The histones of the sperm of Spisula solidissima include a novel, cysteine-containing H-1 histone

Functional genomics in Spiralia

Our understanding of the mechanisms that modulate gene expression in animals is strongly biased by studying a handful of model species that mainly belong to three groups: Insecta, Nematoda and Vertebrata. However, over half of the animal phyla belong to Spiralia, a morphologically and ecologically diverse animal clade with many species of economic and biomedical importance. Therefore, investigating genome regulation in this group is central to uncovering ancestral and derived features in genome functioning in animals, which can also be of significant societal impact. Here, we focus on five aspects of gene expression regulation to review our current knowledge of functional genomics in Spiralia. Although some fields, such as single-cell transcriptomics, are becoming more common, the study of chromatin accessibility, DNA methylation, histone post-translational modifications and genome architecture are still in their infancy. Recent efforts to generate chromosome-scale reference genome assemblies for greater species diversity and optimise state-of-the-art approaches for emerging spiralian research systems will address the existing knowledge gaps in functional genomics in this animal group.

Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin

Variants of the histone H2A occupy distinct locations in the genome. There is relatively little known about the mechanisms responsible for deposition of specific H2A variants. Notable exceptions are chromatin remodelers that control the dynamics of H2A.Z at promoters. Here we review the steps that identified the role of a specific class of chromatin remodelers, including LSH and DDM1 that deposit the variants macroH2A in mammals and H2A.W in plants, respectively. The function of these remodelers in heterochromatin is discussed together with their multiple roles in genome stability.

Sirtuins and Sepsis: Cross Talk between Redox and Epigenetic Pathways

Sepsis and septic shock are the leading causes of death among hospitalized patients in the US. The immune response in sepsis transitions from a pro-inflammatory and pro-oxidant hyper-inflammation to an anti-inflammatory and cytoprotective hypo-inflammatory phase. While 1/3rd sepsis-related deaths occur during hyper-, a vast majority of sepsis-mortality occurs during the hypo-inflammation. Hyper-inflammation is cytotoxic for the immune cells and cannot be sustained. As a compensatory mechanism, the immune cells transition from cytotoxic hyper-inflammation to a cytoprotective hypo-inflammation with anti-inflammatory/immunosuppressive phase. However, the hypo-inflammation is associated with an inability to clear invading pathogens, leaving the host susceptible to secondary infections. Thus, the maladaptive immune response leads to a marked departure from homeostasis during sepsis-phases. The transition from hyper- to hypo-inflammation occurs via epigenetic programming. Sirtuins, a highly conserved family of histone deacetylators and guardians of homeostasis, are integral to the epigenetic programming in sepsis. Through their anti-inflammatory and anti-oxidant properties, the sirtuins modulate the immune response in sepsis. We review the role of sirtuins in orchestrating the interplay between the oxidative stress and epigenetic programming during sepsis.

A Synthetic Approach to Reconstruct the Evolutionary and Functional Innovations of the Plant Histone Variant H2A.W

Diversification of histone variants is marked by the acquisition of distinct motifs and functional properties through convergent evolution.1-4 H2A variants are distinguished by specific C-terminal motifs and tend to be segregated within defined domains of the genome.5,6 Whether evolution of these motifs pre-dated the evolution of segregation mechanisms or vice versa has remained unclear. A suitable model to address this question is the variant H2A.W, which evolved in plants through acquisition of a KSPK motif7 and is tightly associated with heterochromatin.4 We used fission yeast, where chromatin is naturally devoid of H2A.W, to study the impact of engineered chimeras combining yeast H2A with the KSPK motif. Biochemical assays showed that the KSPK motif conferred nucleosomes with specific properties. Despite uniform incorporation of the engineered H2A chimeras in the yeast genome, the KSPK motif specifically affected heterochromatin composition and function. We conclude that the KSPK motif promotes chromatin properties in yeast that are comparable to the properties and function of H2A.W in plant heterochromatin. We propose that the selection of functional motifs confer histone variants with properties that impact primarily a specific chromatin state. The association between a new histone variant and a preferred chromatin state can thus provide a setting for the evolution of mechanisms that segregate the new variant to this state, thereby enhancing the impact of the selected properties of the variant on genome activity.

