Biology subjects

Wei, C.-L.

Publications and source records attributed to Wei, C.-L..

14 recordsLinked to original sources

bioRxiv2026

Short-Read Sequencing Benchmarking with Donor-Specific Assemblies

BackgroundHigh-throughput short-read sequencing has become a core technology for genomics, but the rapid expansion of available platforms has made it increasingly important to benchmark them under standardized conditions. A major challenge is that conventional reference-based comparisons confound true sequencing errors with inherited variation and reference bias, making it difficult to isolate platform-intrinsic performance. ResultsWe benchmarked nine short-read chemistries across seven DNA sequencers using two highly characterized benchmark samples, HG002 and COLO829BL, together with donor-specific assemblies to measure sequencing errors against sample-matched genomic references. This strategy separated authentic platform errors from biological divergence and revealed substantial differences in substitution, indel, read-position, and sequence-context error profiles. Element AVITI UltraQ and Roche SBX-D showed the lowest substitution error rates, whereas Ultima and Roche chemistries exhibited the strongest indel-associated biases. We also found pronounced platform-specific effects in low-complexity regions and trinucleotide contexts, including homopolymer-associated errors and context-dependent substitution skews that are directly relevant to rare-variant detection. In addition, we show that donor-specific references are essential for unbiased base-quality recalibration because they minimize reference bias and more faithfully support cross-platform comparison and low-frequency variant-calling thresholds. ConclusionsDonor-specific assembly-based benchmarking provides a robust framework for measuring true short-read sequencing errors and comparing platforms on a common, sample-matched basis. Our results establish a comprehensive reference for the community and show that authentic error profiles can guide platform selection, quality filtering, and improved detection of rare somatic variation.

bioinformatics↗

bioRxiv2026

Long-read MitoScope reveals tissue-resolved somatic mitochondrial variation and landscape of nuclear-embedded mitochondrial sequences

The mitochondrial genome (mtDNA), rich in repeats and prone to nuclear mitochondrial DNA segments (NUMTs), drives somatic mosaicism implicated in cancer, metabolic syndromes, and neurodegeneration, yet short-read sequencing yields incomplete catalogs, mapping artifacts, and false heteroplasmies. Here, we introduce MitoScope, a scalable long-read workflow to assemble mtDNA, perform high-fidelity variant calling, resolve heteroplasmy, and characterize NUMTs in benchmarking tissues from the Somatic Mosaicism Across Human Tissues (SMaHT) Network. MitoScope shows high sensitivity and precision, determines copy number, and uncovers low-frequency variants. We define an age- and tissue-dependent landscape of mtDNA mosaicism, including low-frequency pathogenic heteroplasmies, a bimodal heteroplasmy spectrum shaped by purifying selection, and age-accumulating deletions enriched for microhomology. Parallel profiling of NUMTs identifies high-confidence events with >2-fold more NUMTs than short-read surveys--with evidence of nonrandom trinucleotide contexts at breakpoints. These findings expose pervasive, tissue-resolved somatic mtDNA and NUMT instability with direct relevance for variant interpretation, aging, and human disease.

genomics↗

bioRxiv2025

An Atlas of Extrachromosomal DNA Structures Illuminates Its Evolution and Biogenesis in Cancer

Extrachromosomal circular DNA (ecDNA) is a prevalent driver of oncogene amplification across diverse types of cancers. Leveraging single-molecule long-read sequencing and a de novo circular genome assembler, ecLego3, we charted a comprehensive atlas of ecDNA structures from longitudinal pairs of primary and recurrent glioblastoma (GBM). Our approach resolved 23 ecDNA genomes representing major oncogenes associated with GBM pathogenesis and revealed a dynamic configuration characterized by pronounced structural variation and multi-species co-existence within individual tumors. Evolutionary trajectories were shaped by hierarchical accrual of structural variants, predominated by deletions and inversions, giving rise to novel oncogene isoforms and enhancer repositioning. Such structural plasticity promotes intratumor heterogeneity and tumor fitness. Multiomic analyses at single cell resolution linked ecDNA abundance and structure to transcriptional output, uncovering non-linear scaling and synergistic co-selection among multiple ecDNA species. Comparative profiling revealed locus-dependent configuration, a contraction of ecDNA diversity upon recurrence, and convergent structural architectures across patients, implicating repeat-mediated genomic rearrangements and replication stress in ecDNA biogenesis. These findings elucidate ecDNA-driven mechanisms of tumor adaptation and highlight new molecular vulnerabilities, informing potential biomarkers and therapeutic strategies for high-grade gliomas.

