Biology subjects

Nordborg, M.

Publications and source records attributed to Nordborg, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Predicting mutation-rate variation across the genome using epigenetic data

Mutation rate variation is a fundamental driver of evolution, yet how it is locally patterned across genomes and structured by chromatin context remains unresolved. Here, we integrate genome-wide profiles of histone marks, DNA methylation and chromatin accessibility in Arabidopsis thaliana with de novo mutation data to model mutation probability at the level of coding sequence (CDS). Using non-negative matrix factorization, we identify 15 combinatorial epigenetic patterns whose graded mixtures stratify CDSs into six classes with distinct mutation probabilities. A generalized linear model based on pattern weights predicts local mutation probability and outperforms models based on sequence context, expression and classical genomic categories. These patterns capture context-dependent variation that is obscured by gene-level summaries and single-feature analyses. Cluster-level differences are partly retained in mutation-accumulation lines, indicating persistence into heritable mutational input. Under hypoxia, stress-responsive chromatin remodeling redistributes epigenetic contexts associated with higher predicted mutation probability toward hypoxia-responsive genes and DNA-repair pathways. Together, our results provide a CDS-resolved and interpretable framework linking combinatorial epigenomic context to mutational input, clarifying how dynamic chromatin states shape local mutation-rate heterogeneity.

bioinformatics↗

bioRxiv2025

Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana

DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements (TEs) in eukaryotes. Numerous examples of cis-elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans-regulators of mCG leading to adaptation. Here, using genome-wide association studies, we identify CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 ALPHA (CDCA7) as a trans-regulator of mCG in natural populations of Arabidopsis thaliana. CDCA7 and its paralog, CDCA7{beta}, directly bind to the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. CDCA7/{beta} selectively regulates mCG and minimally impacts other DDM1-dependent processes such as non-CG methylation and histone variant deposition. We identify the cis-regulatory sequence modulating CDCA7 expression in natural populations and determining the degree of mCG and TE silencing. The geographic distribution of CDCA7 alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Altogether, our findings provide new insight into how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation.

plant biology↗

bioRxiv2025

Life-history trade-offs explain local adaptation in Arabidopsis thaliana

Local adaptation has been demonstrated in many organisms, but the traits involved, and the temporal and spatial scales at which selection acts are generally unknown. We carried out a multi-year study of 200 accessions (natural inbred lines) of Swedish Arabidopsis thaliana using local field sites and a combination of common-garden experiments that measured adult survival and fecundity, and selection experiments that measured fitness over the full life cycle. We found evidence of strong and variable selection, with particular genotypes favored more than five-fold in certain years and locations. Fecundity showed evidence of classical local adaptation, with accessions generally performing better closer to their home. However, relative to other accessions, southern ones usually had the highest fecundity---but were far more sensitive to harsh winters and slug herbivory, which strongly decreased both survival and fecundity. Furthermore, accessions originally sampled on beaches had low fecundity in all common-garden experiments, but massively outperformed all other accessions in the selection experiments, presumably due to an advantage during seedling establishment associated with their very large seeds. We conclude that local adaptation in A. thaliana reflects strong temporally and spatially varying selection on multiple traits, generally involving trade-offs and different life-history strategies, making fitness difficult to predict and measure.

genetics↗

bioRxiv2025

Pannagram: unbiased pangenome alignment and the Mobilome calling

Pangenomes capture genetic variation beyond the scope of single-reference analyses, but interpreting this variation requires approaches that translate whole-genome comparisons into biologically meaningful features. We present Pannagram, a framework combining reference-free linear whole-genome alignment with feature extraction for single-nucleotide polymorphisms (SNPs), structural variants (SVs), and mobile element families (MEFs), together with a library of tools for downstream analysis. Pannagram identifies MEFs by a single criterion, recent mobility, independent of prior transposable element (TE) models or homology. Illustrating its utility through a meta-analysis of pangenome data from 60 insect species, we show that highly similar MEFs, by definition recently active, are frequently shared between species, providing strong evidence for horizontal transfer (HT) orthogonal to sequence similarity and phylogeny. We further find that vectors for such HT include not only viruses but also polintons, supported by cases of polinton HT and by polintons that remain active after insertion of TE cargo.

