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1. From duplication to divergence: Single-cell insights into transcriptional and cis-regulatory landscapes in soybean

   https://doi.org/10.1093/plcell/koaf279  

   Li, Xiang; Zhang, Xuan; Schmitz, Robert J (December 2025, The Plant Cell)

   Abstract Gene duplication is a major source of evolutionary innovation, enabling the emergence of novel expression patterns and functions. Leveraging single-cell genomics, we investigated the transcriptional and cis-regulatory landscapes of duplicated genes in cultivated soybean (Glycine max), which has undergone 2 rounds of whole-genome duplication. Our analysis revealed extensive diversity of transcriptional profiles within and across tissues among duplicated gene pairs. Within-tissue divergence was largely attributable to genetic variation in their associated accessible chromatin regions (ACRs), where cis-regulatory elements reside, whereas cross-tissue divergence was more likely shaped by dynamics in ACR chromatin accessibility profiles across tissues. Distinct duplication mechanisms also likely give rise to different types of cis-regulatory variants, contributing variably to transcriptional divergence. By comparing ACRs associated with gene sets derived from 2 rounds of whole-genome duplication and sharing a common ancestral gene, we found that most ACRs retained one or multiple corresponding duplicated sequences in which mutations gradually accumulated over time, while a subset likely arose de novo. Finally, we traced the evolution of cell-type-specific expression and cell-type-specific ACRs within duplicated gene sets, illustrating a powerful framework for identifying candidate regulatory regions driving cell-type-specific expression. Collectively, our findings highlight the important role of cis-regulatory evolution in shaping transcriptional divergence in a spatiotemporal manner, uncovered with the resolution of single-cell genomics. 

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2. A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus

   https://doi.org/10.1186/s12864-025-12137-0  

   Diaz, Isaac A; Ostovar, Talieh; Chen, Jinfeng; de_Dios, Emmanuel Avila; Piscatella, Ryan; Perez-Alfaro, Ruth S; Zayed, Omar; Saddoris, Sarah; Schmitz, Robert J; Wessler, Susan R; et al (December 2025, BMC Genomics)

   Abstract BackgroundGenetic and epigenetic perturbation of cis-regulatory sequences can shift patterns of gene expression and result in novel phenotypes. Phased genome assemblies now enable the local dissection of linkages between cis-regulatory sequences, including their epigenetic state, and allele-specific gene expression to further characterize gene regulation and resulting phenotypes in heterozygous genomes. ResultsWe assembled a locally phased genome for a mandarin hybrid named ‘Fairchild’ to explore the molecular signatures of allele-specific gene expression. With local genome phasing, genes with allele-specific expression were paired with haplotype-specific chromatin states, including levels of chromatin accessibility, histone modifications, and DNA methylation. We found that 30% of variation in allele-specific expression could be attributed to haplotype associated factors, with allelic levels of chromatin accessibility and three histone modifications in gene bodies having the most influence. Structural variants in promoter regions were also associated with allele-specific expression, including specific enrichments of hAT and MULE-MuDR DNA transposon sequences. Integration of haplotype-resolved genetic and epigenetic landscapes with high-throughput phenotypic analysis of fruit traits in a panel of 154 accessions with mandarin and pummelo ancestry revealed that trait-associated variants were enriched in regions of open chromatin. Mining of trait-associated variants uncovered a Gypsy retrotransposon insertion in a gene that regulates potassium transport and may contribute to the reduction in fruit size that is observed in mandarins. Conclusions​​Using a locally phased assembly of a heterozygous cultivar of citrus, we dissected the interplay between genetic variants and molecular phenotypes to reveal cis-regulatory sequences with potential functional effects on phenotypes relevant for genetic improvement. 

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3. Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei

   https://doi.org/10.1186/s12870-023-04281-0  

   Debernardi, Juan M.; Burguener, German; Bubb, Kerry; Liu, Qiujie; Queitsch, Christine; Dubcovsky, Jorge (December 2023, BMC Plant Biology)

