Spreading of heterochromatin is limited to specific families of maize retrotransposons

Suppressing an auxin efflux transporter enhances rice adaptation to temperate habitats

Rice (Oryza sativa L.), a chilling-sensitive staple crop originating from tropical and subtropical Asia, can be cultivated in temperate regions through the introduction of chilling tolerance traits. However, the molecular mechanisms underlying this adaptation remain largely unknown. Herein, we show that HAN2, a quantitative trait locus, confers chilling tolerance in temperate japonica rice. HAN2 encodes an auxin efflux transporter (OsABCB5) and negatively regulates chilling tolerance, potentially via auxin-mediated signaling pathway. During rice domestication, HAN2 has undergone selective divergence between the indica and temperate japonica subspecies. In temperate japonica rice, the insertion of a Copia long terminal repeat retrotransposon downstream of HAN2 reduces its expression, thereby enhancing chilling tolerance and facilitating adaptation to temperate climates. Introgression of the temperate japonica HAN2 allele into indica rice significantly improves chilling tolerance at both seedling and booting stages. These findings advance our understanding of rice northward expansion and provide a valuable genetic resource for improving yield stability under chilling stress.

PICKLE and HISTONE DEACETYLASE6 coordinately regulate genes and transposable elements in Arabidopsis

Chromatin dynamics play essential roles in transcriptional regulation. The chromodomain helicase DNA-binding domain 3 chromatin remodeler PICKLE (PKL) and HISTONE DEACETYLASE6 (HDA6) are required for transcriptional gene silencing, but their coordinated function in gene repression requires further study. Through a genetic suppressor screen, we found that a point mutation at PKL could partially restore the developmental defects of a weak Polycomb repressive complex 1 (PRC1) mutant (ring1a-2 ring1b-3), in which RING1A expression is suppressed by a T-DNA insertion at the promoter. Compared to ring1a-2 ring1b-3, the expression of RING1A is increased, nucleosome occupancy is reduced, and the histone 3 lysine 9 acetylation (H3K9ac) level is increased at the RING1A locus in the pkl ring1a-2 ring1b-3 triple mutant. HDA6 interacts with PKL and represses RING1A expression similarly to PKL genetically and molecularly in the ring1a-2 ring1b-3 background. Furthermore, we show that PKL and HDA6 suppress the expression of a set of genes and transposable elements (TEs) by increasing nucleosome density and reducing H3K9ac. Genome-wide analysis indicated they possibly coordinately maintain DNA methylation as well. Our findings suggest that PKL and HDA6 function together to reduce H3K9ac and increase nucleosome occupancy, thereby facilitating gene/TE regulation in Arabidopsis (Arabidopsis thaliana).

Epiallelic variation of non-coding RNA genes and their phenotypic consequences

Epigenetic variations contribute greatly to the phenotypic plasticity and diversity. Current functional studies on epialleles have predominantly focused on protein-coding genes, leaving the epialleles of non-coding RNA (ncRNA) genes largely understudied. Here, we uncover abundant DNA methylation variations of ncRNA genes and their significant correlations with plant adaptation among 1001 natural Arabidopsis accessions. Through genome-wide association study (GWAS), we identify large numbers of methylation QTL (methylQTL) that are independent of known DNA methyltransferases and enriched in specific chromatin states. Proximal methylQTL closely located to ncRNA genes have a larger effect on DNA methylation than distal methylQTL. We ectopically tether a DNA methyltransferase MQ1v to miR157a by CRISPR-dCas9 and show de novo establishment of DNA methylation accompanied with decreased miR157a abundance and early flowering. These findings provide important insights into the genetic basis of epigenetic variations and highlight the contribution of epigenetic variations of ncRNA genes to plant phenotypes and diversity.

Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location

Mobilization of transposable elements (TEs) is suppressed by epigenetic mechanisms involving cytosine methylation. However, few studies have focused on clarifying relationships between epigenetic influences of TEs on the adjacent DNA regions and time after insertion of TEs into the genome and/or their chromosomal location. Here we addressed these issues using soybean retrotransposon SORE-1. We analyzed SORE-1, inserted in exon 1 of the GmphyA2 gene, one of the newest insertions in this family so far identified. Cytosine methylation was detected in this element but was barely present in the adjacent regions. These results were correlated, respectively, with the presence and absence of the production of short interfering RNAs. Cytosine methylation profiles of 74 SORE-1 elements in the Williams 82 reference genome indicated that methylation frequency in the adjacent regions of SORE-1 was profoundly higher in pericentromeric regions than in euchromatic chromosome arms and was only weakly correlated with the length of time after insertion into the genome. Notably, the higher level of methylation in the 5' adjacent regions of SORE-1 coincided with the presence of repetitive elements in pericentromeric regions. Together, these results suggest that epigenetic influence of SORE-1 on the adjacent regions is influenced by its location on the chromosome.

DNA methylation signatures of duplicate gene evolution in angiosperms

Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.

Off-target piRNA gene silencing in Drosophila melanogaster rescued by a transposable element insertion

Transposable elements (TE) are selfish genetic elements that can cause harmful mutations. In Drosophila, it has been estimated that half of all spontaneous visible marker phenotypes are mutations caused by TE insertions. Several factors likely limit the accumulation of exponentially amplifying TEs within genomes. First, synergistic interactions between TEs that amplify their harm with increasing copy number are proposed to limit TE copy number. However, the nature of this synergy is poorly understood. Second, because of the harm posed by TEs, eukaryotes have evolved systems of small RNA-based genome defense to limit transposition. However, as in all immune systems, there is a cost of autoimmunity and small RNA-based systems that silence TEs can inadvertently silence genes flanking TE insertions. In a screen for essential meiotic genes in Drosophila melanogaster, a truncated Doc retrotransposon within a neighboring gene was found to trigger the germline silencing of ald, the Drosophila Mps1 homolog, a gene essential for proper chromosome segregation in meiosis. A subsequent screen for suppressors of this silencing identified a new insertion of a Hobo DNA transposon in the same neighboring gene. Here we describe how the original Doc insertion triggers flanking piRNA biogenesis and local gene silencing. We show that this local gene silencing occurs in cis and is dependent on deadlock, a component of the Rhino-Deadlock-Cutoff (RDC) complex, to trigger dual-strand piRNA biogenesis at TE insertions. We further show how the additional Hobo insertion leads to de-silencing by reducing flanking piRNA biogenesis triggered by the original Doc insertion. These results support a model of TE-mediated gene silencing by piRNA biogenesis in cis that depends on local determinants of transcription. This may explain complex patterns of off-target gene silencing triggered by TEs within populations and in the laboratory. It also provides a mechanism of sign epistasis among TE insertions, illuminates the complex nature of their interactions and supports a model in which off-target gene silencing shapes the evolution of the RDC complex.

