Project description:Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to phenotypic diversity, its interaction with genetic variation requires further investigation. MethylC-seq from naturally-occurring Arabidopsis accessions
Project description:Comparative genomic hybridisation of Streptococcus pneumoniae isolates from a single clonal complex, in order to determine genomic diversity. Isolates were selected from a range of tissue types and serotypes in order to cover the full diversity of the clone, and also in order to try and identify tissue-specific genes
Project description:The Global Diversity lines are a resource collection of 87 strains of Drosophila melanogaster (Grenier JK et al 2015. PMID 25673134). In this experiment, whole adult flies from the Global Diversity Lines (87 inbred lines derived from natural populations) were profiled using a spotted-oligo microarray to determine natural variation in gene expression patterns.
Project description:There are very few studies exploring the genetic diversity of tick-borne encephalitis complex viruses. Most of the viruses have been sequenced using capillary electrophoresis, however, very few viruses have been analyzed using deep sequencing to look at the genotypes in each virus population. In this study, different viruses and strains belonging to the tick-borne encephalitis complex were sequenced and genetic diversity was analyzed. Shannon entropy and single nucleotide variants were used to compare the viruses. Then genetic diversity was compared to the phylogenetic relationship of the viruses.
Project description:ZIKV strains belong to three phylogenetic lineages: East African, West African, and Asian/American. RNA virus genomes exist as populations of genetically-related sequences whose heterogeneity may impact viral fitness, evolution, and virulence. The genetic diversity of representative ZIKVs (N=7) from each lineage was examined using next generation sequencing (NGS) paired with downstream Shannon entropy calculation and single nucleotide variant (SNV) analysis. This comprehensive analysis of ZIKV genetic diversity provides insight into the genetic diversity of ZKIV and repository of SNV positions across lineages.
Project description:How functional cellular heterogeneities are regulated is fundamental for understanding the molecular basis of complex organs. Olfactory sensory neurons (OSNs) are an ideal model to investigate the regulation of cellular heterogeneity. The “one-neuron-one-receptor” organization and topographical mapping ensure the detection and precise translation of odor signals to the central neural system. Besides the diversity of OR genes and other molecular guiding axon sorting processes, single-cell transcriptome analysis revealed an OSN subpopulation, defined by Cd36, a lipid receptor gene. The function study exhibited lipid odor identification was impaired in Cd36-deficient mice. In this study, we systematically depicted the transcriptome diversity, spatial distribution, and specific functions of Cd36+ OSNs in the mouse olfactory epithelium. The specific molecular features of Cd36+ OSN we revealed implemented the programmed cellular diversity may be driven by their olfaction function. Furthermore, with the integrative analysis of single-cell transcriptome and epigenome profiles, we revealed the cis and trans regulatory signatures in Cd36+ OSN and identified Tshz1 and Mef2 as the key regulators that may directly regulate and promote the expression of Cd36 and drive the cellular diversity of OSNs. Especially, we demonstrated that Tshz1 is expressed coordinately with the choices of ORs, earlier than the expression of Cd36, which indicates it may act as a pioneer factor that instructs the lineage-specific expression of Cd36 and other genes, eventually leading to the cellular diversity of Cd36+ OSN. Our results provide novel knowledge on the regulation mechanism of cellular diversity of complex organs.
Project description:DNA duplication is intimately connected to setting up post-replicative chromosome structures and events, but molecular details of this coordination are not well understood. A striking example occurs during yeast meiosis, where replication locally influences timing of the DNA double-strand breaks (DSBs) that initiate recombination. We show here that replication-DSB coordination is eliminated by overexpressing Dbf4-dependent Cdc7 kinase (DDK) or removing Tof1 or Csm3, components of the replication fork protection complex (FPC). DDK physically associates with Tof1, and Tof1 is dispensable for replication-DSB coordination if DDK is artificially tethered to replisomes. Furthermore, DDK phosphorylation of the DSB-promoting factor Mer2 is locally coordinated with replication, dependent on Tof1. These findings indicate that DDK recruited by FPC to replisomes phosphorylates chromatin-bound Mer2 in the wake of the replication fork, thus synchronizing replication with an early prerequisite for DSB formation. This may be a general mechanism to ensure spatial and temporal coordination of replication with other chromosomal processes. Ninety-six samples total: 12 time points (each time points contains ChIP and input samples) from Rec114-myc ARS+, Rec114-myc arsM-bM-^HM-^F strains, Rec114-myc tof1M-bM-^HM-^FARS+ and Rec114-myc tof1M-bM-^HM-^F arsM-bM-^HM-^F strains
Project description:DNA duplication is intimately connected to setting up post-replicative chromosome structures and events, but molecular details of this coordination are not well understood. A striking example occurs during yeast meiosis, where replication locally influences timing of the DNA double-strand breaks (DSBs) that initiate recombination. We show here that replication-DSB coordination is eliminated by overexpressing Dbf4-dependent Cdc7 kinase (DDK) or removing Tof1 or Csm3, components of the replication fork protection complex (FPC). DDK physically associates with Tof1, and Tof1 is dispensable for replication-DSB coordination if DDK is artificially tethered to replisomes. Furthermore, DDK phosphorylation of the DSB-promoting factor Mer2 is locally coordinated with replication, dependent on Tof1. These findings indicate that DDK recruited by FPC to replisomes phosphorylates chromatin-bound Mer2 in the wake of the replication fork, thus synchronizing replication with an early prerequisite for DSB formation. This may be a general mechanism to ensure spatial and temporal coordination of replication with other chromosomal processes. Forty-eight samples total: 8 time points from WT ARS+, WT arsM-bM-^HM-^F, DDK OP ARS+, DDK OP arsM-bM-^HM-^F,tof1M-bM-^HM-^F ARS+,tof1M-bM-^HM-^F arsM-bM-^HM-^F strains