   Abstract BackgroundThe genetic information contained in the genome of an organism is organized in genes and regulatory elements that control gene expression. The genomes of multiple plants species have already been sequenced and the gene repertory have been annotated, however,cis-regulatory elements remain less characterized, limiting our understanding of genome functionality. These elements act as open platforms for recruiting both positive- and negative-acting transcription factors, and as such, chromatin accessibility is an important signature for their identification. ResultsIn this work we developed a transgenic INTACT [isolation of nuclei tagged in specific cell types] system in tetraploid wheat for nuclei purifications. Then, we combined the INTACT system together with the assay for transposase-accessible chromatin with sequencing [ATAC-seq] to identify open chromatin regions in wheat root tip samples. Our ATAC-seq results showed a large enrichment of open chromatin regions in intergenic and promoter regions, which is expected for regulatory elements and that is similar to ATAC-seq results obtained in other plant species. In addition, root ATAC-seq peaks showed a significant overlap with a previously published ATAC-seq data from wheat leaf protoplast, indicating a high reproducibility between the two experiments and a large overlap between open chromatin regions in root and leaf tissues. Importantly, we observed overlap between ATAC-seq peaks andcis-regulatory elements that have been functionally validated in wheat, and a good correlation between normalized accessibility and gene expression levels. ConclusionsWe have developed and validated an INTACT system in tetraploid wheat that allows rapid and high-quality nuclei purification from root tips. Those nuclei were successfully used to performed ATAC-seq experiments that revealed open chromatin regions in the wheat genome that will be useful to identify cis-regulatory elements. The INTACT system presented here will facilitate the development of ATAC-seq datasets in other tissues, growth stages, and under different growing conditions to generate a more complete landscape of the accessible DNA regions in the wheat genome. 

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4. A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution

   https://doi.org/10.1038/s41477-025-02106-6  

   Yan, Haidong; Mendieta, John P; Zhang, Xuan; Luo, Ziliang; Marand, Alexandre P; Liang, Yan; Minow, Mark_A A; Zhong, Yun; Jin, Yarong; Jang, Hosung; et al (October 2025, Nature Plants)

   Abstract Cis-regulatory elements (CREs) are essential for regulating gene expression, yet their evolutionary dynamics in plants remain elusive. Here we constructed a single-cell chromatin accessibility atlas forOryza sativafrom 103,911 nuclei representing 126 cell states across nine organs. Comparative genomics betweenO. sativaand 57,552 nuclei from four additional grass species (Zea mays,Sorghum bicolor,Panicum miliaceumandUrochloa fusca) revealed that chromatin accessibility conservation varies with cell-type specificity. Epidermal accessible chromatin regions in the leaf were less conserved compared to other cell types, indicating accelerated regulatory evolution in the L1-derived epidermal layer ofO. sativarelative to other species. Conserved accessible chromatin regions overlapping the repressive histone modification H3K27me3 were identified as potentially silencer-like CREs, as deleting these regions led to up-regulation of gene expression. This study provides a comprehensive epigenomic resource for the rice community, demonstrating the utility of a comparative genomics approach that highlights the dynamics of plant cell-type-specific CRE evolution. 

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5. Common Coronary Artery Disease Risk Variants in Endothelial Regulatory Elements Modulate Tetraspanin 14 Expression and Notch Signaling

   https://doi.org/10.1161/ATVBAHA.125.323330  

   Lee-Kim, Vivian S; Schnitzler, Gavin R; Fang, Shi; Mardani-Kamali, Neeka; Cai, Xiangmeng Shawn; Cui, Ran; Barry, Aurelie E; Zandavi, Miad; Yoo, Hyung-Jin; Kant, Shashi; et al (June 2026, Arteriosclerosis, Thrombosis, and Vascular Biology)

   Coronary artery disease (CAD) is a complex condition and remains the leading cause of mortality worldwide. Genome-wide association studies have identified a CAD risk locus on chromosome 10q23 that is independent of traditional risk factors, providing an opportunity to uncover novel molecular mechanisms contributing to CAD pathogenesis. METHODS: Improved fine-mapping approaches were used to prioritize noncoding variants at the 10q23 locus within the intronic region ofTSPAN14(tetraspanin 14). Regulatory elements harboring lead variants were functionally interrogated using chromatin accessibility, 3-dimensional chromatin organization, and clustered regularly interspaced short palindromic repeats–mediated deletion approaches in endothelial cells (ECs). Subsequently, TSPAN14 function in ECs was assessed using transcriptomic profiling, Notch signaling activation assays, and EC functional assay using gene knockout (KO) cell lines. RESULTS:Fine-mapping identified 2 lead variants, rs17680741 and rs12260962, located within regulatory elements predicted to affectTSPAN14expression in monocytes and ECs, respectively. Chromatin accessibility, organization, and enhancer deletion assays demonstrated EC-specific function for the rs12260962-harboring regulatory element inTSPAN14expression regulation. Loss ofTSPAN14resulted in significant transcriptomic changes related to Notch signaling, heart morphogenesis, cell adhesion, and wound healing. Functionally,TSPAN14 KOECs exhibited impaired cell-cell junction integrity, reduced repair capacity, and diminished mechanosensitive responses. CONCLUSIONS:Together, these data identify a regulatory element harboring CAD-associated variant at the 10q23 locus that modulatesTSPAN14expression and downstream Notch signaling in ECs, thereby linking genetic risk to endothelial dysfunction relevant to CAD pathogenesis. 

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