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Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells

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Title
Identification of potential target genes of USP22 via ChIP-seq and RNA-seq analysis in HeLa cells
Published in
Genetics and Molecular Biology, June 2018
DOI 10.1590/1678-4685-gmb-2017-0164
Pubmed ID
Authors

Zhen Gong, Jianyun Liu, Xin Xie, Xiaoyuan Xu, Ping Wu, Huimin Li, Yaqin Wang, Weidong Li, Jianjun Xiong

Abstract

The ubiquitin-specific protease 22 (USP22) is an oncogene and its expression is upregulated in many types of cancer. In the nucleus, USP22 functions as one subunit of the SAGA to regulate gene transcription. However, the genome-wide USP22 binding sites and its direct target genes are yet clear. In this study, we characterized the potential genomic binding sites of UPS22 and GCN5 by ChIP-seq using specific antibodies in HeLa cells. There were 408 overlapping putative target genes bound by both USP22 and GCN5. Motif analysis showed that the sequences bound by USP22 and GCN5 shared two common motifs. Gene ontology (GO) and pathway analysis indicated that the genes targeted by USP22 and GCN5 were involved in different physiological processes and pathways. Further RNA-seq, GO and pathway analyses revealed that knockdown of UPS22 induced differential expression of many genes that participated in diverse physiological processes, such as metabolic process. Integration of ChIP-seq and RNA-seq data revealed that UPS22 bound to the promoters of 56 genes. These findings may provide new insights into the regulation of USP22 on gene expression during the development of cervical cancer.

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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 > Master 4 18%
Student > Bachelor 3 14%
Student > Ph. D. Student 2 9%
Researcher 2 9%
Professor > Associate Professor 1 5%
Other 0 0%
Unknown 10 45%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 8 36%
Agricultural and Biological Sciences 4 18%
Unknown 10 45%