cancer biology↗

bioRxiv2025

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer

Oncogenesis involves widespread genetic and epigenetic alterations, yet the full spectrum of somatic variation genome-wide remains unresolved. We generated a near-telomere-to-telomere (T2T) diploid assembly of a donor paired with deep short- and long-read sequencing of their melanoma. This revealed that 16% of somatic variants occur in sequences absent from GRCh38, with satellite repeats acting as hotspots for UV-induced damage due to sequence-intrinsic mutability and inefficient repair. Centromere kinetochore domains emerged as focal sites of structural, genetic, and epigenetic variation, leading to remodeling of centromere kinetochore binding domains during tumor evolution. Single-molecule telomere reconstructions uncovered cycles of attrition, deletion, and telomerase-mediated extension that shape cancer telomeres. Finally, diploid chromatin maps exposed that copy number alterations and epimutations, rather than point mutations, predominate in rewiring cancer regulatory programs. These findings define the full landscape of a cancers somatic variation and their functional impact, establishing a blueprint for T2T studies of mosaicism.

genomics↗

bioRxiv2024

Extrachromosomal DNA Associates with Nuclear Condensates and Reorganizes Chromatin Structures to Enhance Oncogenic Transcription

Extrachromosomal, circular DNA (ecDNA) is a prevalent oncogenic alteration in cancer genomes, often associated with aggressive tumor behavior and poor patient outcome. While previous studies proposed a chromatin-based mobile enhancer model for ecDNA-driven oncogenesis, its precise mechanism and impact remains unclear across diverse cancer types. Our study, utilizing advanced multi-omics profiling, epigenetic editing, and imaging approaches in three cancer models, reveals that ecDNA hubs are an integrated part of nuclear condensates and exhibit cancer-type specific chromatin connectivity. Epigenetic silencing of the ecDNA-specific regulatory modules or chemically disrupting liquid-liquid phase separation breaks down ecDNA hubs, displaces MED1 co-activator binding, inhibits oncogenic transcription, and promotes cell death. These findings substantiate the trans-activator function of ecDNA and underscore a structural mechanism driving oncogenesis. This refined understanding expands our views of oncogene regulation and opens potential avenues for novel therapeutic strategies in cancer treatment.

genomics↗

bioRxiv2024

Tri-omic mapping revealed concerted dynamics of 3D epigenome and transcriptome in brain cells

Exploring the genomic basis of transcriptional programs has been a longstanding research focus. Here, we report a high-throughput single-cell tri-omic method to capture chromatin accessibility, interaction, and RNA simultaneously (ChAIR). After validating in cultured cells, we applied ChAIR to brain cells across mouse lifespan and delineated the concerted dynamics of 3D-epigenomic architecture and transcription during maturation and aging. Particularly, ultra-long chromatin megacontacts and promoter-associated 3D-epigenomic states are effective in defining cell identity and revealing spatially-resolved anatomic specificity. Importantly, we found that neurons in different brain regions and non-neuronal cells may undergo divergent genomic mechanisms during differentiation and aging. Our results demonstrated ChAIRs robustness of connecting chromatin folding architecture with cellular property and its potential applications to address complex questions in single-cell resolution and spatial specificity.

genomics↗

bioRxiv2024

Multifaceted roles of cohesin in regulating transcriptional loops

Cohesin is required for chromatin loop formation. However, its precise role in regulating gene transcription remains largely unknown. We investigated the relationship between cohesin and RNA Polymerase II (RNAPII) using single-molecule mapping and live-cell imaging methods in human cells. Cohesin-mediated transcriptional loops were highly correlated with those of RNAPII and followed the direction of gene transcription. Depleting RAD21, a subunit of cohesin, resulted in the loss of long-range (>100 kb) loops between distal (super-)enhancers and promoters of cell-type-specific genes. By contrast, the short-range (<50 kb) loops were insensitive to RAD21 depletion and connected genes that are mostly housekeeping. This result explains why only a small fraction of genes are affected by the loss of long-range chromatin interactions due to cohesin depletion. Remarkably, RAD21 depletion appeared to up-regulate genes located in early initiation zones (EIZ) of DNA replication, and the EIZ signals were amplified drastically without RAD21. Our results revealed new mechanistic insights of cohesins multifaceted roles in establishing transcriptional loops, preserving long-range chromatin interactions for cell-specific genes, and maintaining timely order of DNA replication.

