title: Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals.
abstract: Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play extensive roles in transcriptional regulation. In particular, we have reported that promoter-associated ncRNAs (pancRNAs) activate the partner gene expression via local epigenetic changes.
  
  
  
  Here, we identify thousands of genes under pancRNA-mediated transcriptional activation in five mammalian species in common. In the mouse, 1) pancRNA-partnered genes confined their expression pattern to certain tissues compared to pancRNA-lacking genes, 2) expression of pancRNAs was significantly correlated with the enrichment of active chromatin marks, H3K4 trimethylation and H3K27 acetylation, at the promoter regions of the partner genes, 3) H3K4me1 marked the pancRNA-partnered genes regardless of their expression level, and 4) C- or G-skewed motifs were exclusively overrepresented between-200 and-1 bp relative to the transcription start sites of the pancRNA-partnered genes. More importantly, the comparative transcriptome analysis among five different mammalian species using a total of 25 counterpart tissues showed that the overall pancRNA expression profile exhibited extremely high species-specificity compared to that of total mRNA, suggesting that interspecies difference in pancRNA repertoires might lead to the diversification of mRNA expression profiles.
  
  
  
  The present study raises the interesting possibility that the gain and/or loss of gene-activation-associated pancRNA repertoires, caused by formation or disruption of the genomic GC-skewed structure in the course of evolution, finely shape the tissue-specific pattern of gene expression according to a given species.
authors.affiliation: Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.|Department of Biophysics and Global COE Program, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.|Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-8654, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Uesaka
authors.affiliation: Department of Biophysics and Global COE Program, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.|Department of Life Science, Faculty of Science, Graduate Course in Life Science, Graduate School of Science, Gakushuin University, Tokyo, 171-8588, Japan.
authors.forename: Kiyokazu
authors.initials: K
authors.lastname: Agata
authors.affiliation: Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Aichi, 484-8506, Japan.
authors.forename: Takao
authors.initials: T
authors.lastname: Oishi
authors.affiliation: Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
authors.forename: Kinichi
authors.initials: K
authors.lastname: Nakashima
authors.affiliation: Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan. imamura@scb.med.kyushu-u.ac.jp.|Department of Biophysics and Global COE Program, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan. imamura@scb.med.kyushu-u.ac.jp.
authors.forename: Takuya
authors.initials: T
authors.lastname: Imamura
mesh_terms: D000818:Animals; D001483:Base Sequence; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D008322:Mammals / Q000235:genetics*; D051379:Mice; D059372:Nucleotide Motifs; D009928:Organ Specificity / Q000235:genetics; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D015533:Transcriptional Activation; D059467:Transcriptome
chemical_list: D006657:Histones; D012333:RNA, Messenger; D022661:RNA, Untranslated
keywords: Epigenetic regulation; Evolution; Long non-coding RNA; Species diversity