Differentially-expressed pseudogenes in HIV-1 infection

Aditi Gupta, Charles Brown, Yong Hui Zheng, Christoph Adami

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberA02
Pages (from-to)5191-5205
Number of pages15
JournalViruses
Volume7
Issue number10
DOIs
StatePublished - Jan 1 2015

Fingerprint

Pseudogenes
HIV Infections
HIV-1
Genes
Untranslated RNA
RNA Stability
Gene Expression Regulation
Virus Diseases
Retroviridae
Life Cycle Stages
Computational Biology
Transcriptome
T-Lymphocytes
Gene Expression

Keywords

  • Differential gene expression
  • HIV-1
  • Pseudogenes
  • RNASeq
  • Transcriptome

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

Cite this

Gupta, A., Brown, C., Zheng, Y. H., & Adami, C. (2015). Differentially-expressed pseudogenes in HIV-1 infection. Viruses, 7(10), 5191-5205. [A02]. https://doi.org/10.3390/v7102869

Differentially-expressed pseudogenes in HIV-1 infection. / Gupta, Aditi; Brown, Charles; Zheng, Yong Hui; Adami, Christoph.

In: Viruses, Vol. 7, No. 10, A02, 01.01.2015, p. 5191-5205.

Research output: Contribution to journalArticle

Gupta, A, Brown, C, Zheng, YH & Adami, C 2015, 'Differentially-expressed pseudogenes in HIV-1 infection', Viruses, vol. 7, no. 10, A02, pp. 5191-5205. https://doi.org/10.3390/v7102869
Gupta, Aditi ; Brown, Charles ; Zheng, Yong Hui ; Adami, Christoph. / Differentially-expressed pseudogenes in HIV-1 infection. In: Viruses. 2015 ; Vol. 7, No. 10. pp. 5191-5205.
@article{b6cfabdf4e724a31b6d32c39f7614b8c,
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.",
keywords = "Differential gene expression, HIV-1, Pseudogenes, RNASeq, Transcriptome",
author = "Aditi Gupta and Charles Brown and Zheng, {Yong Hui} and Christoph Adami",
year = "2015",
month = "1",
day = "1",
doi = "10.3390/v7102869",
language = "English (US)",
volume = "7",
pages = "5191--5205",
journal = "Viruses",
issn = "1999-4915",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
number = "10",

}

TY - JOUR

T1 - Differentially-expressed pseudogenes in HIV-1 infection

AU - Gupta, Aditi

AU - Brown, Charles

AU - Zheng, Yong Hui

AU - Adami, Christoph

PY - 2015/1/1

Y1 - 2015/1/1

N2 - 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.

AB - 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.

KW - Differential gene expression

KW - HIV-1

KW - Pseudogenes

KW - RNASeq

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=84942890557&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84942890557&partnerID=8YFLogxK

U2 - 10.3390/v7102869

DO - 10.3390/v7102869

M3 - Article

C2 - 26426037

AN - SCOPUS:84942890557

VL - 7

SP - 5191

EP - 5205

JO - Viruses

JF - Viruses

SN - 1999-4915

IS - 10

M1 - A02

ER -