genomics↗

bioRxiv2021

Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii

Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and 1405 genes in total were affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 273 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 55 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 68 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria, 15 genes encode proteins previously shown to have functions unrelated to photosynthesis, and 190 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, represents a rich resource for gene discovery and protein functional analysis in photosynthesis.

plant biology↗

bioRxiv2021

Subgenomic RNAs as molecular indicators of asymptomatic SARS-CoV-2 infection

In coronaviridae such as SARS-CoV-2, subgenomic RNAs (sgRNA) are replicative intermediates, therefore, their abundance and structures could infer viral replication activity and severity of host infection. Here, we systematically characterized the sgRNA expression and their structural variation in 81 clinical specimens collected from symptomatic and asymptomatic individuals with a goal of assessing viral genomic signatures of disease severity. We demonstrated the highly coordinated and consistent expression of sgRNAs from individuals with robust infections that results in symptoms, and found their expression is significantly repressed in the asymptomatic infections, indicating that the ratio of sgRNAs to genomic RNA (sgRNA/gRNA) is highly correlated with the severity of the disease. Using long read sequencing technologies to characterize full-length sgRNA structures, we also observed widespread deletions in viral RNAs, and identified unique sets of deletions preferentially found primarily in symptomatic individuals, with many likely to confer changes in SARS-CoV-2 virulence and host responses. Furthermore, based on the sgRNA structures, the frequently occurred structural variants in SARS-CoV-2 genomes serves as a mechanism to further induce SARS-CoV-2 proteome complexity. Taken together, our results show that differential sgRNA expression and structural mutational burden both appear to be correlated with the clinical severity of SARS-CoV-2 infection. Longitudinally monitoring sgRNA expression and structural diversity could further guide treatment responses, testing strategies, and vaccine development.

microbiology↗

bioRxiv2020

Sox2 controls neural stem cell self-renewal through a Fos-centered gene regulatory network

The Sox2 transcription factor is necessary for the long-term self-renewal of neural stem cells (NSC). Its mechanism of action is still poorly defined. To identify molecules regulated by Sox2, and acting in mouse NSC maintenance, we transduced, into Sox2-deleted NSC, genes whose expression is strongly downregulated following Sox2 loss (Fos, Jun, Egr2), individually or in combination. Fos alone rescued long-term proliferation, as shown by in vitro cell growth and clonal analysis. Further, pharmacological inhibition of the FOS/JUN AP1 complex binding to its targets, decreased cell proliferation and expression of the putative target Suppressor of cytokine signaling 3 (Socs3). Additionally, Fos requirement for efficient long-term proliferation was demonstrated by the reduction of NSC clones capable of long-term expansion following CRISPR/Cas9-mediated Fos inactivation. Previous work showed that the Socs3 gene is strongly downregulated following Sox2 deletion, and its reexpression by lentiviral transduction rescues long-term NSC proliferation. Fos appears to be an upstream regulator of Socs3, possibly together with Jun and Egr2; indeed, Sox2 reexpression in Sox2-deleted NSC progressively activates both Fos and Socs3 expression; in turn, Fos transduction activates Socs3 expression. Based on available SOX2 ChIPseq and ChIA-PET data, we propose a model whereby Sox2 is a direct activator of both Socs3 and Fos, as well as possibly Jun and Egr2; further, we provide direct evidence for FOS and JUN binding on Socs3 promoter, suggesting direct transcriptional regulation. These results provide the basis for developing a model of a network of interactions, regulating critical effectors of NSC proliferation and long-term maintenance. Significance statementProliferation and maintenance of NSC are essential during normal brain development, and, postnatally, for the maintenance of hippocampal function and memory until advanced age. Little is known about the molecular mechanisms that maintain the critical aspects of NSC biology (quiescence and proliferation) in postnatal age. Our work provides a methodology, transduction of genes deregulated following Sox2 deletion, that allows to test many candidate genes for their ability to sustain NSC proliferation. In principle, this may have interesting implications for identifying targets for pharmacological manipulations. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/995621v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@e9241forg.highwire.dtl.DTLVardef@4276deorg.highwire.dtl.DTLVardef@18a2058org.highwire.dtl.DTLVardef@151b2d2_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2020

