title: Functional prediction of differentially expressed lncRNAs in HSV-1 infected human foreskin fibroblasts.
abstract: One of the most important functions of long noncoding RNAs (lncRNAs) is to control protein coding gene transcription by acting locally in cis, or remotely in trans. Herpes Simplex Virus type I (HSV-1) latently infects over 80 % of the population, its reactivation from latency usually results in productive infections in human epithelial cells, and is responsible for the common cold sores and genital Herpes. HSV-1 productive infection leads to profound changes in the host cells, including the host transcriptome. However, how genome wide lncRNAs expressions are affected by the infection and how lncRNAs expression relates to protein coding gene expression have not been analyzed.
  
  
  
  We analyzed differentially expressed lncRNAs and their potential targets from RNA-seq data in HSV-1 infected human foreskin fibroblast (HFF) cells. Based on correlations of expression patterns of differentially expressed protein-coding genes and lncRNAs, we predicted that these lncRNAs may regulate, either in cis or in trans, the expression of many cellular protein-coding genes.
  
  
  
  Here we analyzed HSV-1 infection induced, differentially expressed lncRNAs and predicted their target genes. We detected 208 annotated and 206 novel differentially expressed lncRNAs. Gene Ontology and Pathway enrichment analyses revealed potential lncRNA targets, including genes in chromatin assembly, genes in neuronal development and neurodegenerative diseases and genes in the immune response, such as Toll-like receptor signaling and RIG-I-like receptor signaling pathways.
  
  
  
  We found that differentially expressed lncRNAs may regulate the expression of many cellular protein-coding genes involved in pathways from native immunity to neuronal development, thus revealing important roles of lncRNAs in the regulation of host transcriptional programs in HSV-1 infected human cells.
authors: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China.
authors: Benxia
authors: B
authors: Hu
authors: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China.
authors: Yongxia
authors: Y
authors: Huo
authors: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China.
authors: Guijun
authors: G
authors: Chen
authors: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China.
authors: Liping
authors: L
authors: Yang
authors: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
authors: Dongdong
authors: D
authors: Wu
authors: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, 650223, China. zhoujm@mail.kiz.ac.cn.
authors: Jumin
authors: J
authors: Zhou
mesh_terms: D005347:Fibroblasts / Q000378:metabolism* / Q000821:virology; D052816:Foreskin / Q000378:metabolism / Q000821:virology*; D005786:Gene Expression Regulation; D006561:Herpes Simplex / Q000235:genetics* / Q000378:metabolism / Q000821:virology; D018259:Herpesvirus 1, Human / Q000235:genetics / Q000502:physiology*; D006801:Humans; D008297:Male; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism
chemical_list: D062085:RNA, Long Noncoding
keywords: HSV-1; In cis; In trans; Long noncoding RNA; RNA-seq