Chromatin network retards nucleoli coalescence

Nuclear bodies are membraneless condensates that may form via liquid-liquid phase separation. The viscoelastic chromatin network could impact their stability and may hold the key for understanding experimental observations that defy predictions of classical theories. However, quantitative studies on the role of the chromatin network in phase separation have remained challenging. Using a diploid human genome model parameterized with chromosome conformation capture (Hi-C) data, we study the thermodynamics and kinetics of nucleoli formation. Dynamical simulations predict the formation of multiple droplets for nucleolar particles that experience specific interactions with nucleolus-associated domains (NADs). Coarsening dynamics, surface tension, and coalescence kinetics of the simulated droplets are all in quantitative agreement with experimental measurements for nucleoli. Free energy calculations further support that a two-droplet state, often observed for nucleoli in somatic cells, is metastable and separated from the single-droplet state with an entropic barrier. Our study suggests that nucleoli-chromatin interactions facilitate droplets’ nucleation but hinder their coarsening due to the coupled motion between droplets and the chromatin network: as droplets coalesce, the chromatin network becomes increasingly constrained. Therefore, the chromatin network supports a nucleation and arrest mechanism to stabilize the multi-droplet state for nucleoli and possibly for other nuclear bodies.

Deep Conservation of Hid-Like RHG Gene Family Homologs in Winged Insects Revealed by “Taxon Hopping” BLAST

Together with sickle (skl), the Drosophila paralogs reaper (rpr), head involution defective (hid), and grim (RHG) control a critical switch in the induction of programmed cell death. RHG homologs have been identified in other dipteran and lepidopteran species but not beyond. Revisiting this issue with a “taxon hopping” BLAST search strategy in current genome and transcriptome resources, I detected high confidence RHG homologs in Coleoptera, Hymenoptera, Hemiptera, and Dictyoptera. Analyses of gene structure and protein sequence conservation revealed aconserved splicing pattern and highly conserved amino acid residues at both the N- and C-terminal ends that identify hid as the most ancestrally organized RHG gene family member in Drosophila. hid-like RHG homologs were also detected in mosquitoes, redefining their michelob_x (mx) genes as an expansion of derived RHG homologs. Only singleton homologs were detected in the large majority of other insect clades. Lepidopteran RHG homologs, however, stand out by producing an evolutionarily-derived splice isoform, identified in previous work, in addition to the newly detected hid-like isoform. Exceptional sequence diversification of select RHG homologs at the family- and genus-level explain their previous elusiveness in important insect genome model species like the red flour beetle Tribolium castaneum and the pea aphid Acyrthosiphon pisum. Combined, these findings expand the minimal age of the RHG gene family by about 100 million years and open new avenues for molecular cell death studies in insects.

Deep conservation of Hid-like RHG gene family homologs in winged insects

ABSTRACTTogether with sickle (skl), the Drosophila paralogs reaper (rpr), head involution defective (hid), and grim (RHG) control a critical switch in the induction of programmed cell death. RHG homologs have been identified in other dipteran and lepidopteran species but not beyond. Revisiting this issue with a “taxon hopping” BLAST search strategy in current genome and transcriptome resources, I detected high confidence RHG homologs in Coleoptera (beetles), Hymenoptera (bees+wasps), Hemiptera (true bugs), termites, and cockroaches. Analyses of gene structure and protein sequence conservation revealed a shared ancestral splicing pattern and highly conserved amino acid residues at both the N- and C-terminal ends that identify hid as the most ancestrally organized RHG gene family member in Drosophila. hid-like RHG homologs were also detected in mosquitoes, redefining their michelob_x (mx) genes as an expansion of derived RHG homologs. Only singleton homologs were detected in the large majority of other insect clades. Lepidopteran RHG homologs, however, stand out by producing an evolutionarily derived splice isoform, identified in previous work, in addition to the newly detected hid-like isoform. Exceptional sequence diversification of select RHG homologs at the family- and genus-level explain their elusiveness in important insect genome model species like the red flour beetle Tribolium castaneum and the pea aphid Acyrthosiphon pisum. Combined, these findings expand the minimal age of the RHG gene family by about 100 million years and open new avenues for molecular cell death studies in insects.

Prediction of mechanical and thermal properties of particle reinforced hydrogel composites using the structural genome approach

In this paper, the structural genome approach is used for multiscale analyses to predict the mechanical and thermal properties of particle reinforced hydrogel composites. First, the structure genome model of particle reinforced hydrogel composites is created by the random sequential adsorption algorithm. Then the mechanical properties and equivalent thermal conductivity of hydrogel composites are numerically studied by the structural genome approach. The effects of particles with different volume fractions and material properties on their mechanical and thermal properties are investigated. From the simulation results, it can be found that within a certain range of volume fraction, the mechanical properties and equivalent thermal conductivity of hydrogel composites are positively correlated with the volume fractions of particles. We also find that with the increase of the mechanical properties and thermal conductivity of particles, the properties of hydrogel can be improved and eventually reach stabilization. The structural genome approach shows excellent efficiency in multiscale structure analysis. It is a convenient method for the simulation of complex soft material composites.

