Oncotarget

Research Papers:

Evidence for the association of chromatin and microRNA regulation in the human genome

Bang-Bao Tao, Xi-Qiang Liu, Wenhao Zhang, Shu Li, Dong Dong, Mang Xiao and Jun Zhong _

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Oncotarget. 2017; 8:70958-70966. https://doi.org/10.18632/oncotarget.20214

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Abstract

Bang-Bao Tao1,*, Xi-Qiang Liu2,*, Wenhao Zhang3,*, Shu Li4,*, Dong Dong6, Mang Xiao5 and Jun Zhong1

1Department of Neurosurgery, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200092, China

2Department of Hepatobiliary-Pancreatic Surgery, Zhejiang Provincial People’s Hospital, Hangzhou 310014, China

3Department of Hematology, Xinhua Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 200092, China

4 Department of Pathophysiology, Wannan Medical College, Wuhu 241002, China

5Department of Otolaryngology Head and Neck Surgery, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou 310027, China

6Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai 200241, China

*These authors have contributed equally to this work

Correspondence to:

Jun Zhong, email: [email protected]

Mang Xiao, email: [email protected]

Keywords: microRNA, histone modification, DNA methylation, chromatin regulation, coordinated action

Received: April 12, 2017    Accepted: May 29, 2017    Published: August 12, 2017

ABSTRACT

Both microRNAs (miRNAs) and chromatin regulation play important roles in cellular processes and they function at different regulatory levels of transcription. Although efforts have been devoted to the investigation of miRNA and chromatin regulation, there’s still no comprehensive work to illustrate their relationships due tothe lack of whole-genome wide datasets in different human cellular contexts. Based on the recently published large-scale epigenetic data, we examined the association between miRNA and epigenetic machinery. Our work confirmed a general relationship between miRNA biogenesis and chromatin features around pre-miRNA genomic regions. Obvious enrichments of DNA methylation and several histone modifications were observed within the pre-miRNA genomic region, which werecorrelated with miRNA expression levels. Furthermore, chromatin features at genepromoter regionsweretightly associated with miRNA regulation. Interestingly, we found that genes with their promoter regions located in the active chromatin state regions tend to have a higher probability to be targeted by miRNAs. This worksuggests that miRNAs and chromatin features are often highly coordinated, which provides a guide to deeply understand the complexity of gene regulation.


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