Transcriptome altered by latent human cytomegalovirus infection on THP-1 cells using RNA-seq.
Human cytomegalovirus (HCMV) has been recognized as a cause of severe, sometimes life-threatening disease in congenitally infected newborns as well as in immunocompromised individuals. However, the molecular mechanisms of the host-virus interaction remain poorly understood. Here, we profiled the expression of mRNAs and long noncoding RNAs (lncRNAs) in THP-1 cells using the emerging RNA-seq to investigate the transcriptional changes during HCMV latent infection. At 4 days post HCMV infection, a total of 169,008,624 sequence reads and 180,616 transcripts were obtained, respectively. Of these transcripts, 1,354 noncoding genes and 12,952 protein-coding genes were observed in Refseq database. Differential gene expression analysis identified 2,153 differentially expressed genes (DEGs) between HCMV-infected and mock-infected THP-1 cells, including 1,098 up-regulated genes and 1,055 down-regulated genes. These regulated genes were involved in pathways of apoptosis, inflammatory response and cell cycle progression, all of which may be implicated in viral pathogenesis. In addition, 646 lncRNAs (208 known lncRNAs and 438 novel lncRNAs) were upregulated and 424 (140 known and 284 novel) were downregulated in infected THP-1 cells. These findings have provided a dynamic scenario of DE candidate genes and lncRNAs at the virus-host interface and clearly warrant further experimental investigation associated with HCMV infection.
Department of Laboratory Medicine, the Second Affiliated Hospital﹠Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China; School of Laboratory Medicine, Wenzhou Medical University; Key Laboratory of Laboratory Medicine, Ministry of Education, China.
Qi
Q
Zhang
Department of Laboratory Medicine, the Second Affiliated Hospital﹠Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China; School of Laboratory Medicine, Wenzhou Medical University; Key Laboratory of Laboratory Medicine, Ministry of Education, China.
Mei-Mei
MM
Lai
Department of Laboratory Medicine, the Second Affiliated Hospital﹠Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China; School of Laboratory Medicine, Wenzhou Medical University; Key Laboratory of Laboratory Medicine, Ministry of Education, China.
Yun-Yan
YY
Lou
Department of Laboratory Medicine, the Second Affiliated Hospital﹠Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China; School of Laboratory Medicine, Wenzhou Medical University; Key Laboratory of Laboratory Medicine, Ministry of Education, China.
Bin-Han
BH
Guo
Department of Laboratory Medicine, the Second Affiliated Hospital﹠Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China.
Hui-Yan
HY
Wang
Department of Laboratory Medicine, the Second Affiliated Hospital﹠Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China; School of Laboratory Medicine, Wenzhou Medical University; Key Laboratory of Laboratory Medicine, Ministry of Education, China. Electronic address: jszhengxq@163.com.
Xiao-Qun
XQ
Zheng
D045744:Cell Line, Tumor; D003587:Cytomegalovirus; D003586:Cytomegalovirus Infections / Q000235:genetics / Q000378:metabolism*; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D062085:RNA, Long Noncoding / Q000096:biosynthesis* / Q000235:genetics; D059467:Transcriptome
D062085:RNA, Long Noncoding
HCMV; RNA-seq; latent infection; lncRNA; mRNA