bioinformatics↗

bioRxiv2024

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorphisms in another accession, or naturally occurring strain. Since then, inventories of genome-wide diversity have been generated at increasingly precise levels. High-density genotype data for A. thaliana, including those from the 1001 Genomes Project, were key to demonstrating the enormous power of GWAS in inbred populations of wild plants, and the comparison of intraspecific polymorphism with interspecific divergence has illuminated many aspects of plant genome evolution. Over the past decade, an increasing number of nearly complete genome sequences have been published for many more accessions. Here, we highlight the diversity of a curated collection of previously published and so far unpublished genome sequences assembled using different types of long reads, including PacBio Continuous Long Reads (CLR), PacBio High Fidelity (HiFi) reads, and Oxford Nanopore Technologies (ONT) reads. This 1001 Genomes Plus (1001G+) resource is being made available at http://1001genomes.org. We invite colleagues with yet unpublished genome assemblies from A. thaliana accessions to contribute to this effort.

genomics↗

bioRxiv2024

Bisulphite sequencing in the presence of cytosine-conversion errors

Bisulphite treatment of DNA converts unmethylated cytosines to thymine, and is a common method to infer the methylation status of cytosines when coupled with sequencing. Tagmentation approaches to bisulphite sequencing use a transposase to simultaneously make double-stranded breaks and ligate adaptors to the resulting fragments, allowing for higher throughput with less starting material. However, it has also been noted that certain tagmentation protocols have an unusually high number unmethylated cytosines that are not converted to thymine. Here we describe this phenomenon in detail, and find that results are consistent with single strand nicks by the transposase, followed by strand displacement of part or all of the DNA fragment, leading to erroneous incorporation of methylated cytosines. Nevertheless we show that these errors can be accounted for in downstream analysis and need not impede biological conclusions. We provide a Python package to allow users to implement this framework. Ultimately the additional effort of accounting for errors must be traded off against the scalability of the protocol in planning experiments.

genomics↗

bioRxiv2024

PTGS is dispensable for the initiation of epigenetic silencing of an active transposon in Arabidopsis

Transposable elements (TEs) are largely repressed in plants through transcriptional gene silencing (TGS), which is maintained by heritable epigenetic silencing marks such as DNA methylation. However, the mechanisms by which silencing is installed in the first place remains poorly understood in plants. Small interfering (si)RNAs and post-transcriptional gene silencing (PTGS) play a role in the initial response by reducing mRNA and protein levels of active TEs and are believed to mediate the initiation of TGS by guiding the first deposition of DNA methylation. To determine how this silencing installation works, we took advantage of EVADE (EVD), an endogenous retroelement in Arabidopsis, which can be used to recapitulate true de novo silencing with a well-established sequence of PTGS followed by a TGS phase. To test whether PTGS is a prerequisite for TGS, active EVD copies were introduced into RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) mutants lacking an essential PTGS component. EVD activity and silencing were monitored across several generations. Unexpectedly, even in the absence of PTGS, TGS and silencing of EVD were still achieved through installation of RNA-directed DNA methylation (RdDM) at EVD regulatory sequences without any prior DNA methylation at its coding sequence. Hence, our study shows that PTGS is dispensable for de novo EVD silencing. Although we cannot rule out that PTGS might facilitate the initiation of TGS, or control TE activity until then, initiation of epigenetic silencing can take place in its absence.

plant biology↗

bioRxiv2024

Towards an unbiased characterization of genetic polymorphism

Our view of genetic polymorphism is shaped by methods that provide a limited and reference-biased picture. Long-read sequencing technologies, which are starting to provide nearly complete genome sequences for population samples, should solve the problem--except that characterizing and making sense of non-SNP variation is difficult even with perfect sequence data. Here we analyze 27 genomes of Arabidopsis thaliana in an attempt to address these issues, and illustrate what can be learned by analyzing whole-genome polymorphism data in an unbiased manner. Estimated genome sizes range from 135 to 155 Mb, with differences almost entirely due to centromeric and rDNA repeats that are difficult to assemble. The completely assembled chromosome arms comprise roughly 120 Mb in all accessions, but are full of structural variants, largely due to transposable elements. Even with only 27 accessions, a pan-genome coordinate system that includes the resulting variation ends up being [~] 70% larger than the size of any one genome. Our analysis reveals an incompletely annotated mobile-ome: we not only detect several novel TE families, but also find that existing TE annotation is a poor predictor of elements that have recently been active. In contrast to this, the genic portion, or "gene-ome", is highly conserved. By annotating each genome using accession-specific transcriptome data, we find that 13% of all (non-TE) genes are segregating in our 27 accessions, but most of these are transcriptionally silenced. Finally, we show that with short-read data we previously massively underestimated genetic variation of all kinds, including SNPs--mostly in regions where short reads could not be mapped reliably, but also where reads were mapped incorrectly. We demonstrate that SNP-calling errors can be biased by the choice of reference genome, and that RNA-seq and BS-seq results can be strongly affected by mapping reads only to a reference genome rather than to the genome of the assayed individual. In conclusion, while whole-genome polymorphism data pose tremendous analytical challenges, they also have the potential to revolutionize our understanding of genome evolution.

