Biology subjects

Springer, N. M.

Publications and source records attributed to Springer, N. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Promoter Structural Variants are Drivers of Genome-Wide Differential Expression in Maize

BackgroundStructural variants (SVs) are large insertions or deletions of DNA sequences. While less numerous than single nucleotide polymorphisms, SVs often account for a greater proportion of nucleotide differences between genomes. Their size and frequent association with repetitive sequences has historically hindered their detection, which has limited the ability to associate this variation with molecular and phenotypic trait variation. While some SVs have been linked to observable traits, it remains unclear whether such effects are rare or broadly distributed across the genome. ResultsTo test for genome-wide relationships between SVs and gene expression, we analyzed genome assemblies and transcriptomic data from 10 tissues across 26 diverse maize inbred lines. We identified SVs amongst these lines and examined variants located within the 1kb promoter region upstream of genes. Thousands of genes showed expression differences associated with promoter SVs, often in a tissue-specific manner. One common feature of these SVs was the presence of transposable element sequences. LTR retrotransposons were enriched amongst promoter SVs associated with differential expression and often reduced expression of the nearby gene. Despite widespread expression changes, we found no enrichment for specific biological functions or pathways among affected genes. ConclusionsOur findings indicate that extant TE-mediated promoter SVs play a significant role in shaping gene expression patterns across the maize genome. However, their phenotypic effects appear limited or context-dependent, suggesting that many variants may have minimal impact outside specific developmental stages or environmental conditions.

genomics↗

bioRxiv2025

SWIF-TE: identifying novel transposable element insertions from short read data

Transposable element (TE) insertion polymorphisms (TIPs) are TEs not in the same location between individuals. TIPs have contributed to genomic and phenomic variation but have been historically difficult to study due to their repetitive nature. Here, we describe a fast and memory-efficient tool to identify novel TIPs from short read sequences. SWIF-TE was able to identify 1,438 insertions at a precision rate of 27% using 0.10 Gb of memory and 0.82 hours of runtime from 15x resequencing data of a non-reference maize inbred. SWIF-TE is a powerful tool for studying TE variation in species with TE-rich genomes.

bioinformatics↗

bioRxiv2025

DNA repair under heat: DNA Polymerase {lambda} modulates heat stress-induced mutagenesis in plants

Mutation rates can increase substantially under environmental stress, known as stress-induced mutagenesis. Specifically, heat stress has been shown to elevate mutation rates, thereby enhancing genetic variability and facilitating adaptation. However, the underlying mechanisms remain elusive in eukaryotes. Here, we investigated how heat stress affects DNA repair and induces mutations both locally and globally through CRISPR-Cas9 targeted DNA breaks and whole genome sequencing analyses in Arabidopsis thaliana. Heat stress was found to enhance CRISPR editing efficiency across all chromatin contexts, with particularly significant increases, up to 29.9-fold, in heterochromatic regions. Moreover, heat stress consistently shifts mutation outcomes toward 1-bp insertions regardless of chromatin states. We identified a heat-inducible, error-prone DNA polymerase, Pol{lambda}, as the key mediator of mutation profile changes. When extending our investigation from targeted mutations to genome-wide effects, we found that increases in global mutation rates under heat stress are also dependent on Pol{lambda}. Single-cell transcriptomic analysis further demonstrated that Pol{lambda} expression is tightly regulated and cell-type specific, with the highest expression levels in central zone meristematic cells. Together, these findings provide practical applications for improving editing efficiency in heterochromatic regions and fundamental insights into heat-induced mutagenesis, establishing Pol{lambda} as a crucial mediator of stress-induced genetic variation in plants.

