Poster abstracts
Poster number 93 submitted by Michael Milligan
Global Intersection of Long Non-Coding RNA (lncRNA) Genes With Processed and Unprocessed Pseudogenes in The Human Genome
Michael Milligan (Wayne State University Center for Molecular Medicine and Genetics), Dr. Leonard Lipovich (Wayne State University Center for Molecular Medicine and Genetics)
Abstract:
Since the completion of the Human Genome Project, a key revelation in post-genomic biology has been the prevalence of non-protein-coding functional elements in the human genome. Highlighted by the ENCODE and FANTOM consortia, these elements include tens of thousands of pseudogenes, as well as comparably numerous long non-coding RNA (lncRNA) genes. Transcription of pseudogenes is still poorly understood, but the field is of great importance for human disease due to the high sequence similarity between pseudogenes and their parental genes, generating the potential for sequence-specific regulation. Recent case studies establish essential functional roles of both pseudogenes and lncRNAs in metazoan systems. Some have even highlighted functional impacts of lncRNA transcription at pseudogene loci on the regulation of the pseudogenes' parental genes. To compute the complete potential regulatory space of integrated pseudogene-lncRNA regulation, we developed and implemented an algorithm, using the PERL programming language, to identify all pseudogenes that are overlapped by lncRNA transcription in both sense and anti-sense orientations. Our algorithm imported three public repositories of pseudogenes: GENCODE v17 (processed and unprocessed; n=15233); UCSC Genome Database (processed only; n=13358) and Yale (processed and unprocessed; n=17216), plus two public lncRNA catalogs: Broad Institute (n=21537) and GENCODE v17 (n=13331). The intersection hence comprised six pseudogene-lncRNA genomewide overlaps. We identified 1167 loci containing genomic-span exon overlaps between all pseudogenes and all lncRNAs with EST and cDNA support. Of these, 374 had bidirectional cDNA support providing evidence of transcription. This project has generated an empirically supported transcriptome list of all pseudogene-lncRNA overlaps in the human genome to serve as a foundation for future curation, parental-gene ontology analysis, and experimental validation of function.
References:
Karro, J. E., Yan, Y., Zheng, D., Zhang, Z., Carriero, N., Cayting, P., . . . Gerstein, M. (2007). Pseudogene.org: A comprehensive database and comparison platform for pseudogene annotation. Nucleic Acids Research, 35(Database issue), D55-D60. doi:10.1093/nar/gkl851
Kalyana-Sundaram, S., Kumar-Sinha, C., Shankar, S., Robinson, D. R., Wu, Y., Cao, X., . . . Chinnaiyan, A. M. (2012). Expressed pseudogenes in the transcriptional landscape of human cancers. Cell, 149(7), 1622-1634. doi:10.1016/j.cell.2012.04.041
Milligan, M. (2014, June). Global Intersection of Long Non-Coding RNA (lncRNA) Genes With Processed and Unprocessed Pseudogenes in The Human Genome. Poster session presented at The 19th Annual Meeting of the RNA Society, Québec City, Canada.
Keywords: LncRNA, Pseudogene, Genomewide