title: Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells.
abstract: Bidirectional promoters are the major source of gene activation-associated noncoding RNA (ncRNA). PC12 cells offer an interesting model for understanding the mechanism underlying bidirectional promoter-mediated cell cycle control. Nerve growth factor (NGF)-stimulated PC12 cells elongate neurites, and are in a reversible cell-cycle-arrested state. In contrast, these cells irreversibly differentiate and cannot re-enter the normal cell cycle after NGF plus cAMP treatment. In this study, using directional RNA-seq, we found that bidirectional promoters for protein-coding genes with promoter-associated ncRNA (pancRNA) were enriched for cAMP response element consensus sequences, and were preferred targets for transcriptional regulation by the transcription factors in the cAMP-dependent pathway. A spindle-formation-associated gene, Nusap1 and pancNusap1 were among the most strictly co-transcribed pancRNA-mRNA pairs. This pancRNA-mRNA pair was specifically repressed in irreversibly differentiated PC12 cells. Knockdown (KD) and overexpression experiments showed that pancNusap1 positively regulated the Nusap1 expression in a sequence-specific manner, which was accompanied by histone acetylation at the Nusap1 promoter. Furthermore, pancNusap1 KD recapitulated the effects of cAMP on cell cycle arrest. Thus, we conclude that pancRNA-mediated histone acetylation contributes to the establishment of the cAMP-induced transcription state of the Nusap1 locus and contributes to the irreversible cell cycle exit for terminal differentiation of PC12 cells.
authors.affiliation: Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Japan Department of Biophysics, Graduate School of Science, Kyoto University, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Yamamoto
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Japan.
authors.forename: Kiyokazu
authors.initials: K
authors.lastname: Agata
authors.affiliation: Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 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, Japan imamura@scb.med.kyushu-u.ac.jp.
authors.forename: Takuya
authors.initials: T
authors.lastname: Imamura
mesh_terms: D000107:Acetylation; D000818:Animals; D001665:Binding Sites; D059447:Cell Cycle Checkpoints / Q000235:genetics; D002454:Cell Differentiation; D002460:Cell Line; D000242:Cyclic AMP / Q000378:metabolism*; D017362:Cyclic AMP Response Element-Binding Protein / Q000378:metabolism; D005786:Gene Expression Regulation; D055785:Gene Knockdown Techniques; D006657:Histones / Q000378:metabolism; D006801:Humans; D020932:Nerve Growth Factor / Q000378:metabolism; D016716:PC12 Cells; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated; D051381:Rats; D020218:Response Elements; D015398:Signal Transduction; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D017362:Cyclic AMP Response Element-Binding Protein; D006657:Histones; D012333:RNA, Messenger; D022661:RNA, Untranslated; D014157:Transcription Factors; D020932:Nerve Growth Factor; D000242:Cyclic AMP