Histone complement of a rapidly evolving chordate Oikopleura dioica: Developmental and sex-specific deployment of novel and universal histone variants and their posttranslational modifications

The packaging of DNA into nucleosomes is a fundamentally conserved property of the eukaryotic nucleus which is evident in the conservation of histone sequences. Nevertheless, it is now clear that histone sequence variants have diversified in many species to assume crucial roles in the regulation of gene expression, DNA repair, chromosome segregation and other processes. While considerable data exist on coding sequences of histones and some selected histone variants in a wide variety of organisms, the information available on total histone gene complements is much more limited. Oikopleura dioica (Od) is a dioecious marine urochordate that occupies a key phylogenetic position near the invertebrate-vertebrate transition with the smallest genome ever found in a chordate (70 Mb). Its short life cycle is characterized by a developmental switch between mitotic and endocycling cells, making O. dioica an attractive model to study the spatial and temporal use of histone variants and posttranslational histone modifications (PTMs) throughout development and in different cell cycle types. We have characterized the complete histone gene complement and the developmental expression of histone genes present in the first assembly of the O. dioica draft genome and identified the major Od PTMs by massspectrometric analysis. Furthermore, we analyzed the dynamics and distribution of phosphorylated H3 variants during mitosis and meiosis of O. dioica and the deposition of the centromeric variant OdCenH3 in mitotic and endocycling cells with respect to centromeric PTMs. The Od histone gene complement displays several features not known from other chordates, including male-specific variants in all of the core histone families, N-terminal H2A.Z splice variants, and a diverse array of H2A variants but absence of the near universal variant H2AX. The results here suggest significant plasticity in histone gene organization, the variation within histone families and the chromosomal distribution of mitotic PTMs within the chordate lineage. This further supports the view that histone gene complements may also evolve adaptively to the specific life history traits, cell cycle regulation and genome architecture of organisms

Histone variant innovation in a rapidly evolving chordate lineage

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Accumulation of mutations in antibody and CD8 T cell epitopes in a B cell depleted lymphoma patient with chronic SARS-CoV-2 infection

Antibodies against the spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) can drive adaptive evolution in immunocompromised patients with chronic infection. Here we longitudinally analyze SARS-CoV-2 sequences in a B cell-depleted, lymphoma patient with chronic, ultimately fatal infection, and identify three mutations in the spike protein that dampen convalescent plasma-mediated neutralization of SARS-CoV-2. Additionally, four mutations emerge in non-spike regions encoding three CD8 T cell epitopes, including one nucleoprotein epitope affected by two mutations. Recognition of each mutant peptide by CD8 T cells from convalescent donors is reduced compared to its ancestral peptide, with additive effects resulting from double mutations. Querying public SARS-CoV-2 sequences shows that these mutations have independently emerged as homoplasies in circulating lineages. Our data thus suggest that potential impacts of CD8 T cells on SARS-CoV-2 mutations, at least in those with humoral immunodeficiency, warrant further investigation to inform on vaccine design

Coincidental SARS-CoV-2 infection and mRNA vaccination: a case report addressing the most important clinical questions

The case describes the coincidental mRNA vaccination and SARS-CoV-2 infection of a 31-year-old physician addressing the theoretical considerations and recommendations for further actions in such a particular constellation that we will expect more often in the near future

Histone variant innovation in a rapidly evolving chordate lineage

Abstract Background Histone variants alter the composition of nucleosomes and play crucial roles in transcription, chromosome segregation, DNA repair, and sperm compaction. Modification of metazoan histone variant lineages occurs on a background of genome architecture that shows global similarities from sponges to vertebrates, but the urochordate, Oikopleura dioica, a member of the sister group to vertebrates, exhibits profound modification of this ancestral architecture. Results We show that a histone complement of 47 gene loci encodes 31 histone variants, grouped in distinct sets of developmental expression profiles throughout the life cycle. A particularly diverse array of 15 male-specific histone variants was uncovered, including a testes-specific H4t, the first metazoan H4 sequence variant reported. Universal histone variants H3.3, CenH3, and H2A.Z are present but O. dioica lacks homologs of macroH2A and H2AX. The genome encodes many H2A and H2B variants and the repertoire of H2A.Z isoforms is expanded through alternative splicing, incrementally regulating the number of acetylatable lysine residues in the functionally important N-terminal "charge patch". Mass spectrometry identified 40 acetylation, methylation and ubiquitylation posttranslational modifications (PTMs) and showed that hallmark PTMs of "active" and "repressive" chromatin were present in O. dioica. No obvious reduction in silent heterochromatic marks was observed despite high gene density in this extraordinarily compacted chordate genome. Conclusions These results show that histone gene complements and their organization differ considerably even over modest phylogenetic distances. Substantial innovation among all core and linker histone variants has evolved in concert with adaptation of specific life history traits in this rapidly evolving chordate lineage.</p

Amino acid composition of HLA-B*08:01-restricted HHV-6B epitopes and their flanking sequences.

<p><b>(A)</b> For 16 confirmed epitopes presented by infected cells, N-terminal flanking amino acid sequences (N8' to N1'), epitope sequences (N1 to N7, C2, C1), and C-terminal flanking sequences (C1' to C8') were aligned. Predefined anchors are shaded in grey. The box indicates that the amino acids at position N7 = C2) of octameric peptides were considered twice; they were included in the calculations shown in panel B as instances of the N7 position and of the C2 position. (B) Amino acid frequency in each position, categorized into different chemical classes of amino acids. AGP, small or not otherwise categorized; LIVM, aliphatic; FYW, aromatic; DE, acidic; CSTNQ, uncharged polar; RKH, basic.</p

Verification of HLA-B*08:01 restriction of HHV-6B peptides.

<p>CD8 T cell clones were tested for specific recognition of 293T kidney cells transiently transfected with HLA-B*08:01 and loaded with the specific cognate peptide. HLA-B*08:01-matched and mismatched LCLs were also tested. IFN-γ was quantified by ELISA. Mean and range of two replicates from one of two experiments is shown. Peptide specificities are indicated by the first three letters of the amino acid sequence (see <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1006991#ppat.1006991.g002" target="_blank">Fig 2</a>), the gene name, and in parentheses the protein name or function.</p

Antigen presentation by cells infected with HHV-6B and HHV-6A.

<p>HLA-B*08:01-matched PHA-activated CD4 T cells were infected with HHV-6B strain HST (panel A) or HHV-6A strain U1102 (panel B). As a further control, the viral replication inhibitor ganciclovir (GCV) was added where indicated. At the indicated time after infection, infected cells were cocultivated with T cell clones of diverse specificities. Data are shown as mean and range of duplicates from one of two experiments.</p

HHV-6-infected cells present HLA-B*08:01-restricted epitopes to CD8 T cells.

<p>(A, B) Analysis of IFN-γ secretion in response to infected cells. PHA-activated primary HLA-B*08:01-positive CD4 T cells were infected with HHV-6B strain HST (panel A) or HHV-6A strain U1102 (panel B), or remained uninfected. After six days, infected cells or controls were cocultivated with CD8 T cell clones of diverse specificities. After overnight coincubation, IFN-γ secretion was measured by ELISA. Mean and range of two replicates is shown. (C–E) Cytotoxic activity in response to infected cells. A T cell clone specific for the DFK epitope from U86 (C,D) or a polyclonal DFK-specific T cell line (E), both from donor 5, were tested against primary CD4 T cells infected with HHV-6B strain HST for six days or parallel controls in a calcein release assay. (C, E) HLA-B8-positive targets. (D) HLA-B8-negative targets.</p