TY - JOUR
T1 - Expressed pseudogenes in the transcriptional landscape of human cancers
AU - Kalyana-Sundaram, Shanker
AU - Kumar-Sinha, Chandan
AU - Shankar, Sunita
AU - Robinson, Dan R.
AU - Wu, Yi Mi
AU - Cao, Xuhong
AU - Asangani, Irfan A.
AU - Kothari, Vishal
AU - Prensner, John R.
AU - Lonigro, Robert J.
AU - Iyer, Matthew K.
AU - Barrette, Terrence
AU - Shanmugam, Achiraman
AU - Dhanasekaran, Saravana M.
AU - Palanisamy, Nallasivam
AU - Chinnaiyan, Arul M.
N1 - Funding Information:
The authors thank Ram-Shankar Mani, Kalpana Ramnarayanan, Joseph Mierwaza, and Sooryanarayana Varambally for technical help and Javed Siddiqui for providing samples. This work was supported, in part, by the National Institutes of Health (R01CA132874), Early Detection Research Network grant UO1 CA111275, Prostate SPORE grant P50CA69568, and the Department of Defense Era of Hope grant BC075023 (A.M.C.). A.M.C. is supported by the Doris Duke Charitable Foundation Clinical Scientist Award and the Prostate Cancer Foundation. A.M.C. is an American Cancer Society Research Professor and A. Alfred Taubman Scholar.
PY - 2012/6/22
Y1 - 2012/6/22
N2 - 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.
AB - 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.
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U2 - 10.1016/j.cell.2012.04.041
DO - 10.1016/j.cell.2012.04.041
M3 - Article
C2 - 22726445
AN - SCOPUS:84862695743
VL - 149
SP - 1622
EP - 1634
JO - Cell
JF - Cell
SN - 0092-8674
IS - 7
ER -