The Virtual Circular Genome Model for Primordial RNA Replication

Our manuscript describes a hypothesis for the replication of primordial RNA genomes by entirely nonenzymatic processes. Our proposal circumvents long standing problems such as the difficulty of copying long templates by nonenzymatic chemistry, the need for defined primers, and the so-called ‘last base addition problem’. Our hypothesis leads to surprising predictions, notably that the replication of an ensemble of oligonucleotides could be mediated by the template-directed extension of all oligos by as little as one nucleotide, on average. We propose experimental tests of our model, and discuss its implications for the origin of life.

The Virtual Circular Genome Model for Primordial RNA Replication

Our manuscript describes a hypothesis for the replication of primordial RNA genomes by entirely nonenzymatic processes. Our proposal circumvents long standing problems such as the difficulty of copying long templates by nonenzymatic chemistry, the need for defined primers, and the so-called ‘last base addition problem’. Our hypothesis leads to surprising predictions, notably that the replication of an ensemble of oligonucleotides could be mediated by the template-directed extension of all oligos by as little as one nucleotide, on average. We propose experimental tests of our model, and discuss its implications for the origin of life.

The use of massively parallel sequencing to study the virome, epigenome and genome of canine and feline cancers

The remarkable advancements in sequencing technologies have allowed the entire mutational landscape of hundreds of different types of human cancers to be defined. This knowledge gives patients two new categories of treatment options, small molecule inhibitors and targeted immunotherapy. Veterinary oncology has been slow to enter the field of genome-wide studies, largely due to costs. Five years ago, the first whole genome of a canine cancer patient was published. Because of NIH support and the steady decline in sequencing costs, the number of published canine tumor sequences has exploded this past year as these projects are being concluded. This dissertation contributes to this growing knowledge. The scope was diverse and included exploration in metagenomics, epigenomics and transcriptomics in canine and feline cancers. This research affirmed previous notions that papillomavirus is not a common cause of feline oral squamous cell carcinoma (FOSCC) and added to the understanding that it is not caused by any other DNA or integrated dsRNA virus. In canin DLCBL (cDLBCL) we provided more evidence that the subgroups seen in human DLBCL (hDLBCL) cannot be faithfully reproduced in the methylome of cDLCBL, likely at a greater scale than DNA mutations, and neurogenic/neuroendocrine, HOX and Wnt pathways were epigenetically targeted. In canin osteosarcoma (OSA) we built upon the genome model by adding loss of heterozygosity data and illustration of metastatic lesions. We also provided support to target the CDK4, Wnt and mTOR pathways. Finally we highlight unexpected discoveries such as the discovery of Epstein Barr virus in FOSCC, stability of the methylome in Golden Retriever DLBCL, epimutations in the TBX pathway in cDLBCL, dysregulation of human melanoma pathways in canine OSA, absence of dysregulation of HER2 in canine OSA, absence of genomic evidence of a telomere maintenance mechanism, recurrent shattering of chr26 in canine OSA and HSP90AB1, MITF and NOTCH2, as potentially actionable genes. These data will provide a significant resource for the community to generate new hypotheses and answer key questions about the molecular drivers of canine and feline malignancies.

Sequence properties of certain GC rich avian genes, their origins and absence from genome assemblies: case studies

Background More and more eukaryotic genomes are sequenced and assembled, most of them presented as a complete model in which missing chromosomal regions are filled by Ns and where a few chromosomes may be lacking. Avian genomes often contain sequences with high GC content, which has been hypothesized to be at the origin of many missing sequences in these genomes. We investigated features of these missing sequences to discover why some may not have been integrated into genomic libraries and/or sequenced. Results The sequences of five red jungle fowl cDNA models with high GC content were used as queries to search publicly available datasets of Illumina and Pacbio sequencing reads. These were used to reconstruct the leptin, TNFα, MRPL52, PCP2 and PET100 genes, all of which are absent from the red jungle fowl genome model. These gene sequences displayed elevated GC contents, had intron sizes that were sometimes larger than non-avian orthologues, and had non-coding regions that contained numerous tandem and inverted repeat sequences with motifs able to assemble into stable G-quadruplexes and intrastrand dyadic structures. Our results suggest that Illumina technology was unable to sequence the non-coding regions of these genes. On the other hand, PacBio technology was able to sequence these regions, but with dramatically lower efficiency than would typically be expected. Conclusions High GC content was not the principal reason why numerous GC-rich regions of avian genomes are missing from genome assembly models. Instead, it is the presence of tandem repeats containing motifs capable of assembling into very stable secondary structures that is likely responsible.