Biology subjects

Ming, L.

Publications and source records attributed to Ming, L..

5 recordsLinked to original sources

bioRxiv2026

GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution

BackgroundDissecting the genetic basis of cell-type-specific gene regulation during gametogenesis remains a major challenge. Population-level studies mask cellular heterogeneity, while the extreme data sparsity of single-cell profiling has precluded robust genetic mapping. ResultsWe present GAMETE (Genetic Architecture Mapping of Epigenetic Traits at single-nucleus resolution), an integrated framework combining MPS-ATAC-seq, a high-throughput single-nucleus ATAC-seq method, with robust computational approaches for genotype inference and genetic mapping from sparse single-nucleus data. Applying GAMETE to hybrid rice pollen, we simultaneously profiled chromatin accessibility and inferred the genotypes of 4,887 individual haploid nuclei, revealing distinct chromatin landscapes across pollen cell types. This uncovered an unexpected elevation of chromatin accessibility at gypsy retrotransposons in microspores preceding their silencing in sperm cells, exposing a surveillance gap that may contribute to genome expansion. The synchronized profiling enabled us to construct a single-cell recombination map, map segregation distortion loci and trace their developmental origins, and identify 16,113 chromatin accessibility QTLs (caQTLs), 48.6% of which exhibited pronounced cell-type specificity. Analysis of introgression lines supported a cell-type-specific trans-acting caQTL regulating the pollen-essential gene DTM1. ConclusionsThis work establishes GAMETE as a broadly applicable framework for dissecting the genetic architecture of chromatin accessibility during gametogenesis without the need for subsequent generations.

genomics↗

bioRxiv2025

Liposome Encapsulation Enables Near-Native Cryo-EM Structural Determination by Shielding Macromolecules from Non-Physiological Interfaces

Cryo-electron microscopy (cryo-EM) has emerged as a very powerful tool for high-resolution structure determination of macromolecule complexes. However, sample preparation remains a major bottleneck in cryo-EM workflows. Most structures were resolved not in a native solution environment, but rather in the non-physiological interfaces such as the air-water interface (AWI), where the folding/unfolding energy landscape of macromolecules may be significantly altered, leading to artifact, preferential orientation, particle disassembly or even denaturation. To address this challenge, we developed a robust, sample-independent method utilizing liposome encapsulation that preserve macromolecules in a solution-like and near native environment throughout sample preparation. Using equine spleen apoferritin and the Escherichia coli (E. coli) ribosome as model systems, we demonstrate efficient particle incorporation into liposomes and successful high-resolution structure determination. Notably, our method yields significantly reduced particle disassembly, denaturation, and preferential orientation compared to samples on holey carbon and graphene grids. We anticipate that this approach will facilitate structural studies of other challenging macromolecular complexes that are sensitive to interfacial effects.

biophysics↗

bioRxiv2024

Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for [~]15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.

genomics↗

bioRxiv2020

MMS2plot: an R package for visualizing multiple MS/MS spectra for groups of modified and non-modified peptides

A large number of post-translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot-gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non-modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools would preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, we describe MMS2plot, an R package for visualizing peptide-spectrum matches (PSMs) for multiple peptides. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. We expect MMS2plot to play an important role in PTM discovery from large-scale proteomics datasets generated by LC (liquid chromatography)-MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL-3 license.

bioinformatics↗

bioRxiv2019

Whole-genome sequencing of 128 camels across Asia provides insights into origin and migration of domestic Bactrian camels

The domestic Bactrian camels were treated as the principal means of locomotion between the eastern and western cultures in history. To address the question of their origin, we performed whole-genome sequencing of 128 camels across Asia, including representative populations of domestic Bactrian camels from the Mongolian Plateau to the Caspian Sea, as well as the extant wild Bactrian camels and dromedaries. The domestic and wild Bactrian camels showed remarkable genetic divergence since they were split from dromedaries, confirming they were separated species. The wild Bactrian camels made also little contribution to the ancestry of domestic ones. Among the domestic Bactrian camels, those from Iran exhibited the largest genetic distance from others, and were the first population to separate in the phylogeny. Although evident admixture was observed between domestic Bactrian camels and dromedaries living around the Caspian Sea, the large genetic distance and basal position of Iranian Bactrian camels could not be explained by introgression alone. Taken together, our study favored the Iranian origin of domestic Bactrian camels, which were then immigrated eastward to Mongolia where the native wild Bactrian camels inhabited. This study illustrated the complex genomic landscape of migration underlying domestication in Bactrian camels.

genomics↗