A5047886547- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- Protein Degradation and Inhibitors
- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Retinoids in leukemia and cellular processes
- Advanced biosensing and bioanalysis techniques
- Plant Virus Research Studies
- Music and Audio Processing
- CRISPR and Genetic Engineering
- Speech and Audio Processing
- Inflammasome and immune disorders
- Protein Structure and Dynamics
- Genomic variations and chromosomal abnormalities
- Cancer Genomics and Diagnostics
- Genetic Mapping and Diversity in Plants and Animals
- Biotin and Related Studies
- Gene expression and cancer classification
- interferon and immune responses
- Cancer-related molecular mechanisms research
- Bioinformatics and Genomic Networks
- Speech Recognition and Synthesis
Southern University of Science and Technology
2021-2025
Jackson Laboratory
2015-2020
Genome Institute of Singapore
2012-2018
Interleukin6 (IL-6) is a key driver of hyperinflammation in COVID-19, and its level strongly correlates with disease progression. To investigate whether variability COVID-19 severity partially results from differential IL-6 expression, functional single-nucleotide polymorphisms (SNPs) were determined Chinese patients mild or severe illness. An Asian-common haplotype defined by promoter SNP rs1800796 intronic SNPs rs1524107 rs2066992 correlated severity. Homozygote carriers C-T-T variant at...
CRISPR/Cas-based transcriptional activators can be enhanced by intrinsically disordered regions (IDRs). However, the underlying mechanisms are still debatable. Here, we examine 12 well-known IDRs fusing them to dCas9-VP64 activator, of which only seven augment activation, albeit independently their phase separation capabilities. Moreover, modular domains (MDs), another class multivalent molecules, though ineffective in enhancing activity on own, show substantial enhancement activation when...
Three-dimensional genome organization reveals that gene regulatory elements, which are linearly distant on the genome, can spatially interact with target genes to regulate their expression. DNA fluorescence in situ hybridization (DNA-FISH) is an efficient method for studying spatial proximity of genomic loci. In this study, we developed optimized Tn5 transposome-based DNA-FISH method, termed Tn5-labeled DNA-FISH. This approach amplifies region and uses a self-assembled transposome...
Transcription factors (TFs) play a crucial role in the regulation of gene expression and structural organization chromatin. They interact with proteins, RNA, chromatin DNA to exert their functions. Therefore, an efficient straightforward experimental approach that simultaneously captures interactions transcription DNA, proteins is essential for studying these regulatory proteins. In this study, we developed novel method, TF-chRDP (Transcription Factor binding Chromatin-associated Protein),...
Abstract The three-dimensional (3D) chromatin structure of Epstein–Barr virus (EBV) within host cells and the underlying mechanisms interaction gene regulation, particularly those involving EBV’s noncoding RNAs (ncRNAs), have remained incompletely characterized. In this study, we employed state-of-the-art techniques 3D genome mapping, including protein-associated analysis with paired-end tag sequencing (ChIA-PET), RNA-associated technique (RDD), super-resolution microscopy, to delineate...
The three-dimensional (3D) organization of chromatin within the nucleus is crucial for gene regulation. However, 3D architectural features that coordinate activation an entire chromosome remain largely unknown. We introduce omics method, RNA-associated DNA-DNA interactions, integrates RNA polymerase II (RNAPII)–mediated regulome with stochastic optical reconstruction microscopy to investigate landscape noncoding roX2 -associated topology equalization achieve dosage compensation. Our findings...
Dear editor, In the past decade, genome-wide characterization of three-dimensional chromatin structure using high-throughput methods has greatly advanced our knowledge in plant genome architecture (Liu and Weigel, 2015; Ouyang et al., 2020). However, due to limitation Illumina paired-end short read, most contacts obtained by Hi-C/ChIA-PET are pairwise, interactions among three or more sites (multi-way) can only be inferred from two-way data. To directly capture multi-way interaction...