genomics↗

bioRxiv2024

On the contribution of genetic heterogeneity to complex traits

Genetic heterogeneity, where different alleles or loci are responsible for similar phenotypes, reduces the power of genome-wide association studies and can cause misleading results. Although many striking examples have been identified, the general importance of genetic heterogeneity for complex traits is unclear. Here, we use a novel interpretative machine-learning approach to look for evidence of genetic heterogeneity in plants and humans. Our approach helps identify new loci/alleles influencing trait variation in several agriculturally important species, and we show that at least 6% of maize eQTL, half of them newly identified, exhibit evidence of allelic heterogeneity. Finally, we search for evidence of synthetic associations in human GWAS data, and find that as many as 3-5% may be affected. Our results highlight the need to take genetic heterogeneity seriously, and provide a simple approach for doing so.

genetics↗

bioRxiv2024

Alternative silencing states of Transposable Elements in Arabidopsis

The DNA methylation/H3K9me2 and Polycomb-group proteins (PcG)-H3K27me3 pathways have long been considered mutually exclusive and specific to TEs and genes, respectively. However, H3K27me3 can be recruited to many TEs in the absence of DNA methylation machinery and sometimes also co-occur with DNA methylation. In this study, we show that TEs can also be solely targeted by H3K27me3 in wild-type Arabidopsis plants. These H3K27me3-marked TEs not only comprise degenerate relics but also seemingly intact copies that display the epigenetic features of responsive PcG target genes as well as an active H3K27me3 regulation. We also show that H3K27me3 can be deposited on newly inserted transgenic TE sequences in a TE-specific manner indicating that silencing is determined in cis. Finally, comparison of Arabidopsis natural accessions reveals the existence of a category of TEs - which we refer to as "bifrons" - that are marked by DNA methylation or H3K27me3 depending on the ecotype. This variation can be linked to intrinsic TE features and to trans- acting factors, and reveals a change in epigenetic status across TE lifespan. Our study sheds light on an alternative mode of TE silencing associated with H3K27me3 instead of DNA methylation in flowering plants. It also suggests dynamic switching between the two epigenetic marks at the species level, a new paradigm that might extend to other multicellular eukaryotes.

molecular biology↗

bioRxiv2023

Widespread transcriptional regulation from within transcribed regions in plants

Much of what we know about eukaryotic transcription stems from animals and yeast, however, plants have evolved separately for 1.6 billion years, leaving ample time for divergence in transcriptional regulation. Here, we set out to elucidate fundamental properties of cis-regulatory sequences in plants. Using massively parallel reporter assays across four plant species, we demonstrate the central role of sequences downstream of the transcription start site (TSS) in transcriptional regulation. Unlike animal enhancers that are position-independent, plant regulatory elements depend on their position, as altering their location relative to the TSS significantly affects transcription. We highlight the importance of the region downstream of the TSS in regulating transcription by identifying a DNA motif that is conserved across vascular plants and is sufficient to enhance gene expression in a dose-dependent manner. The identification of a large number of position-dependent enhancers points to fundamental differences in gene regulation between plants and animals.

