Comparative epigenomics: defining and utilizing epigenomic variations across species, time-course, and individuals

An analysis of methylome evolution in primates

Although the investigation of the epigenome becomes increasingly important, still little is known about the long-term evolution of epigenetic marks and systematic investigation strategies are still lacking. Here, we systematically demonstrate the transfer of classic phylogenetic methods such as maximum likelihood based on substitution models, parsimony, and distance-based to interval-scaled epigenetic data. Using a great apes blood data set, we demonstrate that DNA methylation is evolutionarily conserved at the level of individual CpGs in promotors, enhancers, and genic regions. Our analysis also reveals that this epigenomic conservation is significantly correlated with its transcription factor binding density. Binding sites for transcription factors involved in neuron differentiation and components of AP-1 evolve at a significantly higher rate at methylation than at the nucleotide level. Moreover, our models suggest an accelerated epigenomic evolution at binding sites of BRCA1, chromobox homolog protein 2, and factors of the polycomb repressor 2 complex in humans. For most genomic regions, the methylation-based reconstruction of phylogenetic trees is at par with sequence-based reconstruction. Most strikingly, phylogenetic reconstruction using methylation rates in enhancer regions was ineffective independently of the chosen model. We identify a set of phylogenetically uninformative CpG sites enriched in enhancers controlling immune-related genes.

Advances and Promises of Epigenetics for Forest Trees

The importance of tree genetic variability in the ability of forests to respond and adapt to environmental changes is crucial in forest management and conservation. Along with genetics, recent advances have highlighted “epigenetics” as an emerging and promising field of research for the understanding of tree phenotypic plasticity and adaptive responses. In this paper, we review recent advances in this emerging field and their potential applications for tree researchers and breeders, as well as for forest managers. First, we present the basics of epigenetics in plants before discussing its potential for trees. We then propose a bibliometric and overview of the literature on epigenetics in trees, including recent advances on tree priming. Lastly, we outline the promises of epigenetics for forest research and management, along with current gaps and future challenges. Research in epigenetics could use highly diverse paths to help forests adapt to global change by eliciting different innovative silvicultural approaches for natural- and artificial-based forest management.

EpiAlignment: alignment with both DNA sequence and epigenomic data

Comparative epigenomics, which subjects both epigenome and genome to interspecies comparison, has become a powerful approach to reveal regulatory features of the genome. Thus elucidated regulatory features surpass the information derived from comparison of genomic sequences alone. Here, we present EpiAlignment, a web-based tool to align genomic regions with both DNA sequence and epigenomic data. EpiAlignment takes DNA sequence and epigenomic profiles derived by ChIP-seq from two species as input data, and outputs the best semi-global alignments. These alignments are based on EpiAlignment scores, computed by a dynamic programming algorithm that accounts for both sequence alignment and epigenome similarity. For timely response, the EpiAlignment web server automatically initiates up to 140 computing threads depending on the size of user input data. For users’ convenience, we have pre-compiled the comparable human and mouse epigenome datasets in matched cell types and tissues from the Roadmap Epigenomics and ENCODE consortia. Users can either upload their own data or select pre-compiled datasets as inputs for EpiAlignment analyses. Results are presented in graphical and tabular formats where the entries can be interactively expanded to visualize additional features of these aligned regions. EpiAlignment is available at https://epialign.ucsd.edu/.

A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome

Central questions to epigenome evolution include whether interspecies changes of histone modifications are independent of evolutionary changes of DNA, and if there is dependence whether they depend on any specific types of DNA sequence changes. Here, we present a likelihood approach for testing hypotheses on the co-evolution of genome and histone modifications. The gist of this approach is to convert evolutionary biology hypotheses into probabilistic forms, by explicitly expressing the joint probability of multispecies DNA sequences and histone modifications, which we refer to as a class of Joint Evolutionary Model for the Genome and the Epigenome (JEMGE). JEMGE can be summarized as a mixture model of four components representing four evolutionary hypotheses, namely dependence and independence of interspecies epigenomic variations to underlying sequence substitutions and to underlying sequence insertions and deletions (indels). We implemented a maximum likelihood method to fit the models to the data. Based on comparison of likelihoods, we inferred whether interspecies epigenomic variations depended on substitution or indels in local genomic sequences based on DNase hypersensitivity and spermatid H3K4me3 ChIP-seq data from human and rhesus macaque. Approximately 5.5% of homologous regions in the genomes exhibited H3K4me3 modification in either species, among which approximately 67% homologous regions exhibited local-sequence-dependent interspecies H3K4me3 variations. Substitutions accounted for less local-sequence-dependent H3K4me3 variations than indels. Among transposon-mediated indels, ERV1 insertions and L1 insertions were most strongly associated with H3K4me3 gains and losses, respectively. By initiating probabilistic formulation on the co-evolution of genomes and epigenomes, JEMGE helps to bring evolutionary biology principles to comparative epigenomic studies.

Epigenetic modifications play a significant role in gene regulations and thus heavily influence phenotypic outcomes. Whereas cross-species epigenomic comparisons have been fruitful in revealing the function of epigenetic modifications, it still remains unclear how the epigenome changes across species. A central question in epigenome evolution studies is whether interspecies epigenomic variations rely on genomic changes in cis and, if partially yes, whether different genomic changes have distinct impacts. To tackle this question, we initiated a likelihood-based approach, in which different hypotheses related to the co-evolution of the genome and the epigenome could be converted into probabilistic models. By fitting the models to actual data, each model yielded a likelihood, and the hypothesis corresponded to the largest likelihood was selected as most supported by observed data. In this work, we focused on the influence of two types of underlying sequence changes: substitutions, and insertions and deletions (indels). We quantitatively assessed the dependence of H3K4me3 variations on substitutions and indels between human and rhesus, and separated their relative impacts within each genomic region with H3K4me3. The methodology presented here provides a framework for modeling the epigenome together with the genome and a quantitative approach to test different evolutionary hypotheses.

Coordinate systems for supergenomes

Background

Genome sequences and genome annotation data have become available at ever increasing rates in response to the rapid progress in sequencing technologies. As a consequence the demand for methods supporting comparative, evolutionary analysis is also growing. In particular, efficient tools to visualize-omics data simultaneously for multiple species are sorely lacking. A first and crucial step in this direction is the construction of a common coordinate system. Since genomes not only differ by rearrangements but also by large insertions, deletions, and duplications, the use of a single reference genome is insufficient, in particular when the number of species becomes large.

Results

The computational problem then becomes to determine an order and orientations of optimal local alignments that are as co-linear as possible with all the genome sequences. We first review the most prominent approaches to model the problem formally and then proceed to showing that it can be phrased as a particular variant of the Betweenness Problem. It is NP hard in general. As exact solutions are beyond reach for the problem sizes of practical interest, we introduce a collection of heuristic simplifiers to resolve ordering conflicts.

Conclusion

Benchmarks on real-life data ranging from bacterial to fly genomes demonstrate the feasibility of computing good common coordinate systems.

Electronic supplementary material

The online version of this article (10.1186/s13015-018-0133-4) contains supplementary material, which is available to authorized users.