title: Differentially-Expressed Pseudogenes in HIV-1 Infection.
abstract: Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also directly compete with the parent gene transcripts for mRNA stability and other cell factors, modulating their expression levels. Tissue-specific and cancer-specific differential expression of these "functional" pseudogenes has been reported. To ascertain potential pseudogene:gene interactions in HIV-1 infection, we analyzed transcriptomes from infected and uninfected T-cells and found that 21 pseudogenes are differentially expressed in HIV-1 infection. This is interesting because parent genes of one-third of these differentially-expressed pseudogenes are implicated in HIV-1 life cycle, and parent genes of half of these pseudogenes are involved in different viral infections. Our bioinformatics analysis identifies candidate pseudogene:gene interactions that may be of significance in HIV-1 infection. Experimental validation of these interactions would establish that retroviruses exploit this newly-discovered layer of host gene expression regulation for their own benefit.
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI 48824, USA. agupta@msu.edu.|BEACON Center for the Study of Evolution in Action, Michigan State University, 567Wilson Road, East Lansing, MI 48824, USA. agupta@msu.edu.
authors.forename: Aditi
authors.initials: A
authors.lastname: Gupta
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI 48824, USA. ctbrown@ucdavis.edu.|BEACON Center for the Study of Evolution in Action, Michigan State University, 567Wilson Road, East Lansing, MI 48824, USA. ctbrown@ucdavis.edu.|Department of Computer Science and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, MI 48824, USA. ctbrown@ucdavis.edu.
authors.forename: C Titus
authors.initials: CT
authors.lastname: Brown
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI 48824, USA. zhengyo@msu.edu.|BEACON Center for the Study of Evolution in Action, Michigan State University, 567Wilson Road, East Lansing, MI 48824, USA. zhengyo@msu.edu.
authors.forename: Yong-Hui
authors.initials: YH
authors.lastname: Zheng
authors.affiliation: Department of Microbiology and Molecular Genetics, Michigan State University, 567 Wilson Road, East Lansing, MI 48824, USA. adami@msu.edu.|BEACON Center for the Study of Evolution in Action, Michigan State University, 567Wilson Road, East Lansing, MI 48824, USA. adami@msu.edu.|Department of Physics and Astronomy, Michigan State University, 567 Wilson Road, East Lansing, MI 48824, USA. adami@msu.edu.
authors.forename: Christoph
authors.initials: C
authors.lastname: Adami
mesh_terms: D002460:Cell Line; D020869:Gene Expression Profiling; D015658:HIV Infections / Q000821:virology*; D015497:HIV-1 / Q000254:growth & development*; D054884:Host-Pathogen Interactions; D006801:Humans; D011544:Pseudogenes; D017423:Sequence Analysis, RNA; D013601:T-Lymphocytes / Q000821:virology; D014158:Transcription, Genetic
keywords: HIV-1; RNASeq; differential gene expression; pseudogenes; transcriptome