systems biology↗

bioRxiv2023

Long non-coding RNAs contribute to DNA damage resistance in Arabidopsis thaliana

Efficient repair of DNA lesions is essential for faithful transmission of genetic information between somatic cells and for genome integrity across generations. Plants have multiple, partially redundant and overlapping DNA repair pathways, probably due to the less constricted germline and the inevitable exposure to light including higher energy wavelengths. Many proteins involved in DNA repair and their mode of actions are well described. In contrast, a role for DNA damage-associated RNA components, evident from many other organisms, is less well understood. Here, we have challenged young Arabidopsis thaliana plants with two different types of genotoxic stress and performed de novo assembly and transcriptome analysis. We identified three long non-coding RNAs (lncRNAs) that are lowly or not expressed under regular conditions but up-regulated or induced by DNA damage. To understand their potential role in DNA repair, we generated CRISPR/Cas deletion mutants and found that the absence of the lncRNAs impairs the recovery capacity of the plants from genotoxic stress. The genetic loci are highly conserved among world-wide distributed Arabidopsis accessions and within related species in the Brassicaceae group. Together, these results suggest that the lncRNAs have a conserved function in connection with DNA damage and provide a basis for a mechanistic analysis of their role.

molecular biology↗

bioRxiv2023

Population-level annotation of lncRNAs in Arabidopsis thaliana reveals extensive expression and epigenetic variability associated with TE-like silencing

Long non-coding RNAs (lncRNAs) are understudied and underannotated in plants. In mammals, lncRNA loci are nearly as ubiquitous as protein-coding genes, and their expression is highly variable between individuals of the same species. Using Arabidopsis thaliana as a model, we aimed to understand the true scope of lncRNA transcription across plants from different regions and study its natural variation. We used transcriptome deep sequencing datasets spanning hundreds of natural accessions and several developmental stages to create a population-wide annotation of lncRNAs, revealing thousands of previously unannotated lncRNA loci. While lncRNA transcription is ubiquitous in the genome, most loci appear to be actively silenced and their expression is extremely variable between natural accessions. This high expression variability is largely caused by the high variability of repressive chromatin levels at lncRNA loci. High variability was particularly common for intergenic lncRNAs (lincRNAs), where pieces of transposable elements (TEs) present in 50% of these lincRNA loci are associated with increased silencing and variation, and such lncRNAs tend to be targeted by the TE silencing machinery. We create a population-wide lncRNA annotation in A. thaliana and improve our understanding of plant lncRNA genome biology, raising fundamental questions about what causes transcription and silencing across the genome. One-sentence summarylncRNA loci are plentiful in the A. thaliana genome, but their expression is extremely variable and largely repressed, with TE pieces enriched in intergenic lncRNAs aiding variability and silencing.

genomics↗

bioRxiv2023

Cell-cycle status of male and female gametes during Arabidopsis reproduction

Fertilization in Arabidopsis thaliana is a highly coordinated process that begins with a pollen tube delivering the two sperm cells into the embryo sac. Each sperm cell can then fertilize either the egg or the central cell to initiate embryo or endosperm development, respectively. The success of this double fertilization process requires a tight cell cycle synchrony between the male and female gametes to allow karyogamy (nuclei fusion). However, the cell cycle status of the male and female gametes during fertilization still remains elusive as DNA quantification and DNA replication assays have given conflicting results1-4. Here, to reconcile these results, we quantified the DNA replication state by DNA sequencing and performed microscopic analyses of fluorescent markers covering all the phases of the cell cycle. We show that male and female gametes in Arabidopsis are both arrested prior to DNA replication at maturity and initiate their DNA replication only during fertilization.

