Expressed pseudogenes in the transcriptional landscape of human cancers

Shanker Kalyana-Sundaram, Chandan Kumar-Sinha, Sunita Shankar, Dan R. Robinson, Yi Mi Wu, Xuhong Cao, Irfan A. Asangani, Vishal Kothari, John R. Prensner, Robert J. Lonigro, Matthew K. Iyer, Terrence Barrette, Achiraman Shanmugam, Saravana M. Dhanasekaran, Nallasivam Palanisamy, Arul M. Chinnaiyan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

169 Scopus citations

Abstract

Pseudogene transcripts can provide a novel tier of gene regulation through generation of endogenous siRNAs or miRNA-binding sites. Characterization of pseudogene expression, however, has remained confined to anecdotal observations due to analytical challenges posed by the extremely close sequence similarity with their counterpart coding genes. Here, we describe a systematic analysis of pseudogene "transcription" from an RNA-Seq resource of 293 samples, representing 13 cancer and normal tissue types, and observe a surprisingly prevalent, genome-wide expression of pseudogenes that could be categorized as ubiquitously expressed or lineage and/or cancer specific. Further, we explore disease subtype specificity and functions of selected expressed pseudogenes. Taken together, we provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression, especially in light of the recently described ceRNA networks. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.

Original languageEnglish (US)
Pages (from-to)1622-1634
Number of pages13
JournalCell
Volume149
Issue number7
DOIs
StatePublished - Jun 22 2012

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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