title: Pause-melting misalignment: a novel model for the birth and motif indel of tandem repeats in the mitochondrial genome.
abstract: BACKGROUND
  Tandem repeats (TRs) in the mitochondrial (mt) genome control region have been documented in a wide variety of vertebrate species. The mechanism by which repeated tracts originate and undergo duplication and deletion, however, remains unclear.
  
  
  RESULTS
  We analyzed DNA sequences of mt genome TRs (mtTRs) in the ridged-eye flounder (Pleuronichthys cornutus), and characterized DNA sequences of mtTRs from other vertebrates using the data available in GenBank. Tandem repeats are concentrated in the control regions; however, we found approximately 16.6% of the TRs elsewhere in the mt genome. The flounder mtTRs possess three motif types with hypervariable characteristics at the 3' end of the control region (CR).
  
  
  CONCLUSIONS
  Based on our analysis of this larger dataset of mtTR sequences, we propose a novel model of Pause Melting Misalignment (PMM) to describe the birth and motif indel of tandem repeats. PMM is activated during a pause event in mitochondrial replication in which a dynamic competition between the nascent (N) heavy strand and the displaced (D) heavy strand may lead to the melting of the N-strand from the template (T) light strand. When mispairing occurs during rebinding of the N-strand, one or several motifs can be inserted or deleted in both strands during the next round of mt-replication or repair. This model can explain the characteristics of TRs in available vertebrate mt genomes.
authors: Key Laboratory of Marine Bio-resource Sustainable Utilization (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, Republic of China.
authors: Wei
authors: W
authors: Shi
authors: Xiao-Yu
authors: XY
authors: Kong
authors: Zhong-Ming
authors: ZM
authors: Wang
authors: Shan-Shan
authors: SS
authors: Yu
authors: Hai-Xia
authors: HX
authors: Chen
authors: Elizabeth A
authors: EA
authors: De Stasio
mesh_terms: D000818:Animals; D001483:Base Sequence; D004272:DNA, Mitochondrial / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics*; D019143:Evolution, Molecular; D005432:Flounder / Q000235:genetics; D014644:Genetic Variation; D054629:Genome, Mitochondrial / Q000235:genetics*; D054643:INDEL Mutation; D008957:Models, Genetic; D009691:Nucleic Acid Denaturation; D059372:Nucleotide Motifs / Q000235:genetics*; D020080:Tandem Repeat Sequences / Q000235:genetics*
chemical_list: D004272:DNA, Mitochondrial