plant biology↗

bioRxiv2022

On the Causes of Gene-Body Methylation Variation in Arabidopsis thaliana

Gene-body methylation (gbM) refers to sparse CG methylation of coding regions, which is especially prominent in evolutionarily conserved house-keeping genes. It is found in both plants and animals, but is directly and stably (epigenetically) inherited over multiple generations in the former. Studies in Arabidopsis thaliana have demonstrated that plants originating from different parts of the world exhibit genome-wide differences in gbM, which could reflect direct selection on gbM, but which could also reflect an epigenetic memory of ancestral genetic and/or environmental factors. Here we look for evidence of such factors in F2 plants resulting from a cross between a southern Swedish line with low gbM and a northern Swedish line with high gbM, grown at two different temperatures. Using bisulfite-sequencing data with nucleotide-level resolution on hundreds of individuals, we confirm that CG sites are either methylated (nearly 100% methylation across sampled cells) or unmethylated (approximately 0% methylation across sampled cells), and show that the higher level of gbM in the northern line is due to more sites being methylated. Furthermore, methylation variants almost always show Mendelian segregation, consistent with their being directly and stably inherited through meiosis. To explore how the differences between the parental lines could have arisen, we focused on somatic deviations from the inherited state, distinguishing between gains (relative to the inherited 0% methylation) and losses (relative to the inherited 100% methylation) at each site in the F2 generation. We demonstrate that deviations predominantly affect sites that differ between the parental lines, consistent with these sites being more mutable. Gains and losses behave very differently in terms of the genomic distribution, and are influenced by the local chromatin state. We find clear evidence for different trans-acting genetic polymorphism affecting gains and losses, with those affecting gains showing strong environmental interactions (GxE). Direct effects of the environment were minimal. In conclusion, we show that genetic and environmental factors can change gbM at a cellular level, and hypothesize that these factors can also lead to transgenerational differences between individuals via the inclusion of such changes in the zygote. If true, this could explain genographic pattern of gbM with selection, and would cast doubt on estimates of epimutation rates from inbred lines in constant environments. Author summaryGene-body methylation, the sparse CG methylation that is associated with house-keeping genes, is found in both plants and animals, but can be directly inherited in the former. Recently, we discovered that Arabidopsis thaliana originating from different geographic regions exhibit different patterns of gbM, which could be due to direct selection on gbM, but could also reflect a transgenerational memory of genetic or environmental factors. Here we look for evidence of such factors using a genetic cross between two natural inbred lines: one with high, and one with low gbM. We confirm that methylation states are stably inherited, but also see large somatic deviations from the inherited state, in particular at sites that differ between the parental lines. We demonstrate that these deviations are affected by genetic variants in interaction with the environment, and hypothesize that geographic differences in gbM arise through the inclusion of such deviations in the zygote.

genetics↗

bioRxiv2022

A globally distributed major virus-resistance association in Arabidopsis thaliana

Plant viruses account for enormous agricultural losses worldwide, and the most effective way to combat them is to identify genetic material conferring plant resistance to these pathogens. Aiming to identify genetic associations with responses to infection, we screened a large panel of Arabidopsis thaliana natural inbred lines for four disease-related traits caused by infection by A. thaliana-naive and -adapted isolates of the natural pathogen turnip mosaic virus (TuMV). We detected a strong, replicable association in a 1.5 Mb region on chromosome 2 with a 10-fold increase in relative risk of systemic necrosis. The region contains several plausible causal genes as well as abundant structural variation, including an insertion of a Copia transposon into a Toll/interleukin receptor (TIR-NBS-LRR) coding for a gene involved in defense, that could be either a driver or a consequence of the disease-resistance locus. When inoculated with TuMV, loss-of-function mutant plants of this gene exhibited different symptoms than wild-type plants. The direction and severity of symptom differences depended on the adaptation history of the virus. This increase in symptoms severity was specific for infections with the adapted isolate. Necrosis-associated alleles are found worldwide, and their distribution is consistent with a trade-off between resistance during viral outbreaks and a cost of resistance otherwise, leading to negative frequency-dependent selection.

genetics↗

bioRxiv2022

Locally adaptive temperature response of vegetative growth in Arabidopsis thaliana

We investigated early vegetative growth of natural Arabidopsis thaliana accessions in cold, non-freezing temperatures, similar to temperatures these plants naturally encounter in fall at northern latitudes. We found that accessions from northern latitudes produced larger seedlings than accessions from southern latitudes, partly as a result of larger seed size. However, their subsequent vegetative growth when exposed to colder temperatures was slower. The difference was too large to be explained by random population differentiation, and is thus suggestive of local adaptation, a notion that is further supported by substantial transcriptome and metabolome changes in northern accessions. We hypothesize that the reduced growth of northern accessions is an adaptive response, and a consequence of reallocating resources towards cold acclimation and winter survival.

plant biology↗

bioRxiv2022

Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes

Genome-wide association studies (GWAS) have revealed that the striking natural variation for DNA CHH-methylation (mCHH; H is A, T, or C) of transposons has oligogenic architecture involving major alleles at a handful of known methylation regulators. Here we use a conditional GWAS approach to show that CHG-methylation (mCHG) has a similar genetic architecture -- once mCHH is statistically controlled for. We identify five key trans-regulators that appear to modulate mCHG levels, and show that they interact with a previously identified modifier of mCHH in regulating natural transposon mobilization.

genetics↗