Biology subjects

zhong, s.

Publications and source records attributed to zhong, s..

3 recordsLinked to original sources

bioRxiv2025

MusTer: A Generalizable Microfluidic Platform Combining Multi-Parametric Droplet Sorting and Multi-Droplet Merging in Single-Cell Sequencing

Droplet microfluidics is a core technology that powers high-throughput single cell sequencing. However, the current generation of single-cell microfluidics faces notable limitations, including cell aggregation, suboptimal on-chip reactions that compromise experimental outcomes and elevate background noise, as well as a dependence on costly commercial barcode beads. To address these challenges, we present MusTer, an integrated next-generation platform with multi-parametric singlet droplet sorting and triple-droplet merging capability. MusTers multi-parametric singlet sorting module enables in-line droplet analysis of intrinsic fluorescence peak amplitude, width and interval from single-nucleus- (singlet) or multiple-nuclei (multiplet)-encapsulating droplets, subsequently allowing an effective separation of the singlet droplets from multiplet droplets and empty droplets. MusTers triple-droplet merging module enables precise multi-step reactions, with each step performed under its own optimal conditions, thereby significantly enhancing experimental flexibility and efficiency. We validated MusTers performance by performing single-cell ATAC-seq on maize leaves. The results demonstrate that MusTer significantly reduces the doublet rate, enhances the signal-to-noise ratio, and yields improved cell clustering compared with traditional methods. These results validate MusTers capability to overcome key limitations in droplet-based single-cell analysis, effectively enhancing data quality and reliability, and also paves the way for its use in other challenging sample types and multi-step single-cell assays.

bioengineering↗

bioRxiv2019

Tissue-specific Hi-C analyses of rice, foxtail millet and maize suggest non-canonical function of plant chromatin domains

Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We have also profiled their DNA methylation, open chromatin, histone modification and gene expression to investigate whether chromatin structural dynamics are associated with epigenome features changes. We found that plant global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic that is associated with differential gene expression. Plant domains are largely stable across tissues, while rare domain border changes are often associated with gene activation. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian cells. When comparing synteny gene pairs, we found those maize genes involved in gene island chromatin loops have shorter genomic distances in smaller genomes without gene island loops such as rice and foxtail millet, suggesting that they have conserved functions. Our study revealed that the 3D configuration of the plant chromatin is also complex and dynamic with unique features that need to be further examined.

genomics↗

bioRxiv2017

The fruitENCODE project sheds light on the genetic and epigenetic basis of convergent evolution of climacteric fruit ripening

Fleshy fruit evolved independently multiple times during angiosperm history. Many climacteric fruits utilize the hormone ethylene to regulate ripening. The fruitENCODE project shows there are multiple evolutionary origins of the regulatory circuits that govern climacteric fruit ripening. Eudicot climacteric fruits with recent whole-genome duplications (WGDs) evolved their ripening regulatory systems using the duplicated floral identity genes, while others without WGD utilised carpel senescence genes. The monocot banana uses both leaf senescence and duplicated floral-identity genes, forming two interconnected regulatory circuits. H3K27me3 plays a conserved role in restricting the expression of key ripening regulators and their direct orthologs in both the ancestral dry fruit and non-climacteric fleshy fruit species. Our findings suggest that evolution of climacteric ripening was constrained by limited availability of signalling molecules and genetic and epigenetic materials, and WGD provided new resources for plants to circumvent this limit. Understanding these different ripening mechanisms makes it possible to design tailor-made ripening traits to improve quality, yield and minimize postharvest losses.\n\nOne Sentence SummaryThe fruitENCODE project discovered three evolutionary origins of the regulatory circuits that govern climacteric fruit ripening.

genomics↗