plant biology↗

bioRxiv2024

Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions

Transcription factors (TFs) play important roles in regulation of gene expression and phenotype. A variety of approaches have been utilized to develop gene-regulatory networks (GRNs) to predict the regulatory targets for each TF, such as yeast-one-hybrid (Y1H) screens and gene co-expression network (GCN) analysis. Here we identified potential TF targets and used a reverse genetics approach to test the predictions of several GRNs in maize. Loss-of-function mutant alleles were isolated for 22 maize TFs. These mutants did not exhibit obvious morphological phenotypes. However, transcriptomic profiling identified differentially expressed genes in each of the mutant genotypes, and targeted metabolic profiling indicated variable phenolic accumulation in some mutants. An analysis of expression levels for predicted target genes based on Y1H screens identified a small subset of predicted targets that exhibit altered expression levels. The analysis of predicted targets from GCN-based methods found significant enrichments for prediction sets of some TFs, but most predicted targets did not exhibit altered expression. This could result from false-positive GCN predictions, a TF with a secondary regulatory role resulting in minor effects on gene regulation, or redundant gene regulation by other TFs. Collectively, these findings suggest that loss-of-function for single uncharacterized TFs might have limited phenotypic impacts but can reveal subsets of GRN predicted targets with altered expression.

plant biology↗

bioRxiv2024

Temporally resolved growth patterns reveal novel information about the polygenic nature of complex quantitative traits

Plant height can be an indicator of plant health across environments and used to identify superior genotypes or evaluate abiotic stress factors. Typically plant height is measured at a single time point when plants have reached terminal height for the season. Evaluating plant height using unoccupied aerial vehicles (UAVs) is faster, allowing for measurements throughout the growing season, which facilitates a better understanding of plant-environment interactions and the genetic basis of this complex trait. To assess variation throughout development, plant height data was collected weekly for a panel of [~]500 diverse maize inbred lines over four growing seasons. The variation in plant height throughout the season was significantly explained by genotype, year, and genotype-by-year interactions to varying extents throughout development. Genome-wide association studies revealed significant SNPs associated with plant height and growth rate at different parts of the growing season specific to certain phases of vegetative growth that would not be identified by terminal height associations alone. When plant height growth rates were compared to growth rates estimated from canopy cover, greater Frechet distance stability was observed in plant height growth curves than for canopy cover. This indicated canopy cover may be more useful for understanding environmental modulation of overall plant growth and plant height better for understanding genotypic modulation of overall plant growth. This study demonstrated that substantial information can be gained from high temporal resolution data to understand how plants differentially interact with the environment and can enhance our understanding of the genetic basis of complex polygenic traits.

plant biology↗

bioRxiv2024

Dissecting the temporal phenomics and genomics of maize canopy cover using UAV mediated image capture

Canopy cover is an important agronomic trait influencing photosynthesis, weed suppression, biomass accumulation, and yield. Conventional methods to quantify canopy cover are time and labor-intensive. As such, little is known about how canopy cover develops over time, the stability of canopy cover across environments, or the genetic architecture of canopy cover. We used unoccupied aerial vehicle-mediated image capture to quantify plot-level canopy coverage in maize throughout the growing season. Images of 501 diverse inbred lines were acquired between 300 and 1300 growing degree days in the 2018-2021 growing seasons. We observed that the maize canopy developed following a logistic curve. Phenotypic variation in percent canopy coverage and canopy growth rate was explained by genetic and environmental factors and genotype-by-environment interactions, however the percent of variance explained by each factor varied throughout the growing season. Environmental factors explained the largest portion of trait variance during the adult vegetative growth stage and had a larger impact on canopy growth rates than percent canopy coverage. We conducted multiple genome wide association studies and found that canopy cover is a complex, polygenic trait with a diverse range of marker trait associations throughout development. The change in associations indicated that single time point phenotyping was insufficient to capture the full phenomic and genetic diversity of canopy cover in maize.

plant biology↗

bioRxiv2024

Prioritizing Metabolic Gene Regulators through Multi-Omic Network Integration in Maize

