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

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

doi:10.1590/1678-4685-gmb-2017-0164

Zhen Gong, Weidong Li + Show 7 more

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https://doi.org/10.1590/1678-4685-gmb-2017-0164

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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.

Highlights

Ubiquitin-Specific Peptidase 22 (USP22) belongs to the largest subfamily of ubiquitin-specific proteases (USPs)
To identify the potential gene targets of USP22 and GCN5, the genomic DNA fragments recognized by USP22 and GCN5 were isolated by ChIP using specific antibodies and sequenced
There were 2434 putative target genes bound by USP22 (Table S3), including the known target MTA 1 and CAD (Zhang et al, 2008), and 2256 putative target genes bound by GCN5 (Table S4), respectively

Summary

Introduction

Ubiquitin-Specific Peptidase 22 (USP22) belongs to the largest subfamily of ubiquitin-specific proteases (USPs). There are two kinds of proteins identified as the substrates of USP22, non-histone and histone. It is well known that USP22 can interact with non-histone substrates to stabilize these proteins and inhibit their degradation by proteasome. These substrates include telomeric repeat binding factor 1 (TRF1) (Atanassov et al, 2009), sirtuin 1 (SIRT1) (Lin et al, 2012), cyclooxygenase 2 (COX-2) (Xiao et al, 2015), lysine-specific histone demethylase 1A (KDM1A) (Zhou et al, 2016) and others. USP22 is the subunit of the transcription regulatory SAGA (Spt-Ada-Gcn acetyltransferase) complex (Zhao et al, 2008; Zhang et al, 2008). There is no information on the genome-wide binding sites of USP22 and its direct target genes in cancer cells

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