core histonesX. laevisX. laevisD. melanogasternoneX. laevisCH tailsyesnonononoModeled LH sequenceD. melanogaster H1G. gallus H5G. gallus H5G. gallus H5,D. melanogaster H1X. laevis H1.0bModeled LH structurefrom closed G. gallus LHPDB: 1HST, chain Bfrom open G. gallus LHPDB: 1HST, chain Afrom closed G. gallus LHPDB: 1HST, chain BH5, from closed G. gallus LHPDB: 1HST, chain BH1, from closed G. gallus LHPDB: 1HST, chain Bfrom closed G. gallus LHPDB: 1HST, chain BLH positionoff-dyadoff-dyadon-dyadon-dyadoff-dyadon-dyadPDB ID of model4QLC5NL0The methods used and the sequences studied are given, followed by the details of the structural models derived from the experimental results.CH, core histone; N-DNA, nucleosomal DNA; L-DNA, linker DNA; NMR, nuclear magnetic resonance; PRE, paramagnetic relaxation enhancement; ITC, isothermal titration calorimetry; HADDOCK, High Ambiguity-Driven protein-protein DOCKing; cryo-EM, cryoelectron microscopy; X-ray, X-ray crystallography; FRET, Förster resonance energy transfer; OH footprint, hydroxyl radical footprinting; CL, chemical crosslinking; WT, wild-type.a The Widom 601L N-DNA sequence is the palindrome of the left half of the Widom 601 N-DNA sequence.b The number of bp for each L-DNA arm is given, e.g., 10 + 10 denotes L-DNA1 with 10 bp and L-DNA2 with 10 bp.c Residue ranges are given in parentheses.d The ionic strength is classified as low: ca. 10–20 mM, and medium: ca. 100–150 mM. Open table in a new tab The methods used and the sequences studied are given, followed by the details of the structural models derived from the experimental results. CH, core histone; N-DNA, nucleosomal DNA; L-DNA, linker DNA; NMR, nuclear magnetic resonance; PRE, paramagnetic relaxation enhancement; ITC, isothermal titration calorimetry; HADDOCK, High Ambiguity-Driven protein-protein DOCKing; cryo-EM, cryoelectron microscopy; X-ray, X-ray crystallography; FRET, Förster resonance energy transfer; OH footprint, hydroxyl radical footprinting; CL, chemical crosslinking; WT, wild-type. The nucleosome systems vary in the lengths of the L-DNA arms, which each range from 10 to 30 bp. The sequences of the N-DNA and L-DNA can influence the binding location and the orientation of the LH, which may interact directly with one or both of the L-DNA arms (Öztürk et al., 2016Öztürk M.A. Pachov G.V. Wade R.C. Cojocaru V. Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.Nucleic Acids Res. 2016; 44: 6599-6613Crossref PubMed Scopus (30) Google Scholar). The first chromatosome structure solved (Zhou et al., 2013Zhou B.-R. Feng H. Kato H. Dai L. Yang Y. Zhou Y. Bai Y. Structural insights into the histone H1-nucleosome complex.Proc. Natl. Acad. Sci. USA. 2013; 110: 19390-19395Crossref PubMed Scopus (147) Google Scholar) had a Widom 601 DNA sequence and core histone proteins from Drosophila melanogaster. A common component of the recent structural nucleosome studies is the synthetic 147-bp Widom 601 N-DNA sequence that wraps around the core histones and has a strong core histone octamer binding affinity (Lowary and Widom, 1998Lowary P.T. Widom J. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning.J. Mol. Biol. 1998; 276: 19-42Crossref PubMed Scopus (1202) Google Scholar). The choice of Widom 601 sequence, albeit unnatural, allowed researchers to obtain more stable nucleosomes (Tóth et al., 2013Tóth K. Böhm V. Sellmann C. Danner M. Hanne J. Berg M. Barz I. Gansen A. Langowski J. Histone- and DNA sequence-dependent stability of nucleosomes studied by single-pair FRET.Cytometry A. 2013; 83: 839-846Crossref PubMed Scopus (36) Google Scholar), thereby facilitating structure determination. To the best of our knowledge, the first published report of the sequence of Widom 601 DNA was given in the study of Schalch et al., 2005Schalch T. Duda S. Sargent D.F. Richmond T.J. X-Ray structure of a tetranucleosome and its implications for the chromatin fibre.Nature. 2005; 436: 138-141Crossref PubMed Scopus (594) Google Scholar. A palindromic variant, Widom 601 L, with higher core histone octamer affinity (L indicates that it was generated from the left half of the Widom 601 sequence), was also used by (Bednar et al., 2017Bednar J. Garcia-Saez I. Boopathi R. Cutter A.R. Papai G. Reymer A. Syed S.H. Lone I.N. Tonchev O. Crucifix C. et al.Structure and dynamics of a 197 bp nucleosome in complex with linker histone H1.Mol. Cell. 2017; 66: 384-397.e8Abstract Full Text Full Text PDF PubMed Scopus (155) Google Scholar, Chua et al., 2012Chua E.Y.D. Vasudevan D. Davey G.E. Wu B. Davey C.A. The mechanics behind DNA sequence-dependent properties of the nucleosome.Nucleic Acids Res. 2012; 40: 6338-6352Crossref PubMed Scopus (123) Google Scholar). In the published studies of the structures of LH-nucleosome complexes, the core histones vary in origin, as shown in Table 1. The core histones have flexible tails, which are present in the sequences used in the experiments but often missing in the final structures determined. The extent to which the flexible tails affect LH binding is unknown. Öztürk et al., 2016Öztürk M.A. Pachov G.V. Wade R.C. Cojocaru V. Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome.Nucleic Acids Res. 2016; 44: 6599-6613Crossref PubMed Scopus (30) Google Scholar found that off-dyad binding would mean little interaction of the Gallus gallus gH5 with core histone tails. On the other hand, Zhou et al., 2013Zhou B.-R. Feng H. Kato H. Dai L. Yang Y. Zhou Y. Bai Y. Structural insights into the histone H1-nucleosome complex.Proc. Natl. Acad. Sci. USA. 2013; 110: 19390-19395Crossref PubMed Scopus (147) Google Scholar reported that D. melanogaster H1 methyl groups are affected by paramagnetic relaxation enhancement (PRE) labeling of T119 in the H2A tail, and that the disordered C-terminal tail of H2A folds upon LH binding. These results suggest that further research is required to understand the effects of the core histone tails on LH binding to the nucleosome. Experimentally, the LHs have been studied as full-length proteins and as GD constructs of varying lengths and, in some cases, with mutations to improve stability or switch key isoform residues. The N- and C-terminal domains are highly flexible and, therefore, their removal can be expected to facilitate crystallization. The experimental methods used vary in the level of detail and the amount of information that they provide, as well as the associated uncertainties (for a recent review, see Mackay et al., 2017Mackay J.P. Landsberg M.J. Whitten A.E. Bond C.S. Whaddaya know: a guide to uncertainty and subjectivity in structural biology.Trends Biochem. Sci. 2017; 42: 155-167Abstract Full Text Full Text PDF PubMed Scopus (11) Google Scholar). For the first structure of an LH-nucleosome complex determined, Zhou et al., 2013Zhou B.-R. Feng H. Kato H. Dai L. Yang Y. Zhou Y. Bai Y. Structural insights into the histone H1-nucleosome complex.Proc. Natl. Acad. Sci. USA. 2013; 110: 19390-19395Crossref PubMed Scopus (147) Google Scholar mutated four residues of the D. melanogaster H1 GD and obtained a more stable LH domain, similar to the G. gallus H5 GD. By using a gel shift assay and isothermal titration calorimetry (ITC), they showed that various mutant D. melanogaster H1 constructs (residues 37–132, 45–119, 37–211, and 37–256) have the same nucleosome binding affinities. The authors derived experimental constraints with nuclear magnetic resonance (NMR) shifts and PRE for wild-type and mutant D. melanogaster H1 binding to a nucleosome. The structure of the D. melanogaster H1 GD was modeled by homology, based on the closed conformation of the G. gallus H5 GD in the crystal structure (PDB: 1HST, chain B) and a structural model of an LH GD-nucleosome complex was obtained by docking the LH GD and nucleosome with the HADDOCK program (Dominguez et al., 2003Dominguez C. Boelens R. Bonvin A.M.J.J. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.J. Am. Chem. Soc. 2003; 125: 1731-1737Crossref PubMed Scopus (2168) Google Scholar) using a small number of restraints derived from the combined experimental results. It should be noted that, even though Zhou et al., 2013Zhou B.-R. Feng H. Kato H. Dai L. Yang Y. Zhou Y. Bai Y. Structural insights into the histone H1-nucleosome complex.Proc. Natl. Acad. Sci. USA. 2013; 110: 19390-19395Crossref PubMed Scopus (147) Google Scholar did their experiments with a Widom 601 N-DNA sequence, in their docking calculations they used the nucleosome structure with PDB: 1ZBB, whose DNA sequence is not Widom 601 but a palindromic sequence extracted from PDB: 1KX5 (Schalch et al., 2005Schalch T. Duda S. Sargent D.F. Richmond T.J. X-Ray structure of a tetranucleosome and its implications for the chromatin fibre.Nature. 2005; 436: 138-141Crossref PubMed Scopus (594) Google Scholar). Later, Zhou et al., 2016Zhou B.-R. Feng H. Ghirlando R. Li S. Schwieters C.D. Bai Y. A small number of residues can determine if linker histones are bound on or off dyad in the chromatosome" @default.
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