The evolution and function of transposons in epigenetic regulation in response to the environment

Transposable elements (TEs) make up a major proportion of plant genomes. Despite their prevalence genome-wide, TEs are often tossed aside as "junk DNA" since they rarely cause phenotypes, and epigenetic mechanisms silence TEs to prevent them from causing deleterious mutations through movement. While this bleak picture of TEs in genomes is true on average, a growing number of examples across many plant species point to TEs as drivers of phenotypic diversity and novel stress responses. Examples of TE-influenced phenotypes illustrate the many ways that novel transposition events can alter local gene expression and how this relates to potential variation in plant responses to environmental stress. Since TE families and insertions at the locus level lack evolutionary conservation, advancements in the field will require TE experts across diverse species to identify and utilize TE variation in their own systems as a means of crop improvement.

You shall not pass! A Chromatin barrier story in plants

As in other eukaryotes, the plant genome is functionally organized in two mutually exclusive chromatin fractions, a gene-rich and transcriptionally active euchromatin, and a gene-poor, repeat-rich, and transcriptionally silent heterochromatin. In Drosophila and humans, the molecular mechanisms by which euchromatin is preserved from heterochromatin spreading have been extensively studied, leading to the identification of insulator DNA elements and associated chromatin factors (insulator proteins), which form boundaries between chromatin domains with antagonistic features. In contrast, the identity of factors assuring such a barrier function remains largely elusive in plants. Nevertheless, several genomic elements and associated protein factors have recently been shown to regulate the spreading of chromatin marks across their natural boundaries in plants. In this minireview, we focus on recent findings that describe the spreading of chromatin and propose avenues to improve the understanding of how plant chromatin architecture and transitions between different chromatin domains are defined.

Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading

The organization of the genome into transcriptionally active and inactive chromatin domains requires well-delineated chromatin boundaries and insulator functions in order to maintain the identity of adjacent genomic loci with antagonistic chromatin marks and functionality. In plants that lack known chromatin insulators, the mechanisms that prevent heterochromatin spreading into euchromatin remain to be identified. Here, we show that DNA Topoisomerase VI participates in a chromatin boundary function that safeguards the expression of genes in euchromatin islands within silenced heterochromatin regions. While some transposable elements are reactivated in mutants of the Topoisomerase VI complex, genes insulated in euchromatin islands within heterochromatic regions of the Arabidopsis thaliana genome are specifically down-regulated. H3K9me2 levels consistently increase at euchromatin island loci and decrease at some transposable element loci. We further show that Topoisomerase VI physically interacts with S-adenosylmethionine synthase methionine adenosyl transferase 3 (MAT3), which is required for H3K9me2. A Topoisomerase VI defect affects MAT3 occupancy on heterochromatic elements and its exclusion from euchromatic islands, thereby providing a possible mechanistic explanation to the essential role of Topoisomerase VI in the delimitation of chromatin domains.

The Methylation Inhibitor 5-Aza-2'-Deoxycytidine Induces Genome-Wide Hypomethylation in Rice

DNA methylation is a conserved epigenetic modification which is vital for regulating gene expression and maintaining genome stability in both mammals and plants. Homozygous mutation of rice methyltransferase 1 (met1) gene can cause host death in rice, making it difficult to obtain plant material needed for hypomethylation research. To circumvent this challenge, the methylation inhibitor, 5-Aza-2'-deoxycytidine (AzaD), is used as a cytosine nucleoside analogue to reduce genome wide hypomethylation and is widely used in hypomethylation research. However, how AzaD affects plant methylation profiles at the genome scale is largely unknown. Here, we treated rice seedlings with AzaD and compared the AzaD treatment with osmet1-2 mutants, illustrating that there are similar CG hypomethylation and distribution throughout the whole genome. Along with global methylation loss class I transposable elements (TEs) which are farther from genes compared with class II TEs, were more significantly activated, and the RNA-directed DNA Methylation (RdDM) pathway was activated in specific genomic regions to compensate for severe CG loss. Overall, our results suggest that AzaD is an effective DNA methylation inhibitor that can influence genome wide methylation and cause a series of epigenetic variations.

TE Density: a tool to investigate the biology of transposable elements

BACKGROUND

Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE's potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs' ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly available computational methods that quantify the presence of TEs relative to genes.

RESULTS

Here, we have developed a tool to more easily quantify TE presence relative to genes through the use of only a gene and TE annotation, yielding a new metric we call TE Density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the genome, for each type descriptor of TE (order and superfamily), and for multiple positions and distances relative to the gene (upstream, intragenic, and downstream) over sliding, user-defined windows. In this way, we overcome previous limitations to the study of TE-gene relationships by focusing on all TE types present in the genome, utilizing flexible genomic distances for measurement, and reporting a TE presence metric for every gene in the genome.

CONCLUSIONS

Together, this new tool opens up new avenues for studying TE-gene relationships, genome architecture, comparative genomics, and the tremendous diversity present of the TE world. TE Density is open-source and freely available at: https://github.com/sjteresi/TE_Density .

Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions

The mechanism of the addition of a methyl group to cytosine has been identified as one of several heritable epigenetic mechanisms. In plants, DNA methylation is involved in mediating response to stress, plant development, polyploidy, and domestication through regulation of gene expression. The correlation of epigenetic variation to phenotypic traits expands our understanding toward plant evolution, and provides new source for targeted manipulation in crop improvement. To address the increasing interest to map methylation landscape in plant species, this chapter describes methods to analyze bisulfite sequencing data and identify epigenetic variation between samples. We also detailed guidelines to highlight possible optimizations, as well as ways to tailor parameters according to data and biological variability.

