Abstract:
:Epigenetic information, which can be passed on independently of the DNA sequence, is stored in part in the form of histone posttranslational modifications and specific histone variants. Although complexes necessary for deposition have been identified for canonical and variant histones, information regarding the chromatin assembly pathways outside of the Opisthokonts remains limited. Tetrahymena thermophila, a ciliated protozoan, is particularly suitable to study and unravel the chromatin regulatory layers due to its unique physical separation of chromatin states in the form of two distinct nuclei present within the same cell. Using a functional proteomics pipeline, we carried out affinity purification followed by mass spectrometry of endogenously tagged T. thermophila histones H2A, H2B and variant Hv1.We identified a set of interacting proteins shared among the three analyzed histones that includes the FACT-complex, as well as H2A- or Hv1-specific chaperones. We find that putative subunits of T. thermophila versions of SWR- and INO80-complexes, as well as transcription-related histone chaperone Spt6Tt specifically copurify with Hv1. We also identified importin β6 and the T. thermophila ortholog of nucleoplasmin 1 (cNpl1Tt) as H2A-H2B interacting partners. Our results further implicate Poly [ADP-ribose] polymerases in histone metabolism. Molecular evolutionary analysis, reciprocal affinity purification coupled to mass spectrometry experiments, and indirect immunofluorescence studies using endogenously tagged Spt16Tt (FACT-complex subunit), cNpl1Tt, and PARP6Tt underscore the validity of our approach and offer mechanistic insights. Our results reveal a highly conserved regulatory network for H2A (Hv1)-H2B concerning their nuclear import and assembly into chromatin.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Ashraf K,Nabeel-Shah S,Garg J,Saettone A,Derynck J,Gingras AC,Lambert JP,Pearlman RE,Fillingham Jdoi
10.1093/molbev/msz039subject
Has Abstractpub_date
2019-05-01 00:00:00pages
1037-1055issue
5eissn
0737-4038issn
1537-1719pii
5362030journal_volume
36pub_type
杂志文章abstract::To explore the origin of the diversity observed in natural populations, many studies have investigated the relationship between genotype and phenotype. In yeast species, especially in Saccharomyces cerevisiae, these studies are mainly conducted using recombinant offspring derived from two genetically diverse isolates,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa101
更新日期:2020-09-01 00:00:00
abstract::Functional redundancy in genomes arises from genes with overlapping functions, allowing phenotypes to persist after gene knockouts. Evolutionary redundancy or evolvability of a genome is one step removed, in that functional redundancy is absent but the genome has the potential to evolve to restore a lost phenotype. Ex...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp037
更新日期:2009-06-01 00:00:00
abstract::DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated non...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr041
更新日期:2011-08-01 00:00:00
abstract::A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025892
更新日期:1998-12-01 00:00:00
abstract::Partial and complete genome duplications occurred during evolution and resulted in the creation of new genes and gene families. We identified a novel and intricate human gene family located primarily in regions of segmental duplications on human chromosome 1. We named it NBPF, for neuroblastoma breakpoint family, beca...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi222
更新日期:2005-11-01 00:00:00
abstract::The degree to which an amino acid site is free to vary is strongly dependent on its structural and functional importance. An amino acid that plays an essential role is unlikely to change over evolutionary time. Hence, the evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh194
更新日期:2004-09-01 00:00:00
abstract::Successful fertilization in free-spawning marine organisms depends on the interactions between genes expressed on the surfaces of eggs and sperm. Positive selection frequently characterizes the molecular evolution of such genes, raising the possibility that some common deterministic process drives the evolution of gam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl062
更新日期:2006-10-01 00:00:00
abstract::The complete mitochondrial genome of Tupaia belangeri, a representative of the eutherian order Scandentia, was determined and compared with full-length mitochondrial sequences of other eutherian orders described to date. The complete mitochondrial genome is 16, 754 nt in length, with no obvious deviation from the gene...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026417
更新日期:2000-09-01 00:00:00
abstract::We recently introduced a novel method for estimating selection pressures on proteins, termed "volatility," which requires only a single genome sequence. Some criticisms that have been levied against this approach are valid, but many others are based on misconceptions of volatility, or they apply equally to comparative...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msl021
更新日期:2006-08-01 00:00:00
abstract::The T1 family of retrotransposable elements is interspersed and moderately repeated in five member species of the Anopheles gambiae sibling-species complex and has diverged little since the radiation of the complex. T1 includes two closely related but independent subfamilies, defined by the presence or absence of link...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040599
更新日期:1990-05-01 00:00:00
abstract::Hantaviruses are considered one of the best examples of a long-term association between RNA viruses and their hosts. Based on the appearance of strong host specificity, it has been suggested that hantaviruses cospeciated with the rodents and insectivores they infect since these mammals last shared a common ancestor, a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn234
更新日期:2009-01-01 00:00:00
