Journal of Genetics and Genomics

A universal cost-efficient sample labeling approach for multiplexed single cell RNA-seq based on recombinant HUH-endonuclease-agglutinin tagging

Quanyong Zhang, Maorong Li, et al.

doi: 10.1016/j.jgg.2025.10.004

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Abstract:
Recent advances in single-cell transcriptomics have revolutionized our understanding of cellular diversity and tissue heterogeneity, providing unprecedented insights into biological and medical research. However, the high per-assay cost limits broader applications of this technology. Although sample-labeling strategies enabling multiplexing have emerged, current methods suffer from either impractical complexity for barcoding or high cost for preparing the index labeling reagents. To address these challenges, here we present HEATag, a universal cell membrane labeling approach that combines Duck circovirus HUH endonuclease (DCV) with wheat germ agglutinin (WGA) to efficiently tag cell membranes with indexed single-stranded DNA (indexed ssDNA). The DCV domain enables rapid, sequence-specific conjugation of indexed ssDNA, while the WGA domain ensures robust labeling of fresh or fixed cells across diverse species. This method is compatible with both commercial platforms and custom systems, readily adaptable to various single cell omics workflows. Therefore, HUH-endonuclease-agglutinin tagging (HEATag) provides a universal, cost-effective and scalable solution for high-throughput single-cell studies, enhancing library preparation efficiency and minimizing batch effects for single-cell researchers.

To see and to know: the power of live imaging in illuminating and decoding biological complexity

Miaoling Yang, Zhuo Du

doi: 10.1016/j.jgg.2025.10.003

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Abstract:
Live imaging enables direct observation of dynamic biological processes, capturing their progression from molecular to organismal scales in space and time. Through high-resolution observation, it provides a powerful means to decode biological complexity by revealing dynamic behaviors, spatial patterns, and regulatory changes. This review illustrates the application of live imaging in investigating complex biological processes with spatiotemporal resolution and mechanistic insight. We first highlight the analytical power and integrative strategies of live imaging, and then summarize recent advances that further extend its capacities. We then focus on four complex processes—cell proliferation, lineage regulation, morphogenesis, and atlas construction—to elucidate how live imaging contributes to their decoding through representative studies. We also discuss the conceptual and practical limitations that currently constrain the full interpretive potential of live imaging, underscoring the need for deeper integration between observation, perturbation, and modeling. Looking ahead, live imaging will benefit from both technical refinement and advances in data standardization and visualization, functional quantification, multiscale integration, and the discovery of generalizable principles. Together, these directions advance a more integrative and mechanistic understanding of complex biological processes.

Dissecting the genetic basis of reproductive transition and reproductive growth in wheat by considering accumulated temperature

Liujie Jin, Kening Duo, et al.

doi: 10.1016/j.jgg.2025.09.012

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Abstract:

Maize Chlorotic Leaf Spot1 encodes a fumarylacetoacetate hydrolase essential for carbohydrate partitioning

Ruchang Ren, Sihang Zhao, et al.

doi: 10.1016/j.jgg.2025.10.002

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Abstract:
Carbohydrate partitioning from photosynthetic sources to non-photosynthetic sinks is essential for plant development and crop yield. Using a maize-teosinte BC₂S₃ population, we identify Chlorotic Leaf Spot1 (CLS1), a fumarylacetoacetate hydrolase (FAH) in the tyrosine degradation pathway that plays an essential role in carbohydrate partitioning in maize. CLS1 localizes to the plasma membrane, cytoplasm, and nucleus. Allelic tests and sequence analysis reveal that the teosinte parent CIMMYT8759 carries a weak allele of CLS1, likely due to rare amino acid substitutions at residues 175 and 355. Loss-of-function mutants of CLS1 develop chlorotic leaf spots accompanied by carbohydrate hyperaccumulation, reduced photosynthetic efficiency, chloroplast damage, and impaired transient starch conversion. Critically, cls1 mutants exhibit ectopic callose accumulation and aberrant plasmodesmata ultrastructure at the mesophyll-bundle sheath and bundle sheath-vascular parenchyma interfaces. This defect causes starch granule and soluble sugar accumulation in chlorotic leaf tissues, indicating a disruption of the symplastic transport pathway. Collectively, our results uncover an important role for FAH in plant development and identify CLS1 as a key regulator of symplastic carbohydrate partitioning.

circRNAs derived from a nuclear hormone receptor act differentially on insect metamorphosis and reproduction

Lulu Gao, Qiang Yan, et al.

doi: 10.1016/j.jgg.2025.10.001

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Abstract:
Insects are the most diverse group on earth, partially owing to their metamorphosis and strong fecundity. Circular RNAs (circRNAs) are stable molecules implicated in a broad range of biological processes. However, the regulatory roles of circRNAs in insect metamorphosis and reproduction are unclear. Methoprene-tolerant (Met) is the nuclear receptor of juvenile hormone (JH) that plays dual roles of inhibiting precocious metamorphosis and promoting reproduction. Here, we report that locust Met generates two circRNAs, circMet1 and circMet2, respectively. While circMet1 is highly expressed in the cuticle of late final instar, circMet2 is more abundant in the corpora allata, brain, and fat body of early vitellogenic adults. Interestingly, circMet2 is generated by complementary pairing of Penelope-like remnants across the introns of Met. Moreover, circMet2 functions as a miRNA sponge of four species-specific miRNAs that downregulate Met translation. siRNA-mediated knockdown of circMet1 causes the delay of metamorphosis and retarded vitellogenesis. Loss of circMet2 results in significantly decreased vitellogenin synthesis, along with blocked ovarian growth. These results reveal the differential roles of circMet1 and circMet2 in modulating insect metamorphosis and female reproduction. This study advances our understanding of how circRNAs derived from a single gene exert distinct roles in insect life history.

Single-molecule chromatin profiling reveals cell type-specific A/B compartment alteration and multi-enhancer transcriptional coordination

Luo-Ran Liu, Jia-Yong Zhong, et al.

doi: 10.1016/j.jgg.2025.09.011

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Abstract:
In eukaryotic organisms, the three-dimensional organization and epigenomic landscape of chromatin are fundamental to the regulation of gene expression. Previous studies have provided significant insights into CpG methylation, chromatin accessibility, and the dynamics of 3D architecture. However, a systematic delineation of how these epigenomic features regulate transcriptional activity remains limited. In this study, we develop nanoCAM-seq, a single-molecule sequencing technique designed to simultaneously profile higher-order chromatin interactions, chromatin accessibility, and endogenous CpG methylation. This approach provides an integrative view of chromatin features associated with cis-regulatory elements and reveals their coordinated dynamics during transitions of A/B compartments. Single-molecule analyses using nanoCAM-seq further reveal that promoters characterized by low CpG methylation and high chromatin accessibility more frequently interact with multiple enhancers. Collectively, our findings establish nanoCAM-seq as a powerful approach for resolving the coordinated dynamics of chromatin architecture and epigenetic modifications, offering critical insights into the regulatory mechanisms underlying gene expression.