Assessment of natural DNA methylation variation and its association with economically important traits in dolichos bean (Lablab purpureus L. Var. Lignosus) using AMP-PCR assay

As a prelude to exploit DNA methylation-induced variation, we hypothesized the existence of substantial natural DNA methylation variation and its association with economically important traits in dolichos bean, and tested it using amplified methylation polymorphism-polymerase chain reaction (AMP-PCR) assay. DNA methylation patterns such as internal, external, full and non-methylation were amplified in a set of 64 genotypes using 26 customized randomly amplified polymorphic DNA (RAPD) primers containing 5'CCGG3' sequence. The 64 genotypes included 60 germplasm accessions (GA), two advanced breeding lines (ABLs) and two released varieties. The ABLs and released varieties are referred to as improved germplasm accessions (IGA) in this study. The association of DNA methylation patterns with economically important traits such as days to 50% flowering, raceme length, fresh pods plant^-1, fresh pod yield plant^-1 and 100-fresh seed weight was explored. At least 50 genotypes were polymorphic for DNA methylation patterns at 10 loci generated by seven of the 26 RAPD primers. The GA and IGA differed significantly for total, full and external methylation and the frequency of methylation was higher in GA compared to that in IGA. The genotypes with external methylation produced longer racemes than those with full, internal and non-methylation in that order at polymorphic RAPD-11-242 locus. High pod yielding genotypes had significantly lower frequency of full methylation than low yielding ones. On the contrary, the genotypes that produced heavier fresh seeds harboured higher frequencies of total and externally methylated loci than those that produced lighter fresh seeds.

Drought induces variation in the DNA methylation status of the barley HvDME promoter

Cytosine methylation is an epigenetic modification with essential roles in diverse plant biological processes including vegetative and reproductive development and responsiveness to environmental stimuli. A dynamic process involving DNA methyltransferases and DNA demethylases establishes cytosine DNA methylation levels and distribution along the genome. A DNA demethylase gene from barley (Hordeum vulgare), DEMETER (HvDME), the homologue of the Arabidopsis thaliana DME (AtDME), has been characterized previously and found to respond to drought conditions. Here, the promoter of the HvDME gene was analysed further by in silico and DNA methylation analysis. The effect of drought conditions on the DNA methylation status of HvDME was investigated at single-cytosine resolution using bisulfite sequencing. It was demonstrated that the HvDME promoter can be divided into two discrete regions, in terms of DNA methylation level and density; a relatively unmethylated region proximal to the translational start site that is depleted of non-CG (CHG, CHH) methylation and another distal region, approximately 1500 bp upstream of the translational start site, enriched in CG, as well as non-CG methylation. Drought stress provoked alterations in the methylation status of the HvDME promoter distal region, whereas the DNA methylation of the proximal region remained unaffected. Computational analysis of the HvDME promoter revealed the presence of several putative regulatory elements related to drought responsiveness, as well as transposable elements (TEs) that may affect DNA methylation. Overall, our results expand our investigations of the epigenetic regulation of the HvDME gene in response to drought stress in barley and may contribute to further understanding of the epigenetic mechanisms underlying abiotic stress responses in barley and other cereals.

Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse

BACKGROUND

Trimethylation of histone H3 on lysine 9 (H3K9me3) at satellite DNA sequences has been primarily studied at (peri)centromeric regions, where its level shows differences associated with various processes such as development and malignant transformation. However, the dynamics of H3K9me3 at distal satellite DNA repeats has not been thoroughly investigated.

RESULTS

We exploit the sets of publicly available data derived from chromatin immunoprecipitation combined with massively parallel DNA sequencing (ChIP-Seq), produced by the The Encyclopedia of DNA Elements (ENCODE) project, to analyze H3K9me3 at assembled satellite DNA repeats in genomes of human cell lines and during mouse fetal development. We show that annotated satellite elements are generally enriched for H3K9me3, but its level in cancer cell lines is on average lower than in normal cell lines. We find 407 satellite DNA instances with differential H3K9me3 enrichment between cancer and normal cells including a large 115-kb cluster of GSATII elements on chromosome 12. Differentially enriched regions are not limited to satellite DNA instances, but instead encompass a wider region of flanking sequences. We found no correlation between the levels of H3K9me3 and noncoding RNA at corresponding satellite DNA loci. The analysis of data derived from multiple tissues identified 864 instances of satellite DNA sequences in the mouse reference genome that are differentially enriched between fetal developmental stages.

CONCLUSIONS

Our study reveals significant differences in H3K9me3 level at a subset of satellite repeats between biological states and as such contributes to understanding of the role of satellite DNA repeats in epigenetic regulation during development and carcinogenesis.

The genomic ecosystem of transposable elements in maize

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. Genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between attributes of the genomic environment and the survival of TE copies and families. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences reveal a diversity of survival strategies of TE families. Together these generate a rich ecology of the genome, with each TE family representing the evolution of a distinct ecological niche. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.

Whole-genome variation of transposable element insertions in a maize diversity panel

Intact transposable elements (TEs) account for 65% of the maize genome and can impact gene function and regulation. Although TEs comprise the majority of the maize genome and affect important phenotypes, genome-wide patterns of TE polymorphisms in maize have only been studied in a handful of maize genotypes, due to the challenging nature of assessing highly repetitive sequences. We implemented a method to use short-read sequencing data from 509 diverse inbred lines to classify the presence/absence of 445,418 nonredundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e., LTRs, Helitrons, and TIRs) had different frequency distributions within the population. LTRs with lower LTR similarity were generally more frequent in the population than LTRs with higher LTR similarity, though high-frequency insertions with very high LTR similarity were observed. LTR similarity and frequency estimates of nested elements and the outer elements in which they insert revealed that most nesting events occurred very near the timing of the outer element insertion. TEs within genes were at higher frequency than those that were outside of genes and this is particularly true for those not inserted into introns. Many TE insertional polymorphisms observed in this population were tagged by SNP markers. However, there were also 19.9% of the TE polymorphisms that were not well tagged by SNPs (R2 < 0.5) that potentially represent information that has not been well captured in previous SNP-based marker-trait association studies. This study provides a population scale genome-wide assessment of TE variation in maize and provides valuable insight on variation in TEs in maize and factors that contribute to this variation.

Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

Transposable elements (TEs) have the potential to create regulatory variation both through the disruption of existing DNA regulatory elements and through the creation of novel DNA regulatory elements. In a species with a large genome, such as maize, many TEs interspersed with genes create opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22, or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin, suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2 kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes, we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes, the TEs that carry ACRs exhibit enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes.

Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

Accessible chromatin and unmethylated DNA are associated with many genes and cis-regulatory elements. Attempts to understand natural variation for accessible chromatin regions (ACRs) and unmethylated regions (UMRs) often rely upon alignments to a single reference genome. This limits the ability to assess regions that are absent in the reference genome assembly and monitor how nearby structural variants influence variation in chromatin state. In this study, de novo genome assemblies for four maize inbreds (B73, Mo17, Oh43, and W22) are utilized to assess chromatin accessibility and DNA methylation patterns in a pan-genome context. A more complete set of UMRs and ACRs can be identified when chromatin data are aligned to the matched genome rather than a single reference genome. While there are UMRs and ACRs present within genomic regions that are not shared between genotypes, these features are 6- to 12-fold enriched within regions between genomes. Characterization of UMRs present within shared genomic regions reveals that most UMRs maintain the unmethylated state in other genotypes with only ∼5% being polymorphic between genotypes. However, the majority (71%) of UMRs that are shared between genotypes only exhibit partial overlaps suggesting that the boundaries between methylated and unmethylated DNA are dynamic. This instability is not solely due to sequence variation as these partially overlapping UMRs are frequently found within genomic regions that lack sequence variation. The ability to compare chromatin properties among individuals with structural variation enables pan-epigenome analyses to study the sources of variation for accessible chromatin and unmethylated DNA.

The epiallelic potential of transposable elements and its evolutionary significance in plants

DNA provides the fundamental framework for heritability, yet heritable trait variation need not be completely ‘hard-wired’ into the DNA sequence. In plants, the epigenetic machinery that controls transposable element (TE) activity, and which includes DNA methylation, underpins most known cases of inherited trait variants that are independent of DNA sequence changes. Here, we review our current knowledge of the extent, mechanisms and potential adaptive contribution of epiallelic variation at TE-containing alleles in this group of species. For the purpose of this review, we focus mainly on DNA methylation, as it provides an easily quantifiable readout of such variation. The picture that emerges is complex. On the one hand, pronounced differences in DNA methylation at TE sequences can either occur spontaneously or be induced experimentally en masse across the genome through genetic means. Many of these epivariants are stably inherited over multiple sexual generations, thus leading to transgenerational epigenetic inheritance. Functional consequences can be significant, yet they are typically of limited magnitude and although the same epivariants can be found in nature, the factors involved in their generation in this setting remain to be determined. On the other hand, moderate DNA methylation variation at TE-containing alleles can be reproducibly induced by the environment, again usually with mild effects, and most of this variation tends to be lost across generations. Based on these considerations, we argue that TE-containing alleles, rather than their inherited epiallelic variants, are the main targets of natural selection. Thus, we propose that the adaptive contribution of TE-associated epivariation, whether stable or not, lies predominantly in its capacity to modulate TE mobilization in response to the environment, hence providing hard-wired opportunities for the flexible exploration of the phenotypic space.

This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture

BACKGROUND

Datura stramonium (Jimsonweed) is a medicinally and pharmaceutically important plant in the nightshade family (Solanaceae) known for its production of various toxic, hallucinogenic, and therapeutic tropane alkaloids. Recently, we published a tissue-culture based transformation protocol for D. stramonium that enables more thorough functional genomics studies of this plant. However, the tissue culture process can lead to undesirable phenotypic and genomic consequences independent of the transgene used. Here, we have assembled and annotated a draft genome of D. stramonium with a focus on tropane alkaloid biosynthetic genes. We then use mRNA sequencing and genome resequencing of transformants to characterize changes following tissue culture.

RESULTS

Our draft assembly conforms to the expected 2 gigabasepair haploid genome size of this plant and achieved a BUSCO score of 94.7% complete, single-copy genes. The repetitive content of the genome is 61%, with Gypsy-type retrotransposons accounting for half of this. Our gene annotation estimates the number of protein-coding genes at 52,149 and shows evidence of duplications in two key alkaloid biosynthetic genes, tropinone reductase I and hyoscyamine 6 β-hydroxylase. Following tissue culture, we detected only 186 differentially expressed genes, but were unable to correlate these changes in expression with either polymorphisms from resequencing or positional effects of transposons.

CONCLUSIONS

We have assembled, annotated, and characterized the first draft genome for this important model plant species. Using this resource, we show duplications of genes leading to the synthesis of the medicinally important alkaloid, scopolamine. Our results also demonstrate that following tissue culture, mutation rates of transformed plants are quite high (1.16 × 10- 3 mutations per site), but do not have a drastic impact on gene expression.

DNA Modification Patterns within the Transposable Elements of the Fig (Ficus carica L.) Genome

Transposable element activity can be harmful to the host’s genome integrity, but it can also provide selective advantages. One strategy to cope with transposons is epigenetic control through DNA base modifications. We report the non-canonic DNA modification dynamics of fig (Ficus carica L.) by exploiting high-quality genome reference and related N4-methylcytosine (4mC) and N6-methyladenine (6mA) data. Overall, 1.49% of transposon nucleotides showed either 4mC or 6mA modifications: the 4mC/6mA ratio was similar in Class I and Class II transposons, with a prevalence of 4mC, which is comparable to coding genes. Different percentages of 4mC or 6mA were observed among LTR-retrotransposon lineages and sub-lineages. Furthermore, both the Copia and Gypsy retroelements showed higher modification rates in the LTR and coding regions compared with their neighbour regions. Finally, the unconventional methylation of retrotransposons is unrelated to the number of close genes, suggesting that the 4mC and 6mA frequency in LTR-retrotransposons should not be related to transcriptional repression in the adjacency of the element. In conclusion, this study highlighted unconventional DNA modification patterns in fig transposable elements. Further investigations will focus on functional implications, in regards to how modified retroelements affect the expression of neighbouring genes, and whether these epigenetic markers can spread from repeats to genes, shaping the plant phenotype.

