Biology subjects

Minow, M. A. A.

Publications and source records attributed to Minow, M. A. A..

8 recordsLinked to original sources

bioRxiv2026

Multimodal single cell analysis reveals a link between flowering and leaf initiation

Zea mays (maize) flowering time is genetically determined and a critical yield determinant. Yet mechanistic understanding of maize flowering remains poor. Indeterminate1 (Id1), a zinc-finger transcription factor (TF), is a monocot-conserved master regulator of maize flowering. Epistasis between Id1 and the ZeaCentroradialis-Delayed Flowering1 (Zcn-Dlf1) inductive pathway partly explains ID1 floral control; however, the strong mutant id1- floral delay is not explained by this pathway alone. To better characterize Id1 actions, we performed single-cell assay for transposase-accessible chromatin and single nucleus RNA sequencing (scATAC-seq and snRNA-seq) comparing Id1+ and id1- developing leaves. These analyses reveal id1- chromatin remodeling via TEOSINTE BRANCHED1 CYCLOIDEA PROLIFERATING CELL FACTOR (TCP) and APETALA2/ETHYLENE RESPONSEFACTOR (AP2/ERF) transcription factors and provide candidate direct targets that include AP2/ERF genes. These candidate direct targets include the family of {beta}-glucosidase genes that lose expression in id1-. Unexpectedly, CRISPR/Cas9 {beta}-glucosidase edits produced plants that phenocopied terminal ear1- (te1-) mutants. This phenocopy prompted an investigation into the genetic relationship between id1-, te1- and flowering. Surprisingly, id1- te1- plants exhibited a synergistic floral delay, producing ~90 leaves before inflorescence production. Beyond highlighting hitherto unappreciated Te1 autonomous flowering roles, this genetic synergy raises the hypothesis that meristem leaf primordia cessation underpins maize flowering.

plant biology↗

bioRxiv2026

Cell-type-specific regulatory variation shapes maize heterosis

Heterosis, the superior performance of hybrids over their parents, has been widely exploited to enhance crop productivity, but its underlying regulatory mechanisms remain incompletely understood. In particular, how cis-regulatory elements (CREs) vary between parents and hybrids, and how this variation is organized across cell types, remains largely unresolved. Here we profiled chromatin accessibility in 131,890 nuclei derived from seedlings of three Zea mays (maize) inbred lines and their reciprocal hybrids, resolving 14 major cell types. Parental haplotype comparisons showed that most accessible chromatin regions (ACRs) were sequence-conserved and have similar binarized chromatin accessibility status. At cellular resolution, hybridization broadly attenuated chromatin accessibility cell-type specificity, weakening parental cell-type bias and yielding a more even chromatin accessibility profile across cellular contexts. Chromatin inheritance was strongly cell-type dependent, with non-additive inheritance preferentially concentrated at cell-type-specific ACRs. Although cis effects were most prevalent overall, ACRs with attenuated cell-type specificity in hybrids were enriched for non-additive inheritance and trans effects. Attenuated ACRs were more prone to transcription factor (TF) footprint gains than loci retaining high cell-type specificity, with DNA-BINDING WITH ONE FINGER (DOF) and VASCULAR PLANT ONE ZINC FINGER (VOZ) among the motif families most enriched in high-confidence footprint-gaining events. ACRs with footprint gains were preferentially linked to genes involved in development, hormone responses and growth, including DOF-family gains at GOLDEN2-like (GLK2), where both the motif family and the locus have been implicated in bundle-sheath development and C4 photosynthetic specialization. Together, our findings reveal that parental chromatin accessibility patterns are reconfigured across cell types in maize hybrids, with attenuation of cell-type specificity offering a potential cellular mechanism underlying heterosis.

plant biology↗

bioRxiv2026

Easy-Multiome enables joint profiling of gene expression and chromatin accessibility in single cells

Gene expression and chromatin accessibility provide complementary insights into the regulatory mechanisms that define cell states. Although methods for jointly profiling these modalities exist, plant applications remain limited because of complex workflows, inconsistent performance, and prohibitive costs. Here, we present easy-Multiome, a streamlined single-cell multiomic workflow that integrates a single in situ reverse transcription step into the standard droplet-based scATAC-seq protocol. Using easy-Multiome, we profiled more than 20,000 nuclei from maize seedlings generating paired gene expression and chromatin accessibility data, with approximately 90% of nuclei containing both high-quality RNA and chromatin accessibility profiles. The resulting transcriptome data resolved 16 clusters corresponding to nine major maize seedling cell types and enabled direct characterization of cell-type-specific chromatin accessibility from the same nuclei. Furthermore, easy-Multiome simultaneously captured cell-type-specific transcription factor expression and the accessibility of their cognate DNA-binding motifs, providing direct links between transcriptional programs and regulatory landscapes. Together, these results demonstrate that easy-Multiome enables robust and efficient joint profiling of plant gene expression and chromatin accessibility while requiring only minimal modifications to existing droplet-based scATAC-seq workflows.

genomics↗

bioRxiv2025

Single-cell multi-omic characterization of the soybean root response to cyst nematode infection

Soybean cyst nematodes parasitize soybean roots by inducing the formation of multinucleate syncytia to feed and complete their life cycle. However, the molecular basis of syncytia initiation and development remains limited. Here, we generated an integrated single-nucleus RNA and chromatin accessibility profile of soybean roots from infected and uninfected plants. We profiled 56,448 high-quality nuclei and identified all major root cell types, including distinct subpopulations enriched with syncytial nuclei. Transcriptomic and chromatin accessibility analyses support their procambium cell signature that progresses through distinct stages associated with immune suppression, cell fusion, and endoreduplication. Integrative gene expression and transcription factor motif chromatin accessibility analyses identified CAMTA1, as a potential transcriptional repressor of defense-related genes including receptor-like kinases, whereas MYB, MYB-related, and E2F were identified as potential transcriptional activators that coordinate cell wall remodeling, chromatin modification and DNA replication, respectively, across developmental trajectories. These findings provide mechanistic insights into host reprogramming during nematode parasitism and serve as a foundational resource for engineering nematode-resistant soybean.

