title: Prolyl 4-hydroxylase genes are subjected to alternative splicing in roots of maize seedlings under waterlogging.
abstract: BACKGROUND
  In animals, prolyl 4-hydroxylases (P4Hs) are regarded as oxygen sensors under hypoxia stress, but little is known about their role in the response to waterlogging in maize.
  
  
  METHODS
  A comprehensive genome-wide analysis of P4H genes of maize (zmP4H genes) was carried out, including gene structures, phylogeny, protein motifs, chromosomal locations and expression patterns under waterlogging.
  
  
  RESULTS
  Nine zmP4H genes were identified in maize, of which five were alternatively spliced into at least 19 transcripts. Different alternative splicing (AS) events were revealed in different inbred lines, even for the same gene, possibly because of organ and developmental specificities or different stresses. The signal strength of splice sites was strongly correlated with selection of donor and receptor sites, and ambiguous junction sites due to small direct repeats at the exon/intron junction frequently resulted in the selection of unconventional splicing sites. Eleven out of 14 transcripts resulting from AS harboured a premature termination codon, rendering them potential candidates for nonsense-mediated RNA degradation. Reverse transcription-PCR (RT-PCR) indicated that zmP4H genes displayed different expression patterns under waterlogging. The diverse transcripts generated from AS were expressed at different levels, suggesting that zmP4H genes were under specific control by post-transcriptional regulation under waterlogging stress in the line HZ32.
  
  
  CONCLUSIONS
  Our results provide a framework for future dissection of the function of the emerging zmP4H family and suggest that AS might have an important role in the regulation of the expression profile of this gene family under waterlogging stress.
authors.affiliation: State Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
authors.forename: Xiling
authors.initials: X
authors.lastname: Zou
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Jiang
authors.forename: Yonglian
authors.initials: Y
authors.lastname: Zheng
authors.forename: Meidong
authors.initials: M
authors.lastname: Zhang
authors.forename: Zuxin
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D017398:Alternative Splicing; D000595:Amino Acid Sequence; D003681:Dehydration / Q000201:enzymology / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D008969:Molecular Sequence Data; D018517:Plant Roots / Q000201:enzymology / Q000235:genetics; D011393:Procollagen-Proline Dioxygenase / Q000235:genetics* / Q000378:metabolism; D036226:Seedlings / Q000201:enzymology / Q000235:genetics; D015398:Signal Transduction; D003313:Zea mays / Q000201:enzymology* / Q000235:genetics*
chemical_list: D011393:Procollagen-Proline Dioxygenase