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Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer

Overview of attention for article published in Clinical Epigenetics, March 2018
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Title
Integrated analyses of multi-omics reveal global patterns of methylation and hydroxymethylation and screen the tumor suppressive roles of HADHB in colorectal cancer
Published in
Clinical Epigenetics, March 2018
DOI 10.1186/s13148-018-0458-3
Pubmed ID
Authors

Yimin Zhu, Hanlin Lu, Dandan Zhang, Meiyan Li, Xiaohui Sun, Ledong Wan, Dan Yu, Yiping Tian, Hongchuan Jin, Aifen Lin, Fei Gao, Maode Lai

Abstract

DNA methylation is an important epigenetic modification, associated with gene expression. 5-Methylcytosine and 5-hydroxymethylcytosine are two epigenetic hallmarks that maintain the equilibrium of epigenetic reprogramming. Disequilibrium in genomic methylation leads to carcinogenesis. The purpose of this study was to elucidate the epigenetic mechanisms of DNA methylation and hydroxymethylation in the carcinogenesis of colorectal cancer. Genome-wide patterns of DNA methylation and hydroxymethylation in six paired colorectal tumor tissues and corresponding normal tissues were determined using immunoprecipitation and sequencing. Transcriptional expression was determined by RNA sequencing (RNA-Seq). Groupwise differential methylation regions (DMR), differential hydroxymethylation regions (DhMR), and differentially expressed gene (DEG) regions were identified. Epigenetic biomarkers were screened by integrating DMR, DhMR, and DEGs and confirmed using functional analysis. We identified a genome-wide distinct hydroxymethylation pattern that could be used as an epigenetic biomarker for clearly differentiating colorectal tumor tissues from normal tissues. We identified 59,249 DMRs, 187,172 DhMRs, and 948 DEGs by comparing between tumors and normal tissues. After cross-matching genes containing DMRs or DhMRs with DEGs, we screened seven genes that were aberrantly regulated by DNA methylation in tumors. Furthermore, hypermethylation of the HADHB gene was persistently found to be correlated with downregulation of its transcription in colorectal cancer (CRC). These findings were confirmed in other patients of colorectal cancer. Tumor functional analysis indicated that HADHB reduced cancer cell migration and invasiveness. These findings suggested its possible role as a tumor suppressor gene (TSG). This study reveals the global patterns of methylation and hydroxymethylation in CRC. Several CRC-associated genes were screened with multi-omic analysis. Aberrant methylation and hydroxymethylation were found to be in the carcinogenesis of CRC.

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Mendeley readers

The data shown below were compiled from readership statistics for 22 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 22 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 7 32%
Researcher 6 27%
Professor 2 9%
Student > Bachelor 2 9%
Student > Doctoral Student 1 5%
Other 2 9%
Unknown 2 9%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 9 41%
Medicine and Dentistry 5 23%
Agricultural and Biological Sciences 2 9%
Pharmacology, Toxicology and Pharmaceutical Science 1 5%
Psychology 1 5%
Other 2 9%
Unknown 2 9%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 07 March 2018.
All research outputs
#10,088,671
of 12,612,351 outputs
Outputs from Clinical Epigenetics
#488
of 592 outputs
Outputs of similar age
#205,059
of 273,646 outputs
Outputs of similar age from Clinical Epigenetics
#9
of 12 outputs
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