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Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) has emerged as a powerful technique to study cell-specific epigenetic landscapes and to provide a multidimensional portrait of gene regulation. However, low genomic coverage per cell results …
Read PDFCurrent single-cell profiling technologies enable the capture of multiple cellular modalities, providing valuable insights into complex biological systems. While a substantial amount of single-cell multimodal data has been generated and accumulated, most of these datasets …
Read PDFClustered regularly interspaced short palindromic repeats (CRISPR) screens represent a transformative force in biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications. Traditional screening approaches predominantly hinge on cell …
Read PDFDown syndrome (DS), caused by trisomy of chromosome 21, is the leading genetic cause of intellectual disability, yet the mechanisms disrupting fetal brain development remain unclear. We performed single-cell transcriptomic and chromatin accessibility profiling of …
Read PDFAccurate inference of absolute copy numbers beyond simple gains and losses from single-cell chromatin accessibility (scATAC-seq) data remains challenging, thereby obscuring the distinction between genetic and epigenetically driven oncogenic dependencies. Here, we present TeaCNV, a …
Read PDF<h4>Background</h4>Colorectal cancer (CRC) is shaped by inherited genetic susceptibility, metabolic reprogramming, epigenetic regulation, and tumor microenvironment (TME) heterogeneity. Lactylation has recently emerged as an epigenetic mechanism that links lactate accumulation to chromatin remodeling and transcriptional …
Read PDFSingle-cell ATAC-seq (scATAC-seq) enables the interrogation of chromatin accessibility at cellular resolution, yet its practical utility is often constrained by limited sequencing depth, extreme sparsity, and pervasive technical missingness, which collectively hamper robust cell-state delineation …
Read PDFBulk organelle‑fractionation masks cell‑to‑cell heterogeneity, and existing microfluidic methods cannot reliably reconnect each isolated organelle to its parent cell, an essential capability for multiomics readouts. VacTrap, a high-throughput microfluidic device that isolates and spatially indexes …
Read PDFSingle-cell chromatin accessibility analysis enables high-resolution dissection of regulatory elements and gene regulatory mechanisms. However, standardized and comprehensive analysis workflows remain limited. In this study, we present a streamlined pipeline for analyzing single-cell chromatin accessibility …
Read PDFThe skin acts as the first barrier protecting the human body against the external environment. Transcriptional heterogeneity in human skin is widely confirmed, but the regulatory mechanisms remain largely unexplored. In this study, we employed …
Read PDFEndoplasmic reticulum (ER) stress triggers transcriptional programs that promote either adaptation or apoptosis, yet the epigenetic mechanisms underlying this response remain incompletely understood. Here, integrated multi-omics analyses of unfolded protein response transcription factor knockout cells …
Read PDFDeveloping multiple stress-tolerant crops is the goal of many breeders in the current context of seasonal variability precipitated by the ongoing climate change. Among the most pressing stress, drought is becoming a major concern in …
Read PDFCassava production in sub-Saharan Africa is severely impacted by diseases. Most pathogens require interaction with host susceptibility factors to complete their life cycles and cause disease. Targeted DNA methylation is an epigenetic strategy to alter …
Read PDFZinc is recognized as an important component of immune function in animals, operating through many different mechanisms. Metal transporter Zip14 (Slc39a14) is up-regulated during pro-inflammatory conditions and increases zinc uptake into cells, including enterocytes. As …
Read PDFAssay for transposase-accessible chromatin using sequencing (ATAC-seq) is a cornerstone for epigenomic profiling, yet its potential for genomic characterization remains poorly explored. Here, we systematically benchmarked bulk ATAC-seq against whole-genome sequencing (WGS) to assess its …
Read PDFThe prevalence of neurodevelopmental disorders (NDDs) in children is increasing, yet their underlying causes remain largely unknown. We identified heterozygous mutations in the Polycomb repressive complex 1 (PRC1) E3 ligases RING1 and RNF2 in individuals …
Read PDFChronic inflammation plays a central role in the progression of both infectious and vascular diseases, yet its impact on endothelial cells (ECs), which form the interface between blood and tissue, remains poorly understood. Given their …
Read PDFHuman cerebral organoids derived from induced pluripotent stem cells can recapture early developmental processes and reveal changes involving neurodevelopmental disorders. Mutations in the X-linked methyl-CpG binding protein 2 (MECP2) gene are associated with Rett syndrome, …
Read PDFTrimethylation of histone 3 lysine 4 (H3K4me3) is a mark of active transcription, and its regulatory role in RNA polymerase II-mediated transcription has been well-studied. However, if and how this mark regulates RNA polymerase I …
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