Abstract Background Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML-RARα, a major etiological agent in APL. However, molecular mechanisms underlying role of PML-RARα leukemogenesis remain largely unknown. Results Using an inducible system, we comprehensively analyze 3D genome organization myeloid cells and its reorganization after induction perform additional analyses patient-derived APL with native PML-RARα. We discover that mediates extensive chromatin...
Abstract The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional organization, yet introduce new computational challenges. Thus, we developed MIA-Sig, an algorithmic solution based on signal processing information theory. We demonstrate its ability to de-noise the data, assess statistical significance of complexes, identify topological domains...
Abstract The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These not only offer new insight into high-dimensional organization and gene regulation, but also introduce challenges in data visualization analysis. To overcome these challenges, we developed MCIBox, a toolkit for multi-way interaction (MCI) analysis, including tool platform identifying micro-domains clustered complexes. MCIBox...
Abstract ChIA-Drop is a new experimental method for mapping multiplex chromatin interactions with single-molecule precision by barcoding complexes inside microfluidics droplets, followed pooled DNA sequencing. The reads the same droplet-specific barcodes are inferred to be derived from interaction complex. Here, we describe an integrated computational pipeline, named ChIA-DropBox, that specifically designed reconstructing in each droplet and refining raw sequencing reads, then visualizing...
We describe a microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision. In interaction (multi-ChIA), individual complexes are partitioned into droplets that contain gel bead unique DNA barcode, in which tethered fragments barcoded and amplified sequencing mapping to demarcate contacts. Thus, multi-ChIA has the unprecedented ability uncover at level, been impossible using previous methods rely on analyzing pairwise contacts via...
Single-cell multiomics techniques have been widely applied to detect the key signature of cells. These methods achieved a single-molecule resolution and can even reveal spatial localization. emerging provide insights elucidating features genomic, epigenomic transcriptomic heterogeneity in individual However, they given rise new computational challenges data processing. Here, we describe Single-molecule multiple Omics Pipeline (ScSmOP), universal pipeline for barcode-indexed single-cell...
Chromatin structural domains, or topologically associated domains (TADs), are a general organizing principle in chromatin biology. RNA polymerase II (RNAPII) mediates multiple interactive loops, tethering together as RNAPII-associated interaction (RAIDs) to offer framework for gene regulation. RAID and TAD alterations have been found be with diseases. They can further dissected micro-domains (micro-TADs micro-RAIDs) by clustering single-molecule chromatin-interactive complexes from...
Abstract The single-molecule multiplex chromatin interaction data generated by emerging non-ligation-based 3D genome mapping technologies provide novel insights into high dimensional organization, yet introduce new computational challenges. We developed MIA-Sig ( https://github.com/TheJacksonLaboratory/mia-sig.git ), an algorithmic framework to de-noise the data, assess statistical significance of complexes, and identify topological domains inter-domain contacts. On immunoprecipitation...
Abstract Background Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML/RARα, a major etiological agent in APL. However, molecular mechanisms underlying role of PML/RARα leukemogenesis remains largely unknown. Results Using an inducible system, we comprehensively analyzed 3D genome organization myeloid cells and its reorganization after induction, performed additional analyses patient-derived APL with native PML/RARα. We discovered that mediates extensive...
Abstract In the past decade, genome-wide characterization of three-dimensional chromatin structure in plants using high-throughput methods has greatly advanced our knowledge plant genome architecture (Liu and Weigel, 2015; Ouyang et al., 2020). However, due to limitation Illumina short-read sequencing, contact map obtained by Hi-C/ChIA-PET is pairwise, multi-way interaction can only be inferred from two-way data. To directly capture Arabidopsis, we applied a long-read-based method called...
SUMMARY The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These offer new insight into high-dimensional organization and gene regulation, but also introduce challenges in data visualization analysis. To overcome these challenges, we developed MCIBox, a toolkit for Multi-way Chromatin Interaction (MCI) analysis, including tool platform identifying micro-domains clustered complexes. MCIBox...