Gene regulatory networks (GRNs) link transcription factors (TFs) to the biological processes they control. Assembling them remains difficult because the relevant data types (gene expression, protein-DNA interactions, and genetic variation) are large, heterogeneous, and rarely combined. Here, we developed and benchmarked a framework that integrates these data into TF-function predictions in maize. We assembled four complementary TF-target gene network layers, based on expression, protein-DNA interaction, trans-expression quantitative trait loci (eQTL), and cis-eQTL-supported interaction, from 46 Random Forest (RF)-inferred regulatory networks, 283 protein-DNA interaction assays, and eQTLs derived from 16 million SNPs across 304 inbred lines. Together these layers comprised ~4.6 million interactions. We then compared three strategies for integrating them, benchmarking each against published TF knockout data. A network-based approach, which represents every gene as a low-dimensional vector (embedding) learned from the combined network, outperformed the two overlap-based strategies, annotating over eight times more TFs (~3,000), agreeing most closely with gene knockout responses where predictions existed, and remaining robust when individual layers lacked data. The predictions recovered TF functions and predicted new regulators of hormone, developmental, and metabolic processes, which we prioritized per process and mapped to specific conditions. Using similarity on the low-dimensional vector representation (embedding), we further identified candidate functionally redundant or diverged TF paralogs. Because it relies only on data types now common across species, the framework provides a generalizable template for prioritizing regulatory genes in maize and other plants.

plant biology↗

bioRxiv2023

Mutator transposon insertions within maize genes often provide a novel outward reading promoter

The highly active family of Mutator (Mu) DNA transposons has been widely used for forward and reverse genetics in maize. There are examples of Mu-suppressible alleles which result in conditional phenotypic effects based on the activity of Mu. Phenotypes from these Mu- suppressible mutations are observed in Mu-active genetic backgrounds, but absent when Mu activity is lost. For some Mu-suppressible alleles, phenotypic suppression likely results from an outward-reading promoter within Mu that is only active when the autonomous Mu element is silenced or lost. We isolated 35 Mu alleles from the UniformMu population that represent insertions in 24 different genes. Most of these mutant alleles are due to insertions within gene coding sequences, but several 5 UTR and intron insertions were included. RNA-seq and de novo transcript assembly were utilized to document the transcripts produced from 33 of these Mu insertion alleles. For 20 of the 33 alleles, there was evidence of transcripts initiating within the Mu sequence reading through the gene. This outward-reading promoter activity was detected in multiple types of Mu elements and doesnt depend on the orientation of Mu. Expression analyses of Mu-initiated transcripts revealed the Mu promoter often provides gene expression levels and patterns that are similar to the wild-type gene. These results suggest the Mu promoter may represent a minimal promoter that can respond to gene cis-regulatory elements. Findings from this study have implications for maize researchers using the UniformMu population, and more broadly highlights a strategy for transposons to co-exist with their host. Article SummaryMutator (Mu) transposable elements are a widely used tool for insertional mutagenesis in maize and often insert in the 5 regions of genes. The characterization of transcripts for Mu insertion alleles reveals complex transcripts. These often result in one transcript that covers the first portion of the gene terminating in Mu and a second transcript initiating within Mu covering the latter portion of the gene. This may reflect a strategy for Mu to minimize the consequences of insertions within genes.

plant biology↗

bioRxiv2022

Mapping Responsive Genomic Elements to Heat Stress in a Maize Diversity Panel

Many plant species exhibit genetic variation for tolerating environmental stress. A transcriptome investigation of over 100 maize inbreds revealed many cis- and trans-acting eQTLs that influence the expression response to heat stress. The cis-acting eQTL in response to heat stress are identified in genes with differential responses to heat stress between genotypes as well as genes that are only expressed under heat stress. The cis-acting variants for heat stress responsive expression likely result from distinct promoter activities and the differential heat responses of the alleles were confirmed for selected genes using transient expression assays. Global foot-printing of transcription factor binding was performed in control and heat stress conditions to document regions with heat-enriched transcription factor binding occupancies. Footprints enriched near proximal regions of characterized heat-responsive genes in a large association panel can be utilized for prioritizing functional genomic regions that regulate genotype-specific responses under heat stress.

