title: Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns.
abstract: Periodontitis is the most common chronic inflammatory disease caused by complex interaction between the microbial biofilm and host immune responses. In the present study, high-throughput RNA sequencing was utilized to systemically and precisely identify gene expression profiles and alternative splicing.
  
  
  
  The pooled RNAs of 10 gingival tissues from both healthy and periodontitis patients were analyzed by deep sequencing followed by computational annotation and quantification of mRNA structures.
  
  
  
  The differential expression analysis designated 400 up-regulated genes in periodontitis tissues especially in the pathways of defense/immunity protein, receptor, protease, and signaling molecules. The top 10 most up-regulated genes were CSF3, MAFA, CR2, GLDC, SAA1, LBP, MME, MMP3, MME-AS1, and SAA4. The 62 down-regulated genes in periodontitis were mainly cytoskeletal and structural proteins. The top 10 most down-regulated genes were SERPINA12, MT4, H19, KRT2, DSC1, PSORS1C2, KRT27, LCE3C, AQ5, and LCE6A. The differential alternative splicing analysis revealed unique transcription variants in periodontitis tissues. The EDB exon was predominantly included in FN1, while exon 2 was mostly skipped in BCL2A1.
  
  
  
  These findings using RNA sequencing provide novel insights into the pathogenesis mechanism of periodontitis in terms of gene expression and alternative splicing.
authors.affiliation: Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea.|Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea.
authors.forename: Yong-Gun
authors.initials: YG
authors.lastname: Kim
authors.affiliation: Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Korea.
authors.forename: Minjung
authors.initials: M
authors.lastname: Kim
authors.affiliation: Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea.
authors.forename: Ji Hyun
authors.initials: JH
authors.lastname: Kang
authors.affiliation: Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea.
authors.forename: Hyo Jeong
authors.initials: HJ
authors.lastname: Kim
authors.affiliation: Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea.
authors.forename: Jin-Woo
authors.initials: JW
authors.lastname: Park
authors.affiliation: Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea.
authors.forename: Jae-Mok
authors.initials: JM
authors.lastname: Lee
authors.affiliation: Department of Periodontology, School of Dentistry, Kyungpook National University, Daegu, 41940, Korea.
authors.forename: Jo-Young
authors.initials: JY
authors.lastname: Suh
authors.affiliation: Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea.|Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea.
authors.forename: Jae-Young
authors.initials: JY
authors.lastname: Kim
authors.affiliation: Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Korea. jaehlee@khu.ac.kr.|Department of Maxillofacial Biomedical Engineering, School of Dentistry, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul, 02447, Korea. jaehlee@khu.ac.kr.
authors.forename: Jae-Hyung
authors.initials: JH
authors.lastname: Lee
authors.affiliation: Institute for Hard Tissue and Bone Regeneration, Kyungpook National University, Daegu, 41940, Korea. ylee@knu.ac.kr.|Department of Biochemistry, School of Dentistry, Kyungpook National University, 2177 Dalgubeol-daero, Joong-gu, Daegu, 41940, Korea. ylee@knu.ac.kr.
authors.forename: Youngkyun
authors.identifier: 0000-0001-9049-6908
authors.initials: Y
authors.lastname: Lee
mesh_terms: D017398:Alternative Splicing; D015415:Biomarkers / Q000378:metabolism; D001706:Biopsy; D016022:Case-Control Studies; D055113:Chronic Periodontitis / Q000175:diagnosis / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D005881:Gingiva / Q000378:metabolism / Q000473:pathology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D015415:Biomarkers
keywords: Alternative splicing; Gene expression profile; Periodontitis; Transcriptome sequencing