Epigenetic mechanisms underlying paternal genome elimination

For most sexually reproducing organisms, the two parentally inherited copies of a gene are equivalent in transmission and expression. However, there are exceptions to this rule. Genomic imprinting is an epigenetic process in which expression of one gene copy is favoured depending on its parental origin. One of the most striking cases of genomic imprinting is Paternal Genome Elimination (PGE). PGE is a genomic imprinting phenomenon found in thousands of insect species and involves the silencing and elimination of an entire haploid genome in a parent-of-origin specific manner. Under PGE, both sexes develop from fertilized eggs and initially possess a diploid euchromatic chromosome complement. However, males subsequently eliminate paternally-inherited chromosomes from their germline. Different PGE species vary in the timing of the elimination of the paternal genome, and in whether it becomes transcriptionally silenced or not. As a result, male gene expression varies from haploid to diploid with various intermediates. The recognition and silencing of paternally-inherited genes under PGE appear to be regulated by the same epigenetic machinery as silencing and imprinting in mammals, namely DNA methylation and histone modifications. However, the molecular details are poorly understood. Here, I investigate the epigenetic mechanisms underlying PGE using the citrus mealybug (Planococcus citri, Hemiptera: Pseudococcidae) a small plant-feeding insect, easily reared in laboratory conditions. I utilize molecular, cytogenetic and genomic techniques to address the following questions: i) do levels & patterns of global DNA methylation differ between the sexes and does this play a role in sex-specific gene expression? ii) are key histone-mediated heterochromatin pathways (H3K9me3-HP1 and H3K27me3-PRC2 pathways) involved in the recognition and silencing of the paternal genome in PGE males? iii) do DNA methylation marks differ between paternal and maternal alleles, potentially acting as a distinguisher of parental origin during PGE? Whole genome bisulfite sequencing and transcriptome sequencing reveal evidence of sex-specific DNA methylation and gene expression. However, changes in gene methylation and expression between males and females are not correlated suggesting that this epigenetic modification may not mediate sex-specific expression. Cytogenetic studies in males show that both H3K9me3-HP1 and H3K27me3-PRC2 heterochromatin pathways are involved in the silencing of paternal alleles in PGE males but not in the recognition of paternal alleles during spermatogenesis. Finally, allele-specific bisulfite analysis in Planococcus hybrids suggests that differences in methylation on maternal and paternal alleles could potentially allow recognition of paternal alleles during PGE. My research provides insight into the putative roles of sex-specific and allele-specific epigenetic modifications in the recognition and silencing of the paternal genome during the process of PGE. Additionally, the methylome of a non-social, non-hymenopteran insect broadens understanding of the function(s) and evolution of DNA methylation within arthropods

Bioinformatics: food detective – a practical guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces the idea of computers as tools to help understand aspects of biology. In particular, it looks at how DNA sequences can be used to identify specific organisms, why this is important in the food industry, and how this can be used to help detect food fraud. Analyses are run online using sequence data from the 4273pi project website: 4273pi.org.<br><br>Specifically, this Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how to identify different species based on their specific DNA sequences – their ‘barcodes’. On reading the Guide and completing the exercises, you will be able to: explain what is meant by DNA barcoding; search biological sequence databases using the online program BLAST; judge the reliability of database-search results in terms of their statistical significance; and evaluate the biological implications of search results with reference to food safety

Bioinformatics: the power of computers in biology – a practical guide

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces simple bioinformatics approaches for database searching and sequence analysis. A ‘mystery’ gene is used as an exemplar: we first characterise the gene, then use it to explore the impact of gene loss in humans. Analyses are run both online and at the command line, the latter using Raspberry Pi computers running the 4273<i>π </i>variant of Linux (4273pi.org).<br><br>Specifically, this Guide introduces a popular Web-based tool for searching biological sequence databases, and shows how similar functionality can be achieved using the Linux command line. On reading the Guide and completing the exercises, users will be able to: search biological sequence databases using the online program BLAST, and navigate GenPept sequence records; execute some basic Linux commands to perform a set of simple file-manipulation tasks; perform BLAST searches via the Linux command line; and evaluate the biological implications of search results, with reference to mutations and function