Satellite DNA-Mediated Gene Expression Regulation: Physiological and Evolutionary Implication

Satellite DNAs are tandemly repeated sequences organized in large clusters within (peri)centromeric and/or subtelomeric heterochromatin. However, in many species, satellite DNAs are not restricted to heterochromatin but are also dispersed as short arrays within euchromatin. Such genomic organization together with transcriptional activity seems to be a prerequisite for the gene-modulatory effect of satellite DNAs which was first demonstrated in the beetle Tribolium castaneum upon heat stress. Namely, enrichment of a silent histone mark at euchromatic repeats of a major beetle satellite DNA results in epigenetic silencing of neighboring genes. In addition, human satellite III transcripts induced by heat shock contribute to genome-wide gene silencing, providing protection against stress-induced cell death. Gene silencing mediated by satellite RNA was also shown to be fundamental for the early embryonic development of the mosquito Aedes aegypti. Apart from a physiological role during embryogenesis and heat stress response, activation of satellite DNAs in terms of transcription and proliferation can have an evolutionary impact. Spreading of satellite repeats throughout euchromatin promotes the variation of epigenetic landscapes and gene expression diversity, contributing to the evolution of gene regulatory networks and to genome adaptation in fluctuating environmental conditions.

Ectopic Expression of a Maize Gene Is Induced by Composite Insertions Generated Through Alternative Transposition

Transposable elements (TEs) are DNA sequences that can mobilize and proliferate throughout eukaryotic genomes. Previous studies have shown that in plant genomes, TEs can influence gene expression in various ways, such as inserting in introns or exons to alter transcript structure and content, and providing novel promoters and regulatory elements to generate new regulatory patterns. Furthermore, TEs can also regulate gene expression at the epigenetic level by modifying chromatin structure, changing DNA methylation status, and generating small RNAs. In this study, we demonstrated that Ac/fractured Ac (fAc) TEs are able to induce ectopic gene expression by duplicating and shuffling enhancer elements. Ac/fAc elements belong to the hAT family of class II TEs. They can undergo standard transposition events, which involve the two termini of a single transposon, or alternative transposition events that involve the termini of two different nearby elements. Our previous studies have shown that alternative transposition can generate various genome rearrangements such as deletions, duplications, inversions, translocations, and composite insertions (CIs). We identified >50 independent cases of CIs generated by Ac/fAc alternative transposition and analyzed 10 of them in detail. We show that these CIs induced ectopic expression of the maize pericarp color 2 (p2) gene, which encodes a Myb-related protein. All the CIs analyzed contain sequences including a transcriptional enhancer derived from the nearby p1 gene, suggesting that the CI-induced activation of p2 is affected by mobilization of the p1 enhancer. This is further supported by analysis of a mutant in which the CI is excised and p2 expression is lost. These results show that alternative transposition events are not only able to induce genome rearrangements, but also generate CIs that can control gene expression.

Impact of Transposable Elements on Methylation and Gene Expression across Natural Accessions of Brachypodium distachyon

Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications, such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation, and nearby gene expression in additional plant species. Here, we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for 11 natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated with a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon.

Mapping Regulatory Determinants in Plants

The domestication and improvement of many plant species have frequently involved modulation of transcriptional outputs and continue to offer much promise for targeted trait engineering. The cis-regulatory elements (CREs) controlling these trait-associated transcriptional variants however reside within non-coding regions that are currently poorly annotated in most plant species. This is particularly true in large crop genomes where regulatory regions constitute only a small fraction of the total genomic space. Furthermore, relatively little is known about how CREs function to modulate transcription in plants. Therefore understanding where regulatory regions are located within a genome, what genes they control, and how they are structured are important factors that could be used to guide both traditional and synthetic plant breeding efforts. Here, we describe classic examples of regulatory instances as well as recent advances in plant regulatory genomics. We highlight valuable molecular tools that are enabling large-scale identification of CREs and offering unprecedented insight into how genes are regulated in diverse plant species. We focus on chromatin environment, transcription factor (TF) binding, the role of transposable elements, and the association between regulatory regions and target genes.

A copia-like retrotransposon insertion in the upstream region of the SHATTERPROOF1 gene, BnSHP1.A9, is associated with quantitative variation in pod shattering resistance in oilseed rape

Seed loss resulting from pod shattering is a major constraint in production of oilseed rape (Brassica napus L.). However, the molecular mechanisms underlying pod shatter resistance are not well understood. Here, we show that the pod shatter resistance at quantitative trait locus qSRI.A9.1 is controlled by one of the B. napus SHATTERPROOF1 homologs, BnSHP1.A9, in a doubled haploid population generated from parents designated R1 and R2 as well as in a diverse panel of oilseed rape. The R1 maternal parental line of the doubled haploid population carried the allele for shattering at qSRI.A9.1, while the R2 parental line carried the allele for shattering resistance. Quantitative RT-PCR showed that BnSHP1.A9 was expressed specifically in flower buds, flowers, and developing siliques in R1, while it was not expressed in any tissue of R2. Transgenic plants constitutively expressing either of the BnSHP1.A9 alleles from the R1 and R2 parental lines showed that both alleles are responsible for pod shattering, via a mechanism that promotes lignification of the enb layer. These findings indicated that the allelic differences in the BnSHP1.A9 gene per se are not the causal factor for quantitative variation in shattering resistance at qSRI.A9.1. Instead, a highly methylated copia-like long terminal repeat retrotransposon insertion (4803 bp) in the promotor region of the R2 allele of BnSHP1.A9 repressed the expression of BnSHP1.A9, and thus contributed to pod shatter resistance. Finally, we showed a copia-like retrotransposon-based marker, BnSHP1.A9R2, can be used for marker-assisted breeding targeting the pod shatter resistance trait in oilseed rape.

