title: A conserved unusual posttranscriptional processing mediated by short, direct repeated (SDR) sequences in plants.
abstract: In several stress responsive gene loci of monocot cereal crops, we have previously identified an unusual posttranscriptional processing mediated by paired presence of short direct repeated (SDR) sequences at 5' and 3' splicing junctions that are distinct from conventional (U2/U12-type) splicing boundaries. By using the known SDR-containing sequences as probes, 24 plant candidate genes involved in diverse functional pathways from both monocots and dicots that potentially possess SDR-mediated posttranscriptional processing were predicted in the GenBank database. The SDRs-mediated posttranscriptional processing events including cis- and trans-actions were experimentally detected in majority of the predicted candidates. Extensive sequence analysis demonstrates several types of SDR-associated splicing peculiarities including partial exon deletion, exon fragment repetition, exon fragment scrambling and trans-splicing that result in either loss of partial exon or unusual exonic sequence rearrangements within or between RNA molecules. In addition, we show that the paired presence of SDR is necessary but not sufficient in SDR-mediated splicing in transient expression and stable transformation systems. We also show prokaryote is incapable of SDR-mediated premRNA splicing.
authors.affiliation: College of Agricultural and Life Sciences, Chongqing University, Chongqing 400030, China.
authors.forename: Xiangli
authors.initials: X
authors.lastname: Niu
authors.forename: Di
authors.initials: D
authors.lastname: Luo
authors.forename: Shaopei
authors.initials: S
authors.lastname: Gao
authors.forename: Guangjun
authors.initials: G
authors.lastname: Ren
authors.forename: Lijuan
authors.initials: L
authors.lastname: Chang
authors.forename: Yuke
authors.initials: Y
authors.lastname: Zhou
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Luo
authors.forename: Yuxiang
authors.initials: Y
authors.lastname: Li
authors.forename: Pei
authors.initials: P
authors.lastname: Hou
authors.forename: Wei
authors.initials: W
authors.lastname: Tang
authors.forename: Bao-Rong
authors.initials: BR
authors.lastname: Lu
authors.forename: Yongsheng
authors.initials: Y
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D017353:Gene Deletion; D020440:Gene Duplication; D017343:Genes, Plant / Q000235:genetics; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics*; D012326:RNA Splicing / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D018749:RNA, Plant