plant biology↗

bioRxiv2025

Hybrids reveal accessible chromatin trans genetic associations

Crosses between genetically distant Zea mays (Maize) inbreds cause hybrid vigour (heterosis): an over-dominant increase in vegetative growth and grain yield. Although the contributing loci are unknown, heterosis strength varies polygenically, with crosses between stiff stalk and non-stiff stalk lineages often producing the highly heterotic F1 seed used for agriculture. As F1 genomes conserve the parental cis-regulatory state, F1 trans-interactions between haplotypes underpin F1 trait over-dominance and heterotic gene expression. Gene expression relies upon transcription factors binding cis-regulatory elements in accessible chromatin regions (ACRs) and recruiting RNA POLYMERASE II. Here, assay for transposase accessible chromatin sequencing (ATAC-seq) examined cis-regulatory element chromatin accessibility inheritance in three different F1 parent-offspring pairs, including a representative stiff stalk-by-non-stiff stalk (B73xOh43) cross. Using concatenated reference alignment, we categorized ACR modes of inheritance (additive, dominant, under/over-dominant), revealing that ACRs are largely inherited additively, and, concordantly, that chromatin accessibility has strong narrow-sense heritability. However, mirroring other heterotic phenotypes, the B73xOh43 cross exhibited the most dominant and over-dominant inheritance. Comparing allele-specific parent-to-offspring chromatin accessibility, we identified F1 differentially trans-regulated ACRs. Using a matched chromatin accessible diversity panel, we found B73xOh43 SNPs with more ACR trans-associations than expected due to chance. These trans-regulatory variants revealed how cell-division and anabolism are elevated in heterotic F1 seedlings. This multiple discovery filtering (MDF) approach to trans-regulatory variant detection is genomic modality agnostic and stands to empower trans-relationship dissection in diverse genetic models.

genetics↗

bioRxiv2024

The genetic architecture of cell-type-specific cis-regulation

AbstractGene expression and complex phenotypes are determined by the activity of cis-regulatory elements. However, an understanding of how extant genetic variants affect cis regulation remains limited. Here, we investigated the consequences of cis-regulatory diversity using single-cell genomics of >0.7 million nuclei across 172 Zea mays (maize) inbreds. Our analyses pinpointed cis-regulatory elements distinct to domesticated maize and revealed how historical transposon activity has shaped the cis-regulatory landscape. Leveraging population genetics principles, we fine-mapped [~]22,000 chromatin accessibility-associated genetic variants with widespread cell-type-specific effects. Variants in TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR binding sites were the most prevalent determinants of chromatin accessibility. Finally, integrating chromatin accessibility-associated variants, organismal trait variation, and population differentiation revealed how local adaptation has rewired regulatory networks in unique cellular context to alter maize flowering.

genetics↗

bioRxiv2024

A spatially resolved multiomic single-cell atlas of soybean development

Cis-regulatory elements (CREs) precisely control spatiotemporal gene expression in cells. Using a spatially resolved single-cell atlas of gene expression with chromatin accessibility across ten soybean tissues, we identified 103 distinct cell types and 303,199 accessible chromatin regions (ACRs). Nearly 40% of the ACRs showed cell-type-specific patterns and were enriched for transcription factor (TF) motifs defining diverse cell identities. We identified de novo enriched TF motifs and explored conservation of gene regulatory networks underpinning legume symbiotic nitrogen fixation. With comprehensive developmental trajectories for endosperm and embryo, we uncovered the functional transition of the three sub-cell types of endosperm, identified 13 sucrose transporters sharing the DOF11 motif that were co-up-regulated in late peripheral endosperm and identified key embryo cell-type specification regulators during embryogenesis, including a homeobox TF that promotes cotyledon parenchyma identity. This resource provides a valuable foundation for analyzing gene regulatory programs in soybean cell types across tissues and life stages.

plant biology↗

bioRxiv2021

small RNA can move long distances through plant vasculature to influence gene expression in shoot apical meristems

In plants, small RNA (sRNA) can regulate gene expression via post transcriptional gene silencing (PTGS) or through RNA-directed DNA methylation (RdDM) leading to transcriptional gene silencing (TGS). sRNA is mobile throughout the plant, with movement occurring short distances from cell-to-cell as well as long distances through the vasculature via phloem trafficking. The range of long-distance sRNA mediated signaling from the vasculature to the shoot apical meristem (SAM) is not clear. To investigate this, two independent transgenic approaches were used to examine trafficking of phloem-expressed sRNA to the SAM in Arabidopsis thaliana. First, the phloem companion-cell specific promoter SUC2 was used to drive expression of an inverted repeat complementary to FLOWERING LOCUS D (FD), a flowering time regulator expressed exclusively in the SAM. In a separate experiment, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) target in the SAM stem cells. Both systems provide evidence of a phloem-to-SAM sRNA communication axis connecting distal regions of the plant to the stem cells of the SAM, which ultimately gives rise to all shoot tissues, including gametes. Thus, phloem-to-SAM sRNA movement defines an important link between sRNA expressed in distal regions of the plant and the growing shoot. Importantly, phloem-to-SAM sRNA trafficking may allow somatic sRNA to direct SAM RdDM, fixing transient sRNA expression events into stable epigenetic changes.

plant biology↗