Sex‐specific expression and DNA methylation in a species with extreme sexual dimorphism and paternal genome elimination

Phenotypic differences between sexes are often mediated by differential expression and alternative splicing of genes. However, the mechanisms that regulate these expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex-specific genomic imprinting, paternal genome elimination (PGE), in which the paternal chromosomes in males are highly condensed and eliminated from the sperm. Planococcus citri has no sex chromosomes and both sexual dimorphism and PGE are predicted to be under epigenetic control. We recently showed that P. citri females display a highly unusual DNA methylation profile for an insect species, with the presence of promoter methylation associated with lower levels of gene expression. Here, we therefore decided to explore genome-wide differences in DNA methylation between male and female P. citri using whole-genome bisulphite sequencing. We identified extreme differences in genome-wide levels and patterns between the sexes. Males display overall higher levels of DNA methylation which manifest as more uniform low levels across the genome. Whereas females display more targeted high levels of methylation. We suggest these unique sex-specific differences are due to chromosomal differences caused by PGE and may be linked to possible ploidy compensation. Using RNA-Seq, we identify extensive sex-specific gene expression and alternative splicing, but we find no correlation with cis-acting DNA methylation

Bringing bioinformatics to schools with the 4273pi project

The work was supported by the Science and Technology Facilities Council (STFC) under Grants STFC ST/R000328/1 (including salary to S.A.B., D.B., H.P., T.R.M. and non-salary costs) and STFC ST/T000872/1 (including salary to S.A.B., D.B., K.C., T.R.M. and non-salary costs), the Darwin Trust of Edinburgh (https://darwintrust.bio.ed.ac.uk; including salary to S.A.B. and H.P. and non-salary costs), the Wellcome Trust-University of Edinburgh Institutional Strategic Support Fund under Wellcome Trust Grant number 204804/Z/16/Z (salary to H.P.), a Public Engagement with Genetics Tier 2 Grant from the Genetics Society (https://genetics.org.uk; non-salary costs), the Natural Environment Research Council (NERC) under Grant NE/P000592/1 (including salary to N.C. and M.G.R. and non-salary costs), the Biotechnology and Biological Sciences Research Council (BBSRC) under Grant BB/S018506/1 (including salary to F.A. and non-salary costs), the School of Biological Sciences at the University of Edinburgh (https://www.ed.ac.uk/biology; including salary to S.A.B. and H.P. and non-salary costs) and its Institute of Evolutionary Biology (https://www.ed.ac.uk/biology/evolutionary-biology; non-salary costs), the Access for Rural Communities project (ARC) at University of St Andrews (https://www.st-andrews.ac.uk/study/access/projects/arc; non-salary costs) and the Engineering and Physical Sciences Research Council (EPSRC) under Grant EP/V52038X/1 (including salary to S.A.B. and non-salary costs). E.W.J.W. is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society [208779/Z/17/Z] (including salary to E.W.J.W.).Over the last few decades, the nature of life sciences research has changed enormously, generating a need for a workforce with a variety of computational skills such as those required to store, manage, and analyse the large biological datasets produced by next-generation sequencing. Those with such expertise are increasingly in demand for employment in both research and industry. Despite this, bioinformatics education has failed to keep pace with advances in research. At secondary school level, computing is often taught in isolation from other sciences, and its importance in biological research is not fully realised, leaving pupils unprepared for the computational component of Higher Education and, subsequently, research in the life sciences. The 4273pi Bioinformatics at School project (https://4273pi.org) aims to address this issue by designing and delivering curriculum-linked, hands-on bioinformatics workshops for secondary school biology pupils, with an emphasis on equitable access. So far, we have reached over 180 schools across Scotland through visits or teacher events, and our open education resources are used internationally. Here, we describe our project, our aims and motivations, and the practical lessons we have learned from implementing a successful bioinformatics education project over the last 5 years.Publisher PDFPeer reviewe

