title: Transcriptome analysis of coding and long non-coding RNAs highlights the regulatory network of cascade initiation of permanent molars in miniature pigs.
abstract: In diphyodont mammals, the additional molars (permanent molars) bud off from the posterior-free end of the primary dental lamina compared with successional teeth (replacement teeth) budding off from the secondary dental lamina. The diphyodont miniature pig has proved to be a valuable model for studying human molar morphogenesis. The additional molars show a sequential initiation pattern related to the specific tooth development stage of additional molars in miniature pigs during the morphogenesis of additional molars. However, the molecular mechanisms of the regulatory network of mRNAs and long non-coding RNAs during sequential formation of additional molars remain poorly characterized in diphyodont mammals. Here, we performed RNA-seq and microarray on miniature pigs at three key molar developmental stages to examine their differential gene expression profiles and potential regulatory networks during additional molar morphogenesis.
  
  
  
  We have profiled the differential transcript expression and functional networks during morphogenesis of additional molars in miniature pigs. We also have identified the coding and long non-coding transcripts using Coding-Non-Coding Index (CNCI) and annotated transcripts through mapping to the porcine, Wuzhishan miniature pig, mice, cow and human genomes. Many new unannotated genes plus 450 putative long intergenic non-coding RNAs (lincRNAs) were identified. Detailed regulatory network analyses reveal that WNT and TGF-β pathways are critical in regulating sequential morphogenesis of additional molars.
  
  
  
  This is the first study to comprehensively analyze the spatiotemporal dynamics of coding and long non-coding transcripts during morphogenesis of additional molars in diphyodont mammals. The miniature pig serves as a large model animal to elucidate the relationship between morphogenesis and transcript level during the cascade initiation of additional molars. Our data provide fundamental knowledge and a basis for understanding the molecular mechanisms governing cascade initiation of additional molars, but also provide an important resource for developmental biology research.
authors.affiliation: Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, China.|Department of Oral Basic Science, School of Stomatology, Dalian Medical University, Liaoning, 116044, China.
authors.forename: Fu
authors.initials: F
authors.lastname: Wang
authors.affiliation: Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, China.
authors.forename: Xiaoshan
authors.initials: X
authors.lastname: Wu
authors.affiliation: Department of Oral Basic Science, School of Stomatology, Dalian Medical University, Liaoning, 116044, China.
authors.forename: Min
authors.initials: M
authors.lastname: Yang
authors.affiliation: Department of Oral Basic Science, School of Stomatology, Dalian Medical University, Liaoning, 116044, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Cong
authors.affiliation: Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, China.
authors.forename: Zhipeng
authors.initials: Z
authors.lastname: Fan
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
authors.forename: Jinsong
authors.initials: J
authors.lastname: Wang
authors.affiliation: Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, China.
authors.forename: Chunmei
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Department of Physiology and Pathophysiology, Beijing AnZhen Hospital the Key Laboratory of Remodeling-Related Cardiovascular Diseases, School of Basic Medical Sciences, Capital Medical University, No.10 Xitoutiao, You An Men, Beijing, 100069, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Du
authors.affiliation: Molecular Laboratory for Gene Therapy & Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, 100050, China. slwang@ccmu.edu.cn.|Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China. slwang@ccmu.edu.cn.
authors.forename: Songlin
authors.initials: S
authors.lastname: Wang
mesh_terms: D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D053823:Hedgehog Proteins / Q000235:genetics; D008963:Molar / Q000166:cytology / Q000378:metabolism*; D011247:Pregnancy; D062085:RNA, Long Noncoding / Q000235:genetics*; D013552:Swine; D013556:Swine, Miniature; D016212:Transforming Growth Factor beta / Q000378:metabolism; D060449:Wnt Signaling Pathway / Q000235:genetics
chemical_list: D053823:Hedgehog Proteins; D062085:RNA, Long Noncoding; D016212:Transforming Growth Factor beta
keywords: Additional molar; Cascade initiation; Diphyodont; Gene expression profiling; LincRNA; Miniature pig