plant biology↗

bioRxiv2022

Conserved and variable responses of the HEAT SHOCK FACTOR transcription factor family in maize and Setaria viridis

Responding to the environment is a core aspect of plant growth and development. Mounting an effective response is important for plants to balance growth and survival. The HEAT SHOCK FACTOR (HSF) transcription factor family is a central and required component of plant heat stress responses and acquired thermotolerance. The HSF family has dramatically expanded in plant lineages, often including a repertoire of 20 or more genes. Here we assess the composition and heat responsiveness of the HSF family in Setaria viridis (Setaria), a model C4 panicoid grass, and make targeted comparisons between the HSF families of Setaria and maize. Examples of both conserved and variable expression responses to a heat stress event were observed when comparing the two species. Novel and existing data on chromatin accessibility, histone modifications, and genome-wide DNA binding profiles were utilized to assess the chromatin of HSF family members with distinct responses to heat stress. We observed significant variability for both expression and chromatin state within syntenic and orthologous sets of HSFs between Setaria and maize, as well as between syntenic pairs of maize HSFs retained following its most recent genome duplication event. These observations collectively support a complex scenario of expansion and sub-functionalization within this transcription factor family that has significant untapped potential for better understanding the evolution of large gene families. Significance StatementA comparison of the Heat Shock Factor transcription factors in maize and Setaria reveals examples of consistent and variable expression responses to heat stress and provides insights into the role of chromatin in predicting expression responses.

plant biology↗

bioRxiv2022

Critical Role of Insertion Preference for Invasion Trajectory of Transposons

Transposable elements (TEs) are mobile DNA sequences that have been highly successful at invading eukaryotic genomes. It is unclear how TE families reach high copy number given the expectation that some novel insertions will be deleterious. It has been hypothesized that TE families may evolve to target and insert into specific DNA sequences to adjust the underlying distribution of fitness effects for new insertions. Preferentially inserting into neutral sites could minimize the cumulative deleterious load of a TE family, allowing the mean TE copy number to increase with less risk for host population extinction. To test this hypothesis, we constructed simulations to explore how the transposition probability and insertion preference of a TE family influence the evolution of mean TE copy number and host population size, allowing for extinction. We find that extinction is most common in our simulations under high transposition probabilities, but, as we reduce transposition rates, the risk of extinction persists while the preference for neutral insertion sites is high. In the absence of mechanisms that regulate TE transposition, a preference for neutral insertion sites is not protective and, in fact, actively accelerates both an increase in TE copy number and the time to population extinction.

evolutionary biology↗

bioRxiv2022

Drastic differential CRISPR-Cas9 induced mutagenesis influenced by DNA methylation and chromatin features

CRISPR-Cas9 mediated genome editing has been widely adopted for basic and applied biological research in eukaryotic systems. While many studies considered DNA sequences of CRISPR target sites as the primary determinant for CRISPR mutagenesis efficiency and mutation profiles, increasing evidence revealed the significant role of chromatin context. Nonetheless, most of the prior studies were limited by the lack of sufficient epigenetic resources and/or by only transiently expressing CRISPR-Cas9 in a short time window. In this study, we leveraged the wealth of high-resolution epigenomic resources in Arabidopsis thaliana to address the impact of chromatin features on CRISPR-Cas9 mutagenesis using stable transgenic plants. Our results indicated that DNA methylation and chromatin features could lead to significant variations in mutagenesis efficiency by up to 250 folds. Low mutagenesis efficiencies were mostly associated with repressive heterochromatic features. This repressive effect appeared to persist through cell divisions but could be alleviated through substantial reduction of DNA methylation at CRISPR target sites. Moreover, specific chromatin features, such as H3K4me1, H3.3, and H3.1, appear to be associated with significant variations in CRISPR-Cas9 mutation profiles reflected by the 1 bp insertion rates. Our findings provided strong evidence that specific chromatin features could have significant and lasting impacts on both CRISPR-Cas9 mutagenesis efficiency and DNA double strand break repair outcomes.

