A5101703602- Genomics and Chromatin Dynamics
- Chromosomal and Genetic Variations
- Genomics and Phylogenetic Studies
- Cervical Cancer and HPV Research
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Neuroinflammation and Neurodegeneration Mechanisms
- RNA modifications and cancer
- Autophagy in Disease and Therapy
- Alzheimer's disease research and treatments
- Gene expression and cancer classification
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- Winter Sports Injuries and Performance
- Plant Genetic and Mutation Studies
- Video Surveillance and Tracking Methods
- Extracellular vesicles in disease
- Metabolomics and Mass Spectrometry Studies
- MicroRNA in disease regulation
- Diet and metabolism studies
- Genetic factors in colorectal cancer
- vaccines and immunoinformatics approaches
- Mitochondrial Function and Pathology
- Plant Gene Expression Analysis
- Cancer, Lipids, and Metabolism
Huazhong Agricultural University
2014-2024
Chengdu Sport University
2024
Beijing Sport University
2023-2024
Shanghai Zhangjiang Laboratory
2021
Capital Medical University
1995-2019
Mayo Clinic
2010
East Sussex Healthcare NHS Trust
2007
Long-range chromatin interactions play an important role in transcription regulation. Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) is emerging technology that has unique advantages interaction analysis, and thus provides insight into the study of This article introduces experimental protocol data analysis process ChIA-PET, as well discusses some applications using this technology. It also unveils direction future studies based on Overall we show ChIA-PET...
Autopolyploidy is widespread in higher plants and important for agricultural yield quality. However, the effects of genome duplication on chromatin organization transcriptional regulation are largely unknown plants. Using High-throughput Chromosome Conformation Capture (Hi-C), we showed that autotetraploid Arabidopsis presented more inter-chromosomal interactions fewer short-range compared with its diploid progenitor. In addition, contributed to switching some loose compact structure domains...
Abnormalities of autophagy can result in neurodegenerative disorders such as Alzheimer's disease (AD). Nevertheless, the regulatory mechanisms AD are not well understood. Here, we describe our findings that microRNA (miR)-299-5p functions an inhibitor by suppressing Atg5 and antagonizing caspase-dependent apoptosis. We observed decreased levels miR-299-5p both primary neurons under conditions starvation hippocampi APPswe/PS1dE9 mice. Additionally, low were cerebrospinal fluid patients....
Integration of human papillomavirus (HPV) DNA into the genome is a reputed key driver cervical cancer. However, effects HPV integration on chromatin structural organization and gene expression are largely unknown. We studied cohort 61 samples identified an hot spot in CCDC106 chromosome 19. then selected fresh cancer tissue that contained unique loci at with no episomal performed whole-genome, RNA, immunoprecipitation high-throughput conformation capture (Hi-C) sequencing to identify...
Abstract Immunocytes dynamically reprogram their gene expression profiles during differentiation and immunoresponse. However, the underlying mechanism remains elusive. Here, we develop a single-cell Hi-C method systematically delineate 3D genome dynamic epigenetic atlas of macrophages these processes. We propose “degree disorder” to measure organizational patterns inside topologically-associated domains, which is correlated with chromatin states, expression, structure variability in...
Human papillomavirus (HPV) is predominantly associated with HPV-related cancers, however, the precise mechanisms underlying HPV-host epigenetic architectures in HPV carcinogenesis remain elusive. Here, we employed high-throughput chromosome conformation capture (Hi-C) to comprehensively map HPV16/18-host chromatin interactions. Our study identified transcription factor Sp1 as a pivotal mediator programming By targeting Sp1, active histone modifications (H3K27ac, H3K4me1, and H3K4me3)...
The existence of only natural brown and green cotton fibers (BCF GCF, respectively), as well poor fiber quality, limits the use naturally colored ( Gossypium hirsutum L.). A better understanding pigment regulation is needed to surmount these obstacles. In this work, transcriptome analysis quantitative reverse transcription PCR revealed that 13 9 phenylpropanoid (metabolic) pathway genes were enriched during synthesis, while differential expression flavonoid metabolic occurred among BCF,...