abstract::Employing comparative analysis of the cDNA-coding sequences of the unique preprorelaxin of the Afro-lorisiform Galago crassicaudatus and the Malagasy lemur Varecia variegata and the relaxin-like factor (RLF) of G. crassicaudatus, we demonstrated distinct differences in the dynamics of molecular remodeling of both horm...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003815
更新日期:2001-03-01 00:00:00
abstract::We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that ar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025817
更新日期:1997-07-01 00:00:00
abstract::Recently, Lee et al. (Lee JH, Silhavy JL, Lee JE, et al. (30 co-authors). 2012. Evolutionarily assembled cis-regulatory module at a human ciliopathy locus. Science (335:966-969.) demonstrated that mutation in either of the transmembrane protein encoding genes, TMEM138 or TMEM216, causes phenotypically indistinguishabl...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss215
更新日期:2013-01-01 00:00:00
abstract::C repeats constitute the predominant family of short interspersed repeats (SINEs) in the rabbit genome. Determination of the nucleotide sequence 5' to rabbit zeta-globin genes reveals clusters of C repeats, and analysis of these and other sequenced regions of rabbit chromosomes shows that the C repeats have a strong t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040631
更新日期:1991-01-01 00:00:00
abstract::DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known ins...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa214
更新日期:2021-01-23 00:00:00
abstract::Transposable elements are widespread mobile DNA sequences able to integrate into new locations within genomes. Through transposition and recombination, they significantly contribute to genome plasticity and evolution. They can also regulate gene expression and provide regulatory and coding sequences (CDSs) for the evo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr208
更新日期:2012-02-01 00:00:00
abstract::Database searches of the Caenorhabditis elegans and human genomic DNA sequences revealed genes encoding ribonuclease H1 (RNase H1) and RNase H2 in each genome. The human genome contains a single copy of each gene, whereas C. elegans has four genes encoding RNase H1-related proteins and one gene for RNase H2. By analyz...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004015
更新日期:2002-11-01 00:00:00
abstract::In termites, as in many social insects, some individuals specialize in colony defense, developing diverse weaponry. As workers of the termite Neocapritermes taracua (Termitidae: Termitinae) age, their efficiency to perform general tasks decreases, while they accumulate defensive secretions and increase their readiness...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv273
更新日期:2016-03-01 00:00:00
abstract::Odorant receptors (ORs) are essential for plant-insect interactions. However, despite the global impacts of Lepidoptera (moths and butterflies) as major herbivores and pollinators, little functional data is available about Lepidoptera ORs involved in plant volatile detection. Here, we initially characterized the plant...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa300
更新日期:2020-11-24 00:00:00
abstract::tRNAs are important players in the protein synthesis machinery, where they act as adapter molecules for translating the mRNA codons into the corresponding amino acid sequence. In a series of highly conserved maturation steps, the primary transcripts are converted into mature tRNAs. In the amoebozoan Acanthamoeba caste...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa270
更新日期:2020-10-23 00:00:00
abstract::Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we exam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx098
更新日期:2017-07-01 00:00:00
abstract::As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cha...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq131
更新日期:2010-10-01 00:00:00
abstract::Although evolutionary studies of gene function often rely on RNA interference, the ideal approach would use reverse genetics to create null mutations for cross-species comparisons and forward genetics to identify novel genes in each species. We have used transcription activator-like effector nucleases (TALENs) to faci...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst213
更新日期:2014-02-01 00:00:00
abstract::Morphological innovations like the acquisition of the neural crest as well as gene family expansions by genome duplication are considered as major leaps in the evolution of the vertebrate lineage. Using comparative genomic analyses, we have reconstructed the evolutionary history of the endothelin system, a signaling p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp015
更新日期:2009-04-01 00:00:00
abstract::Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote ad...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz249
更新日期:2020-03-01 00:00:00
abstract::Liver and intestinal flukes of the family Fasciolidae cause zoonotic food-borne infections that impact both agriculture and human health throughout the world. Their evolutionary history and the genetic basis underlying their phenotypic and ecological diversity are not well understood. To close that knowledge gap, we c...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz204
更新日期:2020-01-01 00:00:00
abstract::In this study, we used an empirical example based on 100 mitochondrial genomes from higher teleost fishes to compare the accuracy of parsimony-based jackknife values with Bayesian support values. Phylogenetic analyses of 366 partitions, using differential taxon and character sampling from the entire data matrix of 100...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh014
更新日期:2004-01-01 00:00:00
abstract::The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonpar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004094
更新日期:2002-04-01 00:00:00
abstract::Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu068
更新日期:2014-05-01 00:00:00