Comparative analysis of genome-wide DNA methylation in Neurospora

DNA methylation is an epigenetic mark that plays an important role in genetic regulation in eukaryotes. Major progress has been made in dissecting the molecular pathways that regulate DNA methylation. Yet, little is known about DNA methylation variation over evolutionary time. Here we present an investigation of the variation of DNA methylation and transposable element (TE) content in species of the filamentous ascomycetes Neurospora. We generated genome-wide DNA methylation data at single-base resolution, together with genomic TE content and gene expression data, of 10 individuals representing five closely related Neurospora species. We found that the methylation levels were low (ranging from 1.3% to 2.5%) and varied among the genomes in a species-specific way. Furthermore, we found that the TEs over 400 bp long were targeted by DNA methylation, and in all genomes, high methylation correlated with low GC, confirming a conserved link between DNA methylation and Repeat Induced Point (RIP) mutations in this group of fungi. Both TE content and DNA methylation pattern showed phylogenetic signal, and the species with the highest TE load (N. crassa) also exhibited the highest methylation level per TE. Our results suggest that DNA methylation is an evolvable trait and indicate that the genomes of Neurospora are shaped by an evolutionary arms race between TEs and host defence.

Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements

Transposable elements (TEs) are genomic parasites that selfishly replicate at the expense of host fitness. Fifty years of evolutionary studies of TEs have concentrated on the deleterious genetic effects of TEs, such as their effects on disrupting genes and regulatory sequences. However, a flurry of recent work suggests that there is another important source of TEs' harmful effects-epigenetic silencing. Host genomes typically silence TEs by the deposition of repressive epigenetic marks. While this silencing reduces the selfish replication of TEs and should benefit hosts, a picture is emerging that the epigenetic silencing of TEs triggers inadvertent spreading of repressive marks to otherwise expressed neighboring genes, ultimately jeopardizing host fitness. In this Review, we provide a long-overdue overview of the recent genome-wide evidence for the presence and prevalence of TEs' epigenetic effects, highlighting both the similarities and differences across mammals, insects, and plants. We lay out the current understanding of the functional and fitness consequences of TEs' epigenetic effects, and propose possible influences of such effects on the evolution of both hosts and TEs themselves. These unique evolutionary consequences indicate that TEs' epigenetic effect is not only a crucial component of TE biology but could also be a significant contributor to genome function and evolution.

Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats

Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of “silent” H3K9me3 and “active” H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats. The results show H3K9me3 enrichment at alpha repeats upon heat stress, which correlates with the dynamics of alpha satellite DNA transcription activation, while no change in H3K4me2/3 level is detected. Spreading of H3K9me3 up to 1–2 kb from the insertion sites of the euchromatic alpha repeats is detected, revealing the alpha repeats as modulators of local chromatin structure. In addition, expression of genes containing alpha repeats within introns as well as of genes closest to the intergenic alpha repeats is downregulated upon heat stress. Further studies are necessary to reveal the possible contribution of H3K9me3 enriched alpha repeats, in particular those located within introns, to the silencing of their associated genes.

Taming the Turmoil Within: New Insights on the Containment of Transposable Elements

Transposable elements (TEs) are mobile genetic parasites that can exponentially increase their genomic abundance through self-propagation. Classic theoretical papers highlighted the importance of two potentially escalating forces that oppose TE spread: regulated transposition and purifying selection. Here, we review new insights into mechanisms of TE regulation and purifying selection, which reveal the remarkable foresight of these theoretical models. We further highlight emergent connections between transcriptional control enacted by small RNAs and the contribution of TE insertions to structural mutation and host-gene regulation. Finally, we call for increased comparative analysis of TE dynamics and fitness effects, as well as host control mechanisms, to reveal how interconnected forces shape the differential prevalence and distribution of TEs across the tree of life.

Rice 3D chromatin structure correlates with sequence variation and meiotic recombination rate

Genomes of many eukaryotic species have a defined three-dimensional architecture critical for cellular processes. They are partitioned into topologically associated domains (TADs), defined as regions of high chromatin inter-connectivity. While TADs are not a prominent feature of A. thaliana genome organization, they have been reported for other plants including rice, maize, tomato and cotton and for which TAD formation appears to be linked to transcription and chromatin epigenetic status. Here we show that in the rice genome, sequence variation and meiotic recombination rate correlate with the 3D genome structure. TADs display increased SNP and SV density and higher recombination rate compared to inter-TAD regions. We associate the observed differences with the TAD epigenetic landscape, TE composition and an increased incidence of meiotic crossovers.

Golicz et al. report an increase in single nucleotide polymorphisms and structural variations across and within Topologically Associated Domains (TADs) in the rice genome, which is different to the pattern observed in the human genome. They show that this may be due to epigenetic modifications, transposable elements composition, and meiotic crossovers in the TAD regions.

Epigenomic landscape and epigenetic regulation in maize

Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.

A serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 regulates maize grain yield

Increasing grain yield of maize (Zea mays L.) is required to meet the rapidly expanding demands for maize-derived food, feed, and fuel. Breeders have enhanced grain productivity of maize hybrids by pyramiding desirable characteristics for larger ears. However, loci selected for improving grain productivity remain largely unclear. Here, we show that a serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 (KNR6) determines pistillate floret number and ear length. Overexpression of KNR6 or introgression of alleles lacking the insertions of two transposable elements in the regulatory region of KNR6 can significantly enhance grain yield. Further in vitro evidences indicate that KNR6 can interact with an Arf GTPase-activating protein (AGAP) and its phosphorylation by KNR6 may affect ear length and kernel number. This finding provides knowledge basis to enhance maize hybrids grain yield.

Nested plant LTR retrotransposons target specific regions of other elements, while all LTR retrotransposons often target palindromes and nucleosome-occupied regions: in silico study

Background

Nesting is common in LTR retrotransposons, especially in large genomes containing a high number of elements.

