The evolution of locally adapted chromosome inversion in Mimulus guttatus
Genome assemblies from long read-sequencing reveals insights about adaptive inversions in Mimulus.
Machine learning models reveal the importance of time-point specific cis-regulatory elements in Arabidopsis thaliana wounding response
Plant responses to environmental stimuli require complex gene expression reprogramming regulated at multiple levels. Cis-regulatory elements (CREs) can activate or repress gene expression through transcription factor (TF) binding. Moreover, the temporal nature of stress responses adds another layer of complexity wherein sets of genes are regulated differently based on their timing of expression during stress […]
Discovery of a species-specific partial duplicate gene in Arabidopsis thaliana helps explain how new functions evolve
Gene duplications are common in plants and create a potential repertoire for functional novelty. Gene duplicates can arise from a variety of mechanisms and place the newly copied gene in a new chromatin environment with different regulatory contexts. After gene duplication, several fates are possible, but in the overwhelming majority of cases, one of the […]
Epigenomic atlas in wheat reveals regulatory elements specifying subgenome divergence
Whole-genome duplication or polyploidy is widespread throughout eukaryotes but is most prevalent in flowering plant lineages. The evolutionary processes following polyploidization, such as genome downsizing, biased fractionation, modulation of gene expression, and epigenomic reprogramming, can profoundly affect genome complexity and generate evolutionarily beneficial genetic diversity. Compared to its diploid and tetraploid progenitors, the allohexaploid common […]
Cellular-identity and regulatory variation in model plants at single-nuclei resolution
The cis-regulatory elements facilitate the binding of sequence-specific transcription factors for activating or repressing the expression of target genes. The expression level of each gene may vary in different cell types due to differential regulatory elements within the accessible chromatin regions (ACRs), which can dictate cell-fate decisions and developmental trajectories. Therefore, it has become essential […]
Vision, challenges and opportunities for a Plant Cell Atlas
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the […]
Predicting Adult Complex Traits from Early Development Transcript Data in Maize
Comparative profiling examines roles of DNA regulatory sequences and accessible chromatin during cold stress response in grasses
Physical access to regulatory DNA, including cis-regulatory sequences found within proximal promoters and distal enhancer elements, is a vital property of chromatin. In turn, their access is determined by nucleosome occupancy and posttranslational modification of histone proteins. A continuum of chromatin accessibility states from closed to permissive and open chromatin is a critical determinant of chromatin’s […]
The R-loop: An additional chromatin feature for gene regulation in Arabidopsis
Gene Dosage Balance Immediately following Whole-Genome Duplication in Arabidopsis
Flowering plants have witnessed multiple cycles of whole-genome duplication (WGD) over the past 200 million years of evolution. Typically, WGD increases genome size and gene content, followed by gene loss, or fractionation, depending on functional categories. Certain classes of genes are retained as duplicates for longer periods of evolutionary time. Duplicate genes provide a potential […]