plant biology↗

bioRxiv2022

Limited consequences for loss of RNA-directed DNA methylation in Setaria viridis domains rearranged methyltransferase (DRM) mutants

The Domains Rearranged Methyltransferases (DRMs) are crucial for RNA-directed DNA methylation (RdDM) in plant species. Setaria viridis is a model monocot species with a relatively compact genome that has limited transposable element content. CRISPR-based genome editing approaches were used to create loss-of-function alleles for the two putative functional DRM genes in S. viridis to probe the role of RdDM. The analysis of drm1ab double mutant plants revealed limited morphological consequences for the loss of RdDM. Whole-genome methylation profiling provided evidence for wide-spread loss of methylation in CHH sequence contexts, particularly in regions with high CHH methylation in wild-type plants. Evidence was also found for locus-specific loss of CG and CHG methylation, even in some regions that lack CHH methylation. Transcriptome profiling identified a limited number of genes with altered expression in the drm1ab mutants. The majority of genes with elevated CHH methylation directly surrounding the transcription start site or in nearby promoter regions do not have altered expression in the drm1ab mutant even when this methylation is lost, suggesting limited regulation of gene expression by RdDM. Detailed analysis of the expression of transposable elements identified several transposons that are transcriptionally activated in drm1ab mutants. These transposons likely require active RdDM for maintenance of transcriptional repression. Significance statementMethylation profiling of Setaria viridis plants that lack functional Domains Rearranged Methyltransferase genes reveal widespread loss of DNA methylation in the CHH sequence context. Transcriptome analysis reveals a small set of genes and transposons that are silenced by RNA-directed DNA methylation.

plant biology↗

bioRxiv2021

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

Accessible chromatin regions are critical components of gene regulation but modeling them directly from sequence remains challenging, especially within plants, whose mechanisms of chromatin remodeling are less understood than in animals. We trained an existing deep learning architecture, DanQ, on leaf ATAC-seq data from 12 angiosperm species to predict the chromatin accessibility of sequence windows within and across species. We also trained DanQ on DNA methylation data from 10 angiosperms, because unmethylated regions have been shown to overlap significantly with accessible chromatin regions in some plants. The across-species models have comparable or even superior performance to a model trained within species, suggesting strong conservation of chromatin mechanisms across angiosperms. Testing a maize held out model on a multi-tissue scATAC panel revealed our models are best at predicting constitutively-accessible chromatin regions, with diminishing performance as cell-type specificity increases. Using a combination of interpretation methods, we ranked JASPAR motifs by their importance to each model and saw that the TCP and AP2/ ERF transcription factor families consistently ranked highly. We embedded the top three JASPAR motifs for each model at all possible positions on both strands in our sequence window and observed position- and strand-specific patterns in their importance to the model. With our cross-species "a2z" model it is now feasible to predict the chromatin accessibility and methylation landscape of any angiosperm genome.

bioinformatics↗

bioRxiv2021

The maize gene maternal depression of r1 (mdr1) encodes a DNA glycosylase with maternal and paternal fertility functions

Demethylation of transposons can activate expression of nearby genes and cause imprinted gene expression in endosperm, and it is hypothesized to lead to expression of transposon siRNAs that reinforce silencing in the next generation through transfer either into egg or embryo. Here we describe maternal derepression of r1 (mdr1), which encodes a DNA glycosylase with homology to Arabidopsis DEMETER and which is partially responsible for demethylation of thousands of regions in endosperm. Instead of promoting siRNA expression in endosperm, MDR1 activity inhibits it. Methylation of most repetitive DNA elements in endosperm is not significantly affected by MDR1, with an exception of Helitrons. While maternally-expressed imprinted genes preferentially overlap with MDR1 demethylated regions, the majority of genes that overlap demethylated regions are not imprinted. Double mutant megagametophytes lacking both MDR1 and its close homolog DNG102 result in early seed failure, and double mutant microgametophytes fail pre-fertilization. These data establish DNA demethylation by glycosylases as essential in maize endosperm and pollen and suggest that neither transposon repression nor genomic imprinting are its main function in endosperm.