Chromatin architectural proteins

The accessibility of eukaryotic DNA is dependent upon the hierarchical level of chromatin organization. These include (1) intra-nucleosome interactions, (2) inter-nucleosome interactions and (3) the influence of non-histone chromatin architectural proteins. There appears to be interplay between all these levels, in that one level can override another or that two or more can act in concert. In the first level, the stability of the nucleosome itself is dependent on the number and type of contacts between the core histones and the surrounding DNA, as well as protein-protein interactions within the core histone octamer. Core histone variants, post-translational modifications of the histones, and linker histones binding to the DNA all influence the organization and stability of the nucleosome. When nucleosomes are placed end-to-end in linear chromatin arrays, the second level of organization is revealed. The amino terminal tails of the histone proteins make contacts with adjacent and distant nucleosomes, both within the fiber and between different fibers. The third level of organization is imposed upon these 'intrinsic' constraints, and is due to the influence of chromatin binding proteins that alter the architecture of the underlying fiber. These chromatin architectural proteins can, in some cases, bypass intrinsic constraints and impart their own topological affects, resulting in truly unique, supra-molecular assemblages that undoubtedly influence the accessibility of the underlying DNA. In this review we will provide a brief summary of what has been learned about the intrinsic dynamics of chromatin fibers, and survey the biology and architectural affects of the handful of chromatin architectural proteins that have been identified and characterized. These proteins are likely only a small subset of the architectural proteins encoded within the eukaryotic genome. We hope that an increased understanding and appreciation of the contribution of these proteins to genome accessibility will hasten the identification and characterization of more of these important regulatory factors.

The sperm-specific proteins of the edible oyster (European flat oyster (Ostrea edulis)) are products of proteolytic processing

Extraction of sperm proteins from the bivalve mollusc Ostrea edulis shows them to contain a normal complement of core histones, together with three sperm-specific proteins, OE1 and OE2, plus the shorter OE3, which shows substantial microheterogeneity. OE1 and OE2 have a very similar amino acid composition, cyanogen bromide (CNBr) cleavage yields products of identical size and possesses a trypsin-resistant core peptide, together indicating that they are closely homologous histone H1-like proteins. Western blotting shows that OE1 and OE2 are closely related to the histone H1-like protein PL-II* of Mytilus trossulus. The amino acid composition of OE3 shows it to be a protamine-like PL-IV type protein. Edman degradation of a CNBr peptide from OE2 gave the sequence (M)KAAFAKGLKSGALVRPKGS-which has 85% identity to a sequence located towards the C-terminal end of the globular domain of the PL-II* protein of M. trossulus. An O. edulis sperm cDNA library yielded a clone of 428 bp. A genomic clone including an open reading frame (ORF) of 750 bp was isolated by PCR amplification from genomic DNA. Hypothetical translation showed the ORF to encode OE1 (or OE2) immediately followed by OE3, separated by a proteolytic processing site. This arrangement (a two-protein ORF) is also found in M. trossulus and Ensis minor.

Cysteine-containing histone H1-like (PL-I) proteins of sperm

We have determined the presence of cysteine in the protein PL-I from the sperm of the surf clam Spisula solidissima. The existence of cysteine in this histone H1-related protein is responsible for its previously described aggregation behavior. The location of this residue, within the trypsin-resistant domain of the protein, has been established. We have also shown that cysteine is ubiquitously present in the PL-I proteins from the sperm of other bivalve mollusks but is absent from other PL of smaller molecular mass (PL-II, PL-III, PL-IV). We have also found cysteine to be present in the PL-I from a tunicate (Chelysoma productum) but absent in a PL-I from a fish (Mullus barbatus). The possible significance of the unusual occurrence of cysteine in these histone-H1-related proteins is discussed.

