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Human Genetics

, Volume 111, Issue 6, pp 511–520 | Cite as

A novel approach for identifying candidate imprinted genes through sequence analysis of imprinted and control genes

  • Xiayi Ke
  • Simon N. Thomas
  • David O. Robinson
  • Andrew Collins
Original Investigation

Abstract.

Through the sequence analysis of 27 imprinted human genes and a set of 100 control genes we have developed a novel approach for identifying candidate imprinted genes based on the differences in sequence composition observed. The imprinted genes were found to be associated with significantly reduced numbers of short interspersed transposable element (SINE) Alus and mammalian-wide interspersed repeat (MIR) repeat elements, as previously reported. In addition, a significant association between imprinted genes and increased numbers of low-complexity repeats was also evident. Numbers of the Alu classes AluJ and AluS were found to be significantly depleted in some parts of the flanking regions of imprinted genes. A recent study has proposed that there is active selection against SINE elements in imprinted regions. Alternatively, there may be differences in the rates of insertion of Alu elements. Our study indicates that this difference extends both upstream and downstream of the coding region. This and other consistent differences between the sequence characteristics of imprinted and control genes has enabled us to develop discriminant analysis, which can be used to screen the genome for candidate imprinted genes. We have applied this function to a number of genes whose imprinting status is disputed or uncertain.

Keywords

Sequence Analysis Sine Discriminant Analysis Transposable Element Flank Region 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag 2002

Authors and Affiliations

  • Xiayi Ke
    • 1
  • Simon N. Thomas
    • 1
  • David O. Robinson
    • 1
  • Andrew Collins
    • 1
  1. 1.Human Genetics, Duthie Building (808), University of Southampton, Tremona Road, Southampton, SO16 6YD, UK

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