genetics↗

bioRxiv2021

Plant trait heterosis is quantitatively associated with expression heterosis of plastid ribosomal proteins

The use of hybrids is widespread in agriculture, yet the molecular basis for hybrid vigor (heterosis) remains obscure. To identify molecular components that may contribute to the known higher photosynthetic capacity of maize hybrids, we analyzed proteomic and transcriptomic data from seedling leaf tissues of the hybrid, B73xMo17, and its inbred parents. Subunits of complexes required for protein synthesis in the chloroplast and for the light reactions of photosynthesis were expressed above mid-parent and high-parent levels, respectively. Nuclear and plastid-encoded subunits were expressed similarly and in a dominant pattern with B73 as the high-parent for most proteins. The reciprocal hybrid displayed the same pattern with B73 still the dominant parent. Protein expression patterns were mostly the same in the adult leaf blade. To rank the relevance of expression differences to trait heterosis, we compared seedling leaf protein levels to adult plant heights of 15 hybrids. Expression heterosis (hybrid/mid-parent expression levels) was most positively correlated with plant height heterosis (hybrid/mid-parent plant height) for the plastid-encoded and nuclear-encoded chloroplast ribosomal proteins; the cytosolic ribosomal proteins were slightly less correlated. Ethylene biosynthetic enzymes were expressed below mid-parent levels in the hybrids, and the ethylene biosynthesis mutant, acs2/acs6, largely phenocopied the hybrid proteome, indicating that a reduction in ethylene biosynthesis may mediate the differences between inbreds and their hybrids. Levels of jasmonic acid biosynthetic enzymes were reduced in both acs2/acs6 and the hybrid, and expression heterosis levels of these proteins were the most negatively correlated with plant height heterosis. Significance StatementHeterosis (hybrid vigor) boosts the productivity and resilience of crops and livestock above the levels of both parents, yet its underlying mechanisms remain unknown. We analyzed expression patterns of proteins in maize hybrids and their inbred parents. Differences in several molecular machines and biochemical pathways were found and quantitatively assessed using a panel of 15 hybrids. Seedling leaf chloroplast ribosomal proteins were able to quantitatively infer levels of adult plant heterosis. Expression levels of biosynthetic enzymes for the stress hormone, ethylene, were reduced in hybrids as was previously reported for the dicot Arabidopsis. Mutation of these genes in a maize inbred caused the proteome to resemble a hybrid. Repression of ethylene biosynthesis may be a conserved component of heterosis physiology.

plant biology↗

bioRxiv2021

Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize

Changes in gene expression are important for response to abiotic stress. Transcriptome profiling performed on maize inbred and hybrid genotypes subjected to heat or cold stress identifies many transcript abundance changes in response to these environmental conditions. Motifs that are enriched near differentially expressed genes were used to develop machine learning models to predict gene expression responses to heat or cold. The best performing models utilize the sequences both upstream and downstream of the transcription start site. Prediction accuracies could be improved using models developed for specific co-expression clusters compared to using all up- or down-regulated genes or by only using motifs within unmethylated regions. Comparisons of expression responses in multiple genotypes were used to identify genes with variable response and to identify cis- or trans-regulatory variation. Models trained on B73 data have lower performance when applied to Mo17 or W22, this could be improved by using models trained on data from all genotypes. However, the models have low accuracy for correctly predicting genes with variable responses to abiotic stress. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and provides a framework for developing models to predict expression response to abiotic stress across multiple genotypes. One sentence summaryTranscriptome profiling of maize inbred and hybrid seedlings subjected to heat or cold stress was used to identify key cis-regulatory elements and develop models to predict gene expression responses.

plant biology↗

bioRxiv2020

Population Level Variation of Transposable Elements 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 non-redundant TEs that were previously annotated in four genome assemblies including B73, Mo17, PH207, and W22. Different orders of TEs (i.e. LTRs, Helitrons, 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.

plant biology↗