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Your search keyword '"Hebing Chen"' showing total 4 results
Start Over Author "Hebing Chen" Publisher public library of science
4 results on '"Hebing Chen"'

1. Genome-wide identification and analysis of A-to-I RNA editing events in the malignantly transformed cell lines from bronchial epithelial cell line induced by α-particles radiation

Author

Pingkun Zhou, Qiaowei Liu, Tao Li, Lukuan You, Xiaohua Chen, Hebing Chen, Hao Li, Yi Hu, Lingling Li, and Xiaochen Bo

Subjects
0301 basic medicine, RNA editing, Adenosine, Molecular biology, Carcinogenesis, Cell Lines, Gene Expression, Artificial Gene Amplification and Extension, medicine.disease_cause, Genome, Biochemistry, Polymerase Chain Reaction, 0302 clinical medicine, Sequencing techniques, Gene expression, Medicine and Health Sciences, DNA sequencing, Cell Line, Transformed, Multidisciplinary, High-Throughput Nucleotide Sequencing, RNA sequencing, Alpha Particles, Cell biology, Nucleic acids, Cell Transformation, Neoplastic, Oncology, 030220 oncology & carcinogenesis, Medicine, Biological Cultures, Research Article, Science, Bronchi, Biology, Research and Analysis Methods, Cell Line, 03 medical and health sciences, Downregulation and upregulation, medicine, Genetics, Cancer Genetics, Humans, Biology and life sciences, Genome, Human, RNA, Transformed Cell Lines, Epithelial Cells, Oncogenes, Inosine, 030104 developmental biology, Molecular biology techniques, Cell culture
Abstract

Adenosine (A) to inosine (I) RNA editing is the most prevalent RNA editing mechanism in humans and plays critical roles in tumorigenesis. However, the effects of radiation on RNA editing were poorly understood, and a deeper understanding of the radiation-induced cancer is imperative. Here, we analyzed BEP2D (a human bronchial epithelial cell line) and radiation-induced malignantly transformed cell lines with next generation sequencing. By performing an integrated analysis of A-to-I RNA editing, we found that single-nucleotide variants (SNVs) might induce the downregulation of ADAR2 enzymes, and further caused the abnormal occurrence of RNA editing in malignantly transformed cell lines. These editing events were significantly enriched in differentially expressed genes between normal cell line and malignantly transformed cell lines. In addition, oncogenes CTNNB1 and FN1 were highly edited and significantly overexpressed in malignantly transformed cell lines, thus may be responsible for the lung cancer progression. Our work provides a systematic analysis of RNA editing from cell lines derived from human bronchial epithelial cells with high-throughput RNA sequencing and DNA sequencing. Moreover, these results provide further evidence for RNA editing as an important tumorigenesis mechanism.

Published
2019

2. iFORM: Incorporating Find Occurrence of Regulatory Motifs

Author

Xiaochen Bo, Chao Ren, Feng Liu, Hebing Chen, Wenjie Shu, Zhangyi Ouyang, and Bite Yang

Subjects
0301 basic medicine, Epigenomics, Computer science, lcsh:Medicine, Gene Expression, Social Sciences, Biochemistry, Database and Informatics Methods, Sociology, Consortia, Transcriptional regulation, lcsh:Science, Regulation of gene expression, Multidisciplinary, Applied Mathematics, Simulation and Modeling, Genomics, Genomic Databases, Physical Sciences, Sequence Analysis, Algorithms, Research Article, Cell Binding, Cell Physiology, Computational biology, ENCODE, Research and Analysis Methods, Response Elements, DNA sequencing, 03 medical and health sciences, Sequence Motif Analysis, DNA-binding proteins, Genetics, Humans, Gene Regulation, Binding site, Nucleotide Motifs, Molecular Biology Techniques, Sequencing Techniques, Transcription factor, Molecular Biology, lcsh:R, Biology and Life Sciences, Computational Biology, Proteins, Cell Biology, Sequence Analysis, DNA, Genome Analysis, Regulatory Proteins, 030104 developmental biology, Biological Databases, Gene Expression Regulation, lcsh:Q, Mathematics, Software, Transcription Factors
Abstract

Accurately identifying the binding sites of transcription factors (TFs) is crucial to understanding the mechanisms of transcriptional regulation and human disease. We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use and efficient tool for scanning DNA sequences with TF motifs described as position weight matrices (PWMs). Both performance assessment with a receiver operating characteristic (ROC) curve and a correlation-based approach demonstrated that iFORM achieves higher accuracy and sensitivity by integrating five classical motif discovery programs using Fisher's combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and the tool has demonstrated its utility in further elucidating individual roles of functional elements. Both the source and binary codes for iFORM can be freely accessed at https://github.com/wenjiegroup/iFORM. The identified TF binding sites across human cell and tissue types using iFORM have been deposited in the Gene Expression Omnibus under the accession ID GSE53962.

Published
2016

3. Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome.

Author

Hebing Chen, Yao Tian, Wenjie Shu, Xiaochen Bo, and Shengqi Wang

Subjects
*CHROMATIN, *NUCLEOPROTEINS, *GENOMES, *GENES, *GENETICS
Abstract

Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCFbinding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome. [ABSTRACT FROM AUTHOR]

Published
2012
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4. Biological Responses to Perfluorododecanoic Acid Exposure in Rat Kidneys as Determined by Integrated Proteomic and Metabonomic Studies.

Author

Hongxia Zhang, Lina Ding, Xuemei Fang, Zhimin Shi, Yating Zhang, Hebing Chen, Xianzhong Yan, and Jiayin Dai

Subjects
IMMUNOMODULATORS, LABORATORY rats, KIDNEY physiology, PROTEOMICS, IMMUNOTOXICOLOGY, HEPATOTOXICOLOGY, AMINO acid metabolism, METHYLHISTIDINES, CARBOXYLIC acids
Abstract

Background: Perfluorododecanoic acid (PFDoA) is a perfluorinated carboxylic chemical (PFC) that has broad applications and distribution in the environment. While many studies have focused on hepatotoxicity, immunotoxicity, and reproductive toxicity of PFCAs, few have investigated renal toxicity. Methodology/Principal Findings: Here, we used comparative proteomic and metabonomic technologies to provide a global perspective on renal response to PFDoA. Male rats were exposed to 0, 0.05, 0.2, and 0.5 mg/kg/day of PFDoA for 110 days. After 2-D DIGE and MALDI TOF/TOF analysis, 79 differentially expressed proteins between the control and the PFDoA treated rats (0.2 and 0.5 mg-dosed groups) were successfully identified. These proteins were mainly involved in amino acid metabolism, the tricarboxylic acid cycle, gluconeogenesis, glycolysis, electron transport, and stress response. Nuclear magnetic resonance-based metabonomic analysis showed an increase in pyruvate, lactate, acetate, choline, and a variety of amino acids in the highest dose group. Furthermore, the profiles of free amino acids in the PFDoA treated groups were investigated quantitatively by high-coverage quantitative iTRAQ-LC MS/MS, which showed levels of sarcosine, asparagine, histidine, 1-methylhistidine, Ile, Leu, Val, Trp, Tyr, Phe, Cys, and Met increased markedly in the 0.5 mg dosed group, while homocitrulline, a-aminoadipic acid, b-alanine, and cystathionine decreased. Conclusion/Significance: These observations provide evidence that disorders in glucose and amino acid metabolism may contribute to PFDoA nephrotoxicity. Additionally, &agr;2u globulin may play an important role in protecting the kidneys from PFDoA toxicity. [ABSTRACT FROM AUTHOR]

Published
2011
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