Results

We analyzed 12 plant genomes and obtained 1491 pairs of nested and original (pre-existing) LTR retrotransposons. We systematically analyzed mutual nesting of individual LTR retrotransposons and found that certain families, more often belonging to the Ty3/gypsy than Ty1/copia superfamilies, showed a higher nesting frequency as well as a higher preference for older copies of the same family ("autoinsertions"). Nested LTR retrotransposons were preferentially located in the 3'UTR of other LTR retrotransposons, while coding and regulatory regions (LTRs) are not commonly targeted. Insertions displayed a weak preference for palindromes and were associated with a strong positional pattern of higher predicted nucleosome occupancy. Deviation from randomness in target site choice was also found in 13,983 non-nested plant LTR retrotransposons.

Conclusions

We reveal that nesting of LTR retrotransposons is not random. Integration is correlated with sequence composition, secondary structure and the chromatin environment. Insertion into retrotransposon positions with a low negative impact on family fitness supports the concept of the genome being viewed as an ecosystem of various elements.

Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize

Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes.

Many Facets of Dynamic Plasticity in Plants

The evolutionary processes that transitioned plants to land-based habitats also incorporated a multiplicity of strategies to enhance resilience to the greater environmental variation encountered on land. The sensing of light, its quality, quantity, and duration, is central to plant survival and, as such, serves as a central network hub. Similarly, plants as sessile organisms that can encounter isolation must continually assess their reproductive options, requiring plasticity in propagation by self- and cross-pollination or asexual strategies. Irregular fluctuations and intermittent extremes in temperature, soil fertility, and moisture conditions have given impetus to genetic specializations for network resiliency, protein neofunctionalization, and internal mechanisms to accelerate their evolution. We review some of the current advancements made in understanding plant resiliency and phenotypic plasticity mechanisms. These mechanisms incorporate unusual nuclear-cytoplasmic interactions, various transposable element (TE) activities, and epigenetic plasticity of central gene networks that are broadly pleiotropic to influence resiliency phenotypes.

Monitoring the interplay between transposable element families and DNA methylation in maize

DNA methylation and epigenetic silencing play important roles in the regulation of transposable elements (TEs) in many eukaryotic genomes. A majority of the maize genome is derived from TEs that can be classified into different orders and families based on their mechanism of transposition and sequence similarity, respectively. TEs themselves are highly methylated and it can be tempting to view them as a single uniform group. However, the analysis of DNA methylation profiles in flanking regions provides evidence for distinct groups of chromatin properties at different TE families. These differences among TE families are reproducible in different tissues and different inbred lines. TE families with varying levels of DNA methylation in flanking regions also show distinct patterns of chromatin accessibility and modifications within the TEs. The differences in the patterns of DNA methylation flanking TE families arise from a combination of non-random insertion preferences of TE families, changes in DNA methylation triggered by the insertion of the TE and subsequent selection pressure. A set of nearly 70,000 TE polymorphisms among four assembled maize genomes were used to monitor the level of DNA methylation at haplotypes with and without the TE insertions. In many cases, TE families with high levels of DNA methylation in flanking sequence are enriched for insertions into highly methylated regions. The majority of the >2,500 TE insertions into unmethylated regions result in changes in DNA methylation in haplotypes with the TE, suggesting the widespread potential for TE insertions to condition altered methylation in conserved regions of the genome. This study highlights the interplay between TEs and the methylome of a major crop species.

The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum

Acquisition and rearrangement of host genes by transposable elements (TEs) is an important mechanism to increase gene diversity as exemplified by the ∼3000 Pack-Mutator-like TEs in the rice genome which have acquired gene sequences (Pack-MULEs), yet remain enigmatic. To identify signatures of functioning Pack-MULEs and Pack-MULE evolution, we generated transcriptome, translatome, and epigenome datasets and compared Pack-MULEs to genes and other TE families. Approximately 40% of Pack-MULEs were transcribed with 9% having translation evidence, clearly distinguishing them from other TEs. Pack-MULEs exhibited a unique expression profile associated with specificity in reproductive tissues that may be associated with seed traits. Expressed Pack-MULEs resemble regular protein-coding genes as exhibited by a low level of DNA methylation, association with active histone marks and DNase I hypersensitive sites, and an absence of repressive histone marks, suggesting that a substantial fraction of Pack-MULEs are potentially functional in vivo. Interestingly, the expression capacity of Pack-MULEs is independent of the local genomic environment, and the insertion and expression of Pack-MULEs may have altered the local chromosomal expression pattern as well as counteracted the impact of recombination on chromosomal base composition, which has profound consequences on the evolution of chromosome structure.

Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses

This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.

Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation

Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell - vegetative cell (VC) - of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation.

Does the Presence of Transposable Elements Impact the Epigenetic Environment of Human Duplicated Genes?

Epigenetic modifications have an important role to explain part of the intra- and inter-species variation in gene expression. They also have a role in the control of transposable elements (TEs) whose activity may have a significant impact on genome evolution by promoting various mutations, which are expected to be mostly deleterious. A change in the local epigenetic landscape associated with the presence of TEs is expected to affect the expression of neighboring genes since these modifications occurring at TE sequences can spread to neighboring sequences. In this work, we have studied how the epigenetic modifications of genes are conserved and what the role of TEs is in this conservation. For that, we have compared the conservation of the epigenome associated with human duplicated genes and the differential presence of TEs near these genes. Our results show higher epigenome conservation of duplicated genes from the same family when they share similar TE environment, suggesting a role for the differential presence of TEs in the evolutionary divergence of duplicates through variation in the epigenetic landscape.

Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice

Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on five factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.

The transcriptome of zinc deficient maize roots and its relationship to DNA methylation loss

BACKGROUND

Zinc (Zn) is an essential micronutrient of all organisms. Deficiency of zinc causes disturbance in crucial plant functions, as a high number of enzymes, including transcription factors, depend on zinc for proper performance. The plant responses to zinc deficiency are associated with increased high affinity Zn uptake and translocation, as well as efficient usage of the remaining zinc, but have not been characterized in molecular detail in maize.