A 75-year-old woman presented with left ventricular apical ballooning syndrome mimicking acute anterior myocardial infarction. She had a long history of chest tightness and was undergoing contrast stress echocardiogram because frequent re-admissions pain, all normal ECGs troponins. standard dobutamine/atropine protocol been used. The patient developed central crushing marked ST elevation, transient slowing heart rate ballooning. admitted to the coronary care unit received thrombolysis....
Understanding chromatin interactions is important because they create chromosome conformation and link the cis- trans- regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing a genome-wide high-throughput technology that detects associated specific protein of interest. We developed ChIA-PET Tool data analysis in 2010. Here, we present updated version (V3) as computational package process...
It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied investigate three-dimensional (3D) genome organizations gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) a new technology with high efficiency cost-effectiveness for whole-genome chromosome capture. Here, we introduce DLO tool, flexible versatile pipeline processing...
This study aims to explore the relationship between blood biochemical indexes and injury risk of elite male athletes in racing ice sports. The compared demographic indexes, monthly injuries, longitudinal tracking data. non-linear was analyzed using an unrestricted cubic spline. Generalized estimating equations estimated relative (OR) occurrence. Receiver operating characteristics area under curve determined diagnostic accuracy. In snow sledding group, when creatine kinase rises 489.46 u/L or...
Abstract Background It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied investigate genome organizations gene regulation. Digestion-Ligation-Only Hi-C (DLO Hi-C) a new technology with high efficiency effective cost for whole-genome chromosome conformation capture. Results Here, we introduce DLO Tool, flexible versatile...
Abstract Understanding chromatin interactions is important since they create chromosome conformation and link the cis- trans-regulatory elements to their target genes for transcriptional regulation. Chromatin Interaction Analysis with Paired-End Tag (ChIA-PET) sequencing a genome-wide high-throughput technology that detects associated specific protein of interest. Previously we developed ChIA-PET Tool in 2010 data analysis. Here present updated version (V3), computational package process...
Abstract MN Background: Breast cancer is the second leading cause of death women worldwide. One major challenges for a better prognosis breast patients ineffectiveness chemotherapy and drug resistance. To investigate mechanisms resistance, resistant cell lines have been established with various anticancer agents. We found that FASN, an important metabolic enzyme overexpressed in aggressive carcinomas, t responsible part resistance phenotype cells. Our findings show blockage FASN augments...
Abstract Summary CoolBox is a Python package for interactive genomic data exploration based on Jupyter notebook. It provides ggplot2-like Application Programming Interface (API) visualization, and Jupyter/ipywidgets Graphical User (GUI) exploration. versatile multi-omics explorer supporting most types of formats generated by various sequencing technologies like RNA-Seq, ChIP-Seq, ChIA-PET Hi-C. Availability implementation purely implemented with Python, the GUI widget in notebook ipywidgets...
Background: Integration of human papillomavirus (HPV) DNA into genome is the reputed key driver cervical cancer. However, effects HPV integration on chromatin structural organization and gene expression are largely unknown in such Methods: We investigated a cohort 61 samples for analysis. And selected fresh cancer tissue from set clinical whose only contained unique loci at CCDC106 no episomal DNA. A combination WGS, RNA-seq, ChIP-seq Hi-C data analysis were applied to identify mechanisms...
Accurate collection and analysis of ground reaction force (GRF) data are crucial for optimizing the technical movements speed skaters; however, it has been a challenge limitations experimental equipment application scenarios. Therefore, we proposed novel approach estimating GRF based on kinematics obtained from markerless video tracking systems achieved low errors compared with data. Our method allows further biomechanical analysis, including muscle power, during skating competitions.
<p indent=0mm>Studies on the 3D genomics could facilitate understanding of relationship between genome structure and functions. Based different research purposes, a variety chromatin three-dimensional conformation capture methods have been developed, greatly promoting progress research. This review aims to systematically introduce summarize various methods. The are generally divided into three categories. first category is based proximity ligation sequencing, including 3C, Hi-C, <italic>in...
Abstract The highly organized three-dimensional genome is crucial for gene transcription. However, it remains elusive how the order of architecture related to its function. Here, we developed a single-cell Hi-C method and proposed TAD “degree disorder” as measure organizational patterns, which correlated with chromatin epigenetic states, expression co-regulation, structure variability in individual cells. Upon Mycobacterium tuberculosis infection, NF-κB enters into nucleus, binds target...