title: Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies.
abstract: The human genome contains thousands of retrocopies, mostly as processed pseudogenes, which were recently shown to be prevalently transcribed. In particular, those specifically acquired in the human lineage are able to modulate gene expression in a manner that contributed to the evolution of human-specific traits. Therefore, knowledge of the human-specific retrocopies that are transcribed or their full-length transcript structure contributes to better understand human genome evolution. In this study, we identified 16 human-specific retrocopies that harbor 5' CpG islands by in silico analysis and showed that 12 were transcribed in normal tissues and cancer cell lines with a variety of expression patterns, including cancer-specific expression. Determination of the structure of the transcripts associated with the retrocopies revealed that none were transcribed from their 5' CpG islands, but rather, from inside the 3' UTR and the nearby 5' flanking region of the retrocopies as well as the promoter of neighboring genes. The multiple forms of the transcripts, such as chimeric and individual transcripts in both the sense and antisense orientation, might have introduced novel post-transcriptional regulation into the genome during human evolution. These results shed light on the potential role of human-specific retrocopies in the evolution of gene regulation and genomic disorders.
authors.affiliation: Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan.
authors.forename: Saori
authors.initials: S
authors.lastname: Mori
authors.affiliation: Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan.
authors.forename: Masaaki
authors.initials: M
authors.lastname: Hayashi
authors.affiliation: Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan.
authors.forename: Shun
authors.initials: S
authors.lastname: Inagaki
authors.affiliation: Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan.
authors.forename: Takuji
authors.initials: T
authors.lastname: Oshima
authors.affiliation: Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Tateishi
authors.affiliation: Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Kami-Ina, Nagano, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Fujii
authors.affiliation: Epigenomics Division, Frontier Agriscience and Technology Center, Faculty of Agriculture, Shinshu University, Kami-Ina, Nagano, Japan Department of Interdisciplinary Genome Sciences and Cell Metabolism, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Kami-Ina, Nagano, Japan ssuzuki@shinshu-u.ac.jp.
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Suzuki
mesh_terms: D020413:3' Untranslated Regions; D045744:Cell Line, Tumor; D018899:CpG Islands; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics*; D018626:Retroelements; D048348:Reverse Transcription
chemical_list: D020413:3' Untranslated Regions; D012333:RNA, Messenger; D018626:Retroelements