Macrofaunal Diversity and Community Structure of the DeSoto Canyon and Adjacent Slope

Macrofauna within the DeSoto Canyon, northern Gulf of Mexico (GOM), along the canyon wall and axis, and on the adjacent slope, were sampled along with sediment, terrain, and water mass parameters. Within the canyon, abundance and species richness decreased with depth, while evenness increased. Cluster analysis identified three depth-related groups within the canyon that conformed to previously established bathymetric boundaries: stations at 464 - 485 m, 669 - 1834 m, and > 2000 m. Abundance differed between depth groups. Species richness was lowest for the deepest group and evenness was lowest for the shallowest. Community structure within the canyon most related to fluorometry and oxygen saturation, combined with any of salinity, particulate organic carbon, sediment organic carbon, or slope. Canyon wall abundances were higher than the canyon axis or adjacent slope. Community structure differed between all three habitat types. Ordination of community structure suggests a longitudinal pattern that potentially tracks with increasing sea-surface chlorophyll that occurs in the eastward direction across the northern GOM. Canyon and slope differences may result from seasonal water masses entrained by canyon topography characterized by high salinity, oxygen saturation, fluorometry, and turbidity. Higher fluorescence and turbidity in the canyon did not translate into higher sediment organic matter. Flushing along canyon wall channels and the canyon axis may explain the low organic matter. Differences in abundance and structure between the canyon wall and axis may result from microhabitat heterogeneity due to potential hydrocarbon seepage, organically enriched sediment deposits along channels, or remnant influence from the Deepwater Horizon blowout.

ecology↗

bioRxiv2018

ChIA-PIPE: A fully automated pipeline for ChIA-PET data analysis and visualization

ChIA-PET enables the genome-wide discovery of chromatin interactions involving specific protein factors, with base-pair resolution. Interpreting ChIA-PET data depends on having a robust analytic pipeline. Here, we introduce ChIA-PIPE, a fully automated pipeline for ChIA-PET data processing, quality assessment, analysis, and visualization. ChIA-PIPE performs linker filtering, read mapping, peak calling, loop calling, chromatin-contact-domain calling, and can resolve allele-specific peaks and loops. ChIA-PIPE also automates quality-control assessment for each dataset. Furthermore, ChIA-PIPE generates input files for visualizing 2D contact maps with Juicebox and HiGlass, and provides a new dockerized visualization tool for high-resolution, browser-based exploration of peaks and loops. With minimal adjusting, ChIA-PIPE can also be suited for the analysis of other related chromatin-mapping data.

bioinformatics↗

bioRxiv2018

Multiplex Chromatin Interaction Analysis with Single-Molecule Precision

We describe a microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision. In multiplex chromatin interaction analysis (multi-ChIA), individual chromatin complexes are partitioned into droplets that contain a gel bead with unique DNA barcode, in which tethered chromatin DNA fragments are barcoded and amplified for sequencing and mapping to demarcate chromatin contacts. Thus, multi-ChIA has the unprecedented ability to uncover multiplex chromatin interactions at single-molecule level, which has been impossible using previous methods that rely on analyzing pairwise contacts via proximity ligation. We demonstrate that multiplex chromatin interactions predominantly contribute to topologically associated domains, and clusters of gene promoters and enhancers provide a fundamental topological framework for co-transcriptional regulation.

genomics↗

bioRxiv2017

Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome

Acquired genomic structural variants (SVs) are major hallmarks of the cancer genome. Their complexity has been challenging to reconstruct from short-read sequencing data. Here, we exploit the long-read sequencing capability of the nanopore platform using our customized pipeline, Picky, to reveal SVs of diverse architecture in a breast cancer model. From modest sequencing coverage, we identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses and uncovered repetitive DNA as the major source of variation. Examination of the genome-wide breakpoints at nucleotide-resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with propensity for inter-chromosomal connectivity and transcriptional regulation. Furthermore, an over-representation of reciprocal translocations from chromosomal double-crossovers was observed through phased SVs. The comprehensive characterization of SVs using the robust long-read sequencing approach in cancer cohorts will facilitate strategies to monitor genome stability during tumor evolution and improve therapeutic intervention.

genomics↗