Ontology highlight
ABSTRACT: In this study, we describe a systematic analysis of pseudogene 'transcription' from an RNA-Seq resource of 293 samples, from 13 cancer and normal tissue types. We observed a highly prevalent, genome-wide expression of pseudogenes that could be categorized as universally expressed or lineage- and/or cancer-specific. We also explored disease subtype specificity and functions of selected expressed pseudogenes. 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. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.
PROVIDER: phs000525.v1.p1 | EGA |
REPOSITORIES: EGA
Kalyana-Sundaram Shanker S Kumar-Sinha Chandan C Shankar Sunita S Robinson Dan R DR Wu Yi-Mi YM Cao Xuhong X Asangani Irfan A IA Kothari Vishal V Prensner John R JR Lonigro Robert J RJ Iyer Matthew K MK Barrette Terrence T Shanmugam Achiraman A Dhanasekaran Saravana M SM Palanisamy Nallasivam N Chinnaiyan Arul M AM
Cell 20120601 7
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 ty ...[more]