Cell-by-cell maps reveal hidden complexity of genomic imprinting in maize

Genomic imprinting, the curious phenomenon in which a gene is expressed depending on which parent it was inherited from, was first discovered in maize nearly a century ago. Now, a team of researchers in China has taken one of the most detailed looks yet at how this epigenetic oddity plays out inside a developing corn kernel, and their findings suggest the phenomenon is far more intricate than earlier studies could ever reveal. By combining two cutting-edge techniques, spatial transcriptomics and single-nucleus RNA sequencing, the scientists mapped allele-specific gene expression across the maize endosperm at unprecedented cellular resolution, uncovering a landscape of parental influence that shifts dramatically from one cell type to another.

The study, published in the journal Genome Biology, was led by Junpeng Shi of Sun Yat-sen University together with colleagues at Shandong Agricultural University, the Chinese Academy of Sciences and other institutions. The endosperm, the triploid tissue that nourishes the developing embryo and ultimately makes up most of what we eat when we consume corn, has long been recognized as the primary arena for genomic imprinting in plants. Because it contains two maternal genome copies and one paternal copy, the endosperm provides a natural system in which researchers can distinguish whether a gene’s transcripts came from the mother or the father, simply by counting the relative abundance of parental alleles.

Previous efforts to catalog imprinted genes in maize relied on bulk RNA sequencing of endosperm tissue that had been painstakingly dissected by hand. Those studies identified hundreds of candidate imprinted genes, but they averaged expression signals across an entire tissue that is anything but uniform. The endosperm is a mosaic of specialized cell types, each with distinct developmental roles, and averaging across them risks blurring the very signals that matter. The new work set out to resolve that heterogeneity directly, asking whether imprinting looks the same in every endosperm cell or whether it, too, is compartmentalized.

To answer that question, the researchers deployed two complementary technologies. The first was 10x Visium spatial transcriptomics, which captures gene expression while preserving information about where in the tissue each transcript was detected. The second was single-nucleus RNA sequencing, or snRNA-seq, which profiles the transcriptomes of individual nuclei, allowing each cell’s identity to be inferred from its expression signature. Crucially, the team applied both methods to reciprocal maize kernels, meaning kernels produced by crossing two inbred lines in both directions, so that the maternal and paternal genomes could be swapped and parental origin of each allele tracked unambiguously.

The combined datasets revealed six major endosperm cell types, providing the most granular cellular atlas of this tissue to date. When the researchers examined allele-specific expression, the pattern of transcripts attributable to one parent versus the other, they found something striking: this expression was strongly cell-type specific. Roughly two-thirds of the genes showing allele-specific expression were detected in only a single endosperm cell type. In other words, the parental bias governing a gene’s activity is not a fixed property of the gene itself but depends heavily on which cellular neighborhood that gene happens to be operating in.

The two technologies proved highly consistent with one another. Nearly 70 percent of the imprinted genes identified through spatial profiling could be validated at the cell-type level using single-nucleus sequencing, a concordance rate that strengthens confidence in both platforms and in the biological conclusions drawn from them. Yet when the team compared imprinted gene sets across the different endosperm cell types, they found that fewer than half of the imprinted genes were shared among multiple cell types. The implication is profound: the imprinting landscape of the endosperm is substantially shaped by spatial position and cellular identity, not merely by the epigenetic state inherited from the gametes.

The study also addressed a long-standing question about the balance of parental influence. In maize endosperm, paternally expressed genes, those that preferentially silence the maternal copy and express the paternal one, outnumbered maternally expressed genes by approximately twofold. This asymmetry adds to evidence that the paternal genome exerts a stronger transcriptional imprint on endosperm development than the maternal genome, at least in terms of the number of genes affected, though the functional consequences of that imbalance remain an open question for future work.

Among the most intriguing discoveries was a maternally expressed long non-coding RNA located within a region of the genome where the maternal copy is hypomethylated, meaning it carries fewer DNA methylation marks than the paternal copy. This lncRNA sits alongside Mez1, one of the canonical, best-characterized imprinted genes in maize, which is known to reside in a differentially methylated region. The co-localization of a novel imprinted non-coding RNA with a classic imprinted protein-coding gene in a shared hypomethylated landscape suggests that these loci may be subject to coordinated epigenetic regulation, hinting at regulatory architectures that earlier bulk approaches simply could not see.

Technically, the work demonstrates how modern genomics can dissect a phenomenon that has resisted fine-scale analysis for decades. Allele-specific expression analysis requires distinguishing transcripts from two highly similar genome copies, and doing so in spatially resolved or single-cell data adds layers of computational complexity, from assigning nuclei to cell types to correcting for the uneven coverage typical of single-cell libraries. By validating spatial results against single-nucleus data, and by using reciprocal crosses to control for the effects of the specific inbred lines, the team built a methodologically robust framework that other plant researchers can now adapt to their own systems.

The broader significance of the study lies in what it says about the developmental logic of imprinting. The authors conclude that post-fertilization endosperm differentiation, the process by which the initially uniform triploid tissue diversifies into specialized cell types, actively shapes the spatial and cellular landscape of genomic imprinting in maize. Rather than being a static epigenetic legacy of fertilization, imprinting emerges as a dynamic, context-dependent program that unfolds as the kernel develops. The comprehensive resource generated by the team, including cell-type atlases, allele-specific expression catalogs, DNA methylation data and lncRNA annotations, is expected to serve as a foundation for investigating the functional roles of imprinting during kernel development, work that could ultimately inform efforts to improve seed traits in one of the world’s most important crops.

Subject of Research: Cell-type-resolved mapping of genomic imprinting and allele-specific expression in developing maize endosperm using spatial transcriptomics and single-nucleus RNA sequencing

Article Title: Spatial and single-nucleus transcriptomics reveal the complexity of genomic imprinting in maize

Article References: Li, T., Jiang, Y., Zhang, M., Zhu, K., Jiang, S., Yang, X., Liu, H., Wang, J., Dong, X., & Shi, J. (2026). Spatial and single-nucleus transcriptomics reveal the complexity of genomic imprinting in maize. Genome Biology. https://doi.org/10.1186/s13059-026-04291-9

Image Credits: AI Generated

DOI: 10.1186/s13059-026-04291-9

Keywords: maize, genomic imprinting, spatial transcriptomics, single-nucleus RNA sequencing, allele-specific expression, endosperm, epigenetics, DNA methylation, long non-coding RNA, Mez1, plant genetics, seed development