RESULTS

The high affinity transporter genes ZmZIP3,4,5,7 and 8 and nicotianamine synthases, primarily ZmNAS5, were identified as primary up-regulated in maize roots upon prolonged Zn deficiency. In addition to down-regulation of genes encoding enzymes involved in pathways regulating reactive oxygen species and cell wall-related genes, a massive up-regulation of the sucrose efflux channel genes SWEET13a,c was identified, despite that in -Zn sugar is known to accumulate in shoots. In addition, enzymes involved in DNA maintenance methylation tended to be repressed, which coincided with massively reduced DNA methylation in Zn-deficient roots. Reduced representation bisulfate sequencing, which revealed base-specific methylation patterns in ~ 14% of the maize genome, identified a major methylation loss in -Zn, mostly in transposable elements. However, hypermethylated genome regions in -Zn were also identified, especially in both symmetrical cytosine contexts. Differential methylation was partially associated with differentially expressed genes, their promoters, or transposons close to regulated genes. However, hypomethylation was associated with about equal number of up- or down-regulated genes, questioning a simple mechanistic relationship to gene expression.

CONCLUSIONS

The transcriptome of Zn-deficient roots identified genes and pathways to cope with the deficiency and a major down-regulation of reactive oxygen metabolism. Interestingly, a nutrient-specific loss of DNA methylation, partially related to gene expression in a context-specific manner, may play a role in long-term stress adaptation.

Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels

Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5′ ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ∼100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 × 10⁻⁵). The density of syntenic genes (i.e., those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e., those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny.

Winter-dormant shoot apical meristem in poplar trees shows environmental epigenetic memory

Trees have a long lifespan and must continually adapt to environmental pressures, notably in the context of climate change. Epigenetic mechanisms are doubtless involved in phenotypic plasticity and in stress memory; however, little evidence of the role of epigenetic processes is available for trees growing in fields. Here, we analyzed the possible involvement of epigenetic mechanisms in the winter-dormant shoot apical meristem of Populus × euramericana clones in memory of the growing conditions faced during the vegetative period. We aimed to estimate the range of genetic and environmentally induced variations in global DNA methylation and to evaluate their correlation with changes in biomass production, identify differentially methylated regions (DMRs), and characterize common DMRs between experiments. We showed that the variations in global DNA methylation between conditions were genotype dependent and correlated with biomass production capacity. Microarray chip analysis allowed detection of DMRs 6 months after the stressful summer period. The 161 DMRs identified as common to three independent experiments most notably targeted abiotic stress and developmental response genes. Results are consistent with a winter-dormant shoot apical meristem epigenetic memory of stressful environmental conditions that occurred during the preceding summer period. This memory may facilitate tree acclimation.

Shaping Plant Adaptability, Genome Structure and Gene Expression through Transposable Element Epigenetic Control: Focus on Methylation

In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to insertion in essential genes. The current review focuses on the effects of methylation on TEs and their genomic context, and how this type of epigenetic control affects plant adaptability when plants are faced with different stresses and changes. TEs mobilize in response to stress elicitors, including biotic and abiotic cues, but also developmental transitions and ‘genome shock’ events like polyploidization. These events transitionally lift TE repression, allowing TEs to move to new genomic locations. When TEs fall close to genes, silencing through methylation can spread to nearby genes, resulting in lower gene expression. The presence of TEs in gene promoter regions can also confer stress inducibility modulated through alternative methylation and demethylation of the TE. Bursts of transposition triggered by events of genomic shock can increase genome size and account for differences seen during polyploidization or species divergence. Finally, TEs have evolved several mechanisms to suppress their own repression, including the use of microRNAs to control genes that promote methylation. The interplay between silencing, transient TE activation, and purifying selection allows the genome to use TEs as a reservoir of potential beneficial modifications but also keeps TEs under control to stop uncontrolled detrimental transposition.

Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat

BACKGROUND

Fungal plant pathogens pose major threats to crop yield and sustainable food production if they are highly adapted to their host and the local environment. Variation in gene expression contributes to phenotypic diversity within fungal species and affects adaptation. However, very few cases of adaptive regulatory changes have been reported in fungi and the underlying mechanisms remain largely unexplored. Fungal pathogen genomes are highly plastic and harbor numerous insertions of transposable elements, which can potentially contribute to gene expression regulation. In this work, we elucidated how transposable elements contribute to variation in melanin accumulation, a quantitative trait in fungi that affects survival under stressful conditions.

RESULTS

We demonstrated that differential transcriptional regulation of the gene encoding the transcription factor Zmr1, which controls expression of the genes in the melanin biosynthetic gene cluster, is responsible for variation in melanin accumulation in the fungal plant pathogen Zymoseptoria tritici. We show that differences in melanin levels between two strains of Z. tritici are due to two levels of transcriptional regulation: (1) variation in the promoter sequence of Zmr1 and (2) an insertion of transposable elements upstream of the Zmr1 promoter. Remarkably, independent insertions of transposable elements upstream of Zmr1 occurred in 9% of Z. tritici strains from around the world and negatively regulated Zmr1 expression, contributing to variation in melanin accumulation.

CONCLUSIONS

Our studies identified two levels of transcriptional control that regulate the synthesis of melanin. We propose that these regulatory mechanisms evolved to balance the fitness costs associated with melanin production against its positive contribution to survival in stressful environments.

Coevolution between transposable elements and recombination

One of the most striking patterns of genome structure is the tight, typically negative, association between transposable elements (TEs) and meiotic recombination rates. While this is a highly recurring feature of eukaryotic genomes, the mechanisms driving correlations between TEs and recombination remain poorly understood, and distinguishing cause versus effect is challenging. Here, we review the evidence for a relation between TEs and recombination, and discuss the underlying evolutionary forces. Evidence to date suggests that overall TE densities correlate negatively with recombination, but the strength of this correlation varies across element types, and the pattern can be reversed. Results suggest that heterogeneity in the strength of selection against ectopic recombination and gene disruption can drive TE accumulation in regions of low recombination, but there is also strong evidence that the regulation of TEs can influence local recombination rates. We hypothesize that TE insertion polymorphism may be important in driving within-species variation in recombination rates in surrounding genomic regions. Furthermore, the interaction between TEs and recombination may create positive feedback, whereby TE accumulation in non-recombining regions contributes to the spread of recombination suppression. Further investigation of the coevolution between recombination and TEs has important implications for our understanding of the evolution of recombination rates and genome structure.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'.