title: The landscape of alternative splicing in buccal mucosa squamous cell carcinoma.
abstract: OBJECTIVE
  Alternative splicing (AS) is a key regulatory mechanism in the process of protein synthesis generating transcriptome and proteome diversity. In this study, we attempted to identify alternative splicing in a pair of BMSCC cancer and adjacent normal tissue using RNAseq datasets and also assessed the potential of these datasets to provide quantitative measurements for alternative splicing levels.
  
  
  METHODS
  We performed high-throughput sequencing of buccal mucosal cancer and healthy tissue cDNA library which resulted in a transcriptome map of BMSCC cancer. RNAseq analysis was performed to assess alternative splicing complexity in cancer tissue and to search splice junction sequences that represent candidate 'new' splicing events. The splice junctions were predicted by SpliceMap software and putative assembled transcripts validated using the RT-PCR. We also analyzed the coding potential of alternative spliced candidate by HMMER.
  
  
  RESULTS
  We detected a total of 11 novel splice junctions derived mostly from alternate 5' splice site; including two of them which contained new translation initiation sites (TISs). We have identified novel IgG pseudogene and a fusion transcript of MEMO1 and RPS9, which were further confirmed by PCR from genomic DNA. We also found novel putative long non-coding RNA (lncRNA), which is antisense to SPINK5 gene. The coding potential of these AS variants revealed that alternative splicing caused premature termination, insertion/deletion of amino acid (s) or formation of novel N-terminus.
  
  
  CONCLUSIONS
  Differential splicing of these novel AS variants between cancer and adjacent normal tissue suggests their involvement in BMSCC cancer development and progression.
authors.affiliation: Department of Animal Biotechnology, College of Veterinary Science & Animal Husbandry, Anand Agricultural University, Anand-388 001, Gujarat, India.
authors.forename: Tejas M
authors.initials: TM
authors.lastname: Shah
authors.forename: Amrutlal K
authors.initials: AK
authors.lastname: Patel
authors.forename: Vaibhav D
authors.initials: VD
authors.lastname: Bhatt
authors.forename: Ajai K
authors.initials: AK
authors.lastname: Tripathi
authors.forename: Siddharth
authors.initials: S
authors.lastname: Shah
authors.forename: Vangipuram
authors.initials: V
authors.lastname: Shankar
authors.forename: Chaitanya G
authors.initials: CG
authors.lastname: Joshi
mesh_terms: D017398:Alternative Splicing; D001483:Base Sequence; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D017931:DNA Primers; D006801:Humans; D009061:Mouth Mucosa / Q000378:metabolism*; D009062:Mouth Neoplasms / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D017931:DNA Primers; D012333:RNA, Messenger