title: Global detection and identification of developmental stage specific transcripts in mouse brain using subtractive cross-screening algorithm.
abstract: BACKGROUND
  Pre-mRNA splicing is a crucial step for genetic regulation and accounts largely for downstream translational diversity. The current time of biological research is characterized by advances in functional genomics study and the understanding of the pre-mRNA splicing process has thus become a major portal for biologists to gain insights into the complex gene regulatory mechanism. The intranuclear alternative splicing process can form a variety of genomic transcripts that modulate the growth and development of an organism, particularly in the immune and neural systems.
  
  
  METHODS
  In the current study, we investigated and identified alternative splicing transcripts at different stages of embryonic mouse brain morphogenesis using subtractive cross-screening algorithm.
  
  
  RESULTS
  A total of 195 candidate transcripts were found during organogenesis; 1629 identified at fetus stage, 116 in juvenile and 148 transcripts from adulthood. To document our findings, we developed a database named DMBAS, which can be accessed through the link: http://173.234.48.5/DMBAS. We further investigated the alternative splicing products obtained in our experiment and noted the existence of chromosome preference between prenatal and postnatal transcripts. Additionally, the distribution of splicing sites and the splicing types were found to have distinct genomic features at varying stages of brain development. The majority of identified alternative splices (72.3%) at fetus stage were confirmed later using separate RNA-seq data sets.
  
  
  CONCLUSIONS
  This study is a comprehensive profiling of alternative splicing transcripts of mouse brain morphogenesis using advanced computational algorithm. A series of developmental stage specific transcripts, as well as their splicing sites and chromosome preferences were revealed in the current study. Our findings and the related online database would form a solid foundation for studies of broader biological significance and paved the way for future investigations in relevant human brain diseases.
authors.affiliation: College of Life Sciences, Central China Normal University, Wuhan, PR China. Electronic address: lvyinice@mails.ccnu.edu.cn.
authors.forename: Yi
authors.initials: Y
authors.lastname: Lv
authors.forename: Zhixiang
authors.initials: Z
authors.lastname: Zuo
authors.forename: Xiao
authors.initials: X
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D000818:Animals; D001921:Brain / Q000254:growth & development* / Q000378:metabolism*; D033481:Chromosomes, Mammalian; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D051379:Mice; D009024:Morphogenesis; D009928:Organ Specificity; D012322:RNA Precursors / Q000235:genetics*; D016415:Sequence Alignment
chemical_list: D012322:RNA Precursors
keywords: AS; Alternative splicing; EST; NCBI; National Center for Biotechnology Information; Nervous system development; Splice database; Splice sites; alternative splicing; expressed sequence tag; mRNA; message RNA