­­­­­­Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

Funder: Leverhulme Trust; funder-id: http://dx.doi.org/10.13039/501100000275Funder: Medical Research Council; funder-id: http://dx.doi.org/10.13039/501100000265Funder: Natural Environment Research Council; funder-id: http://dx.doi.org/10.13039/501100000270Cytosine methylation is an ancient epigenetic modification yet its function and extent within genomes is highly variable across eukaryotes. In mammals, methylation controls transposable elements and regulates the promoters of genes. In insects, DNA methylation is generally restricted to a small subset of transcribed genes, with both intergenic regions and transposable elements (TEs) depleted of methylation. The evolutionary origin and the function of these methylation patterns are poorly understood. Here we characterise the evolution of DNA methylation across the arthropod phylum. While the common ancestor of the arthropods had low levels of TE methylation and did not methylate promoters, both of these functions have evolved independently in centipedes and mealybugs. In contrast, methylation of the exons of a subset of transcribed genes is ancestral and widely conserved across the phylum, but has been lost in specific lineages. A similar set of genes is methylated in all species that retained exon-enriched methylation. We show that these genes have characteristic patterns of expression correlating to broad transcription initiation sites and well-positioned nucleosomes, providing new insights into potential mechanisms driving methylation patterns over hundreds of millions of years

Design, delivery and evaluation of a bioinformatics education workshop for 13-16-year-olds

Funding: Science and Technology Facilities Council (STFC) under Grants ST/R000328 and ST/T000872, the Natural Environment Research Council (NERC) under Grant NE/P000592/1, the Darwin Trust of Edinburgh and the Access for Rural Communities project (ARC) at the University of St Andrews.Bioinformatics is the use of computers in biology, particularly to analyse DNA and protein sequences and associated data. Bioinformatics has become crucial to most areas of life sciences research. However, bioinformatics education has not kept up with the pace of these advances. To help address this problem, we have designed an open-access bioinformatics workshop for secondary school biology pupils. The workshop is linked to the curriculum in Scotland, addressing learning objectives for Scottish Qualifications Authority Higher Biology and Human Biology. Furthermore, it aims to inspire pupils more generally and includes critical evaluation of evidence as a more generic skill. We delivered this workshop to biology pupils of seven schools in Scotland and conducted evaluations of pupil and teacher feedback. Quantitative pupil and teacher feedback suggest the workshop is useful and enjoyable, with no significant difference between pupils identifying as female and pupils identifying as male. Qualitative responses suggest the workshop gives an increased knowledge of the field of bioinformatics and its importance in everyday life, and that pupils enjoy working in groups. Teachers also highlight the importance of hands-on experience in the classroom. We conclude the workshop is successful in its aims and is suitable for wider deployment.Publisher PDFPeer reviewe

Widespread conservation and lineage-specific diversification of genome-wide DNA methylation patterns across arthropods

Cytosine methylation is an ancient epigenetic modification yet its function and extent within genomes is highly variable across eukaryotes. In mammals, methylation controls transposable elements and regulates the promoters of genes. In insects, DNA methylation is generally restricted to a small subset of transcribed genes, with both intergenic regions and transposable elements (TEs) depleted of methylation. The evolutionary origin and the function of these methylation patterns are poorly understood. Here we characterise the evolution of DNA methylation across the arthropod phylum. While the common ancestor of the arthropods had low levels of TE methylation and did not methylate promoters, both of these functions have evolved independently in centipedes and mealybugs. In contrast, methylation of the exons of a subset of transcribed genes is ancestral and widely conserved across the phylum, but has been lost in specific lineages. A similar set of genes is methylated in all species that retained exon-enriched methylation. We show that these genes have characteristic patterns of expression correlating to broad transcription initiation sites and well-positioned nucleosomes, providing new insights into potential mechanisms driving methylation patterns over hundreds of millions of years