Project description:Archaea, together with Bacteria, represent the two main divisions of life on Earth, with many of the defining characteristics of the more complex eukaryotes tracing their origin to evolutionary innovations first made in their archaeal ancestors. One of the most notable such features is nucleosomal chromatin, although archaeal histones and chromatin differ significantly from those of eukaryotes. Despite increased interest in archaeal histones in recent years, the properties of archaeal chromatin have been little studied using genomic tools. Here, we adapt the ATAC-seq assay to the archaeal context and use it to map the accessible landscape of the genome of the euryarchaeote Haloferax volcanii. We integrate the resulting datasets with genome-wide maps of active transcription and single-stranded DNA (ssDNA), and find that while H. volcanii promoters exist in a preferentially accessible state, modulation of transcriptional activity is not associated with changes in promoter accessibility, unlike the typical situation in eukaryotes. Applying orthogonal single-molecule footprinting methods, we quantify the absolute levels of physical protection of H. volcanii, and find that archaeal nucleosomal chromatin is at its baseline comparably to slightly more open than that of eukaryotes. We also evaluate the degree of coordination of transcription within archaeal operons and make the unexpected observation that some CRISPR arrays are associated with highly prevalent ssDNA structures. These results provide a foundation for the future functional studies of archaeal chromatin.
Project description:Archaea are ubiquitous prokaryotes with a wide range of habitats, important roles in ecology, biotechnology and potentially even human health. Despite that, our understanding of archaeal cell biology is still rather limited, partially because the application of systems biology approaches is lacking behind the other domains of life. Here we introduce/announce the Archaeal Proteome Project (ArcPP), a community effort that aims for the comprehensive analysis of archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we have re-analyzed more than 2 TB of MS result files (>20 Mio. spectra) using state-of-the-art bioinformatic tools, increasing peptide spectrum matches and leading to the secure identification of >3000 proteins. This dataset is part of the Archaeal Proteome Project dataset
Project description:The formation of new species is often a consequence of genetic incompatibilities accumulated between populations during allopatric divergence. When divergent taxa interbreed, these incompatibilities impact physiology and have a direct cost resulting in reduced hybrid fitness. Recent surveys of gene regulation in interspecific hybrids have revealed anomalous expression across large proportions of the genome, with 30-70% of all genes apparently misexpressed, mostly in the direction of down-regulation. However, since most of these studies have focused on pairs of species exhibiting high degrees of reproductive isolation, the association between regulatory disruption and reduced hybrid fitness prior to species formation remains unclear. Within the copepod species Tigriopus californicus, interpopulation hybrids show reduced fitness associated with mitochondrial dysfunction. Here we show that in contrast to studies of interspecific hybrids, only 1.2% of the transcriptome was misexpressed in interpopulation hybrids of T. californicus, and nearly 80% of misexpressed genes were overexpressed rather than underexpressed. Moreover, many of the misexpressed genes were components of functional pathways impacted by mitonuclear incompatibilities in hybrid T. californicus (e.g., oxidative phosphorylation and antioxidant response). We also show that the magnitude of hybrid misregulation is not dependent on levels of protein sequence divergence, even though the latter is correlated with expression divergence between parental populations. Our results suggest that hybrid breakdown at early stages of speciation may result from initial incompatibilities amplified by the cost of compensatory physiological responses.
Project description:Here, we produced a set of interspecific F1 triploid hybrid plants between Oryza sativa, ssp. japonica (2nâ=â2xâ=â24, genome AA) and the tetraploid form of O. punctata (2nâ=â4xâ=â48, genome, BBCC), and conducted RNA-seq transcriptome profiling of the hybrids and their exact parental plants. We analyzed both homeolog expression bias and overall gene expression level difference in the hybrids relative to the in silico âhybridsâ (parental mixtures). We found that approximately 16% (2,541) of the 16,112 expressed genes in leaf tissue of the F1 hybrids showed nonadditive expression, which were specifically enriched in photosynthesis-related pathways. Interestingly, changes in the maternal homeolog expression, including non-stochastic silencing, were the major causes for altered homeolog expression partitioning in the F1 hybrids. Our findings have provided further insights into the transcriptome response to interspecific hybridization and heterosis.
