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Background  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.    Methods  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.    Results  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 .    Conclusions  These findings using RNA sequencing provide novel insights into the pathogenesis mechanism of periodontitis in terms of gene expression and alternative splicing.    Electronic supplementary material  The online version of this article (doi:10.1186/s40246-016-0084-0) contains supplementary material, which is available to authorized users.

Transcriptome sequencing of gingival biopsies from chronic periodontitis patients reveals novel gene expression and splicing patterns