Histone H1 variants as sperm-specific nuclear proteins of Rana catesbeiana, and their role in maintaining a unique condensed state of sperm chromatin

Amino acid analyses of nuclear basic proteins of an anuran amphibian, Rana catesbeiana, revealed that they are comprised of a full set of core histones and three types of lysine-rich, sperm-specific proteins. On the basis of their amino-acid compositions and partial amino-acid sequences of their trypsin-resistant cores, the sperm-specific proteins could be defined as members of the histone H1 family. Both micrococcal nuclease digestion and electron microscopy indicated that sperm chromatin consists of nucleosomal and fibrillar DNA structures which are irregularly interspersed with each other. When sperm nuclei were incubated with nucleoplasmin, nuclei decondensed to some extent, and the sperm-specific H1s were removed, but not completely. The residual sperm-specific histone H1 variants were also found in reconstituted male pronuclear chromatin, comprising regularly spaced nucleosomes. We conclude that sperm-specific histone H1 variants are essential for chromatin condensation in the sperm nuclei, but that their complete removal is not necessary for the remodeling into somatic chromatin that takes place after fertilization.

A precursor-product relationship in molluscan sperm proteins from Ensis minor

A cDNA library prepared from mRNA extracted from immature male gonads of the bivalve mollusc Ensis minor (razor shell) was probed with a 133-bp reverse-transcriptase PCR product corresponding to a segment of the sperm protein EM6 [Giancotti, V., Russo, E., Gasparini, M., Serrano, D., Del Piero, D., Thorne, A. W., Cary, P.D. & Crane-Robinson, C. (1993) Eur. J. Biochem. 136, 509-516]. A single 1.5-kb clone was found to encode both sperm proteins EM1 and EM6. Mass spectrometry was used to define the C-terminus of EM1, and since the N-terminus of EM6 is known from Edman degradation, this showed that the pentapeptide NTNNS must be lost on proteolytic processing. Both EM1 and EM6 contain highly repeated amino acid sequences, suggestive of extended structures. EM1 contains seven tandem repeats of the dipeptide S(K/R), followed by six potential cdc2 phosphorylation sites and seven repeats of the octapeptide KRSASKKR, with occasional K/R substitutions. EM6 contains a globular domain preceded by 17 almost identical uninterupted tandem repeats of the motif KKRSXSRKRSAS, where X is charged. Its C-terminus contains 15 short basic clusters. Assignment of EM1 and EM6 to the established categories of molluscan sperm proteins [PLI, PLII, PLIII, PLIV; Ausio, J. (1992) Mol. Cell. Biochem. 115, 163-172] is discussed.

Molluscan sperm proteins: Ensis minor

The three major proteins, EM1, EM5 and EM6, from the mature sperm of the bivalve mollusc Ensis minor have been partially sequenced in order to establish which category they belong to and their potential for phosphorylation. Protein EM1 is protamine-like with about 50% basic amino acids, some of which are included in SK(R) repeats. Three SPXX potential phosphorylation sites were observed in the N-terminal domain. EM1 does not fold (Giancotti et al. (1983) Eur. J. Biochem. 136, 509-516). Protein EM6 (approx. 270 residues) is histone H1-like, having a globular domain homologous to other H1 family proteins. The N-domain of EM6 contains SK(R) repeats like EM1, but there are few, if any, SPXX sites in the chain. Proteins EM1 and EM6 are the two proteins specific for mature sperm. Protein EM5, of about 150 residues and present at lower levels than EM1 and EM6, is also an H1-family molecule. A sequence from its globular domain shows close homology to chicken H5 and to sea urchin somatic H1. Its presence may relate to the existence of a low level of nucleosomal structure.

Biochemical properties of histone-like proteins of procyclic Trypanosoma brucei brucei

Four histone-like proteins a, b, c, d were extracted with 0.2 M H2SO4 from soluble nuclear chromatin of Trypanosoma brucei brucei procyclic culture forms and purified by FPLC reversed phase chromatography. The amino acid composition of these proteins and their electrophoretic mobilities in three different gel systems strongly indicated their core histone nature. Similarities were found between a, b, c and d with the core histones H3, H2A, H2B and H4 of higher eukaryotes, respectively. On the other hand, these proteins also showed differences as compared to higher eukaryotes; proteins a and d clearly differed from their counterparts H3 and H4 on the basis of their hydrophobic properties. The results indicate the occurrence of core histone variants in T.b. brucei which may influence DNA-histone and histone-histone interactions as well as the chromatin compaction in the nucleus of this protozoan parasite.