Project description:Changes in gene regulation rapidly accumulate between species and may contribute to reproductive isolation through misexpression of genes in interspecific hybrids. Hybrid misexpression, defined by expression levels outside the range of both parental species, is thought to be a result of cis- and trans-acting regulatory changes that interact in the hybrid, or arise from changes in the relative abundance of various tissues or cell types due to defects in developmental. Here, we show that misexpressed genes in a sterile interspecific Saccharomyces yeast hybrid result from a heterochronic shift in the timing of the normal meiotic gene expression program. By tracking nuclear divisions, we find that S. cerevisiae initiates meiosis earlier than its closest known relative, S. paradoxus, yet both species complete meiosis at the same time. Although the hybrid up- and down-regulates genes in a similar manner to both parents, the hybrid meiotic program occurs earlier than both parents. The timing shift results in a heterochronic pattern of misexpression throughout meiosis I and the beginning of meiosis II. Coincident with the timing of misexpression, we find an increase in the relative abundance of opposing cis and trans-acting changes and compensatory changes, as well as a transition from predominantly trans-acting to cis-acting expression divergence over the course of meiosis. However, misexpression does not appear to be a direct consequence of cis- and trans-acting regulatory divergence. Our results demonstrate that hybrid misexpression in yeast results from a heterochronic shift in the meiotic gene expression program.
Project description:Using the Illumina HiSeq 2000 platform, 39,598; 32,403and 42,208 genes were identified in flower buds of B. carinata cv.W29, B. napus cv. Zhongshuang 11 and their hybrids, respectively. The differentially expressed genes (DEGs) were significantly enriched in pollen wall assembly, pollen exine formation, pollen development, pollen tube growth, pollination, gene transcription, macromolecule methylation and translation, which might be associated with impaired fertility in the F1 hybrid. These results will shed light on the mechanisms underlying the low fertility of the interspecific hybrids and expand our knowledge of interspecific hybridization.
Project description:Diverse studies including protemoics, genome-wide binding, and transcriptional profiling of the model halophile Halobacterium salinarum suggest that its putative histone protein acts not as a chromatin protein but a direct and indirect transcriptional regulator. Here, we characterise the putative histone (HstA) of another model halophile (Haloferax volcanii) with ChIP-Seq to understand its genome-wide binding, and compare it with binding patterns seen from histones, nucleoid-associated proteins, and transcription factors of Halobacterium salinarum, other archaea, and eukaryotes. Analysis of this data by visual inspection, start site occupancy profiles, DNA motif searching, and dinucleotide periodicity suggests that the binding mode of halophilic histones shares features with TFs, NAPs, and more typical archaeal/eukaryotic histones.
Project description:Ribosome profiling performed on interspecific hybrids of Sacharromyces cerevisiae and S. paradoxus in order to identify allele-specific expression indicative of cis-regulatory divergence at the level of mRNA abundance and protein translation.
Project description:Changes in gene regulation rapidly accumulate between species and may contribute to reproductive isolation through misexpression of genes in interspecific hybrids. Hybrid misexpression, defined by expression levels outside the range of both parental species, is thought to be a result of cis- and trans-acting regulatory changes that interact in the hybrid, or arise from changes in the relative abundance of various tissues or cell types due to defects in developmental. Here, we show that misexpressed genes in a sterile interspecific Saccharomyces yeast hybrid result from a heterochronic shift in the timing of the normal meiotic gene expression program. By tracking nuclear divisions, we find that S. cerevisiae initiates meiosis earlier than its closest known relative, S. paradoxus, yet both species complete meiosis at the same time. Although the hybrid up- and down-regulates genes in a similar manner to both parents, the hybrid meiotic program occurs earlier than both parents. The timing shift results in a heterochronic pattern of misexpression throughout meiosis I and the beginning of meiosis II. Coincident with the timing of misexpression, we find an increase in the relative abundance of opposing cis and trans-acting changes and compensatory changes, as well as a transition from predominantly trans-acting to cis-acting expression divergence over the course of meiosis. However, misexpression does not appear to be a direct consequence of cis- and trans-acting regulatory divergence. Our results demonstrate that hybrid misexpression in yeast results from a heterochronic shift in the meiotic gene expression program. We analyzed three biological replicates of the parental yeast strains, S. cerevisiae and S. paradoxus, and four replicates of their hybrid over four developmental time points. Two hybrid replicates contain MATa from S. cerevisiae and MATalpha from S. paradoxus. The other two hybrid replicates are reciprocal crosses. The developmental time points are T0, which serves as a control, and is the moment cells enter sporulation media. M1 is the beginning of meiosis I. M1/M2 is the overlap of the end of meiosis I and the beginning of meiosis II. M2 is the end of meiosis II.