Gene capture by Helitron transposons reshuffles the transcriptome of maize

Genetics. 2012 Mar;190(3):965-75. doi: 10.1534/genetics.111.136176. Epub 2011 Dec 14.


Helitrons are a family of mobile elements that were discovered in 2001 and are now known to exist in the entire eukaryotic kingdom. Helitrons, particularly those of maize, exhibit an intriguing property of capturing gene fragments and placing them into the mobile element. Helitron-captured genes are sometimes transcribed, giving birth to chimeric transcripts that intertwine coding regions of different captured genes. Here, we perused the B73 maize genome for high-quality, putative Helitrons that exhibit plus/minus polymorphisms and contain pieces of more than one captured gene. Selected Helitrons were monitored for expression via in silico EST analysis. Intriguingly, expression validation of selected elements by RT-PCR analysis revealed multiple transcripts not seen in the EST databases. The differing transcripts were generated by alternative selection of splice sites during pre-mRNA processing. Selection of splice sites was not random since different patterns of splicing were observed in the root and shoot tissues. In one case, an exon residing in close proximity but outside of the Helitron was found conjoined with Helitron-derived exons in the mature transcript. Hence, Helitrons have the ability to synthesize new genes not only by placing unrelated exons into common transcripts, but also by transcription readthrough and capture of nearby exons. Thus, Helitrons have a phenomenal ability to "display" new coding regions for possible selection in nature. A highly conservative, minimum estimate of the number of new transcripts expressed by Helitrons is ~11,000 or ~25% of the total number of genes in the maize genome.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alternative Splicing
  • Amino Acid Sequence
  • Base Sequence
  • DNA Transposable Elements*
  • Expressed Sequence Tags / chemistry
  • Gene Expression Profiling*
  • Gene Expression Regulation, Plant
  • Gene Order
  • Molecular Sequence Data
  • Plant Roots / genetics
  • Plant Shoots / genetics
  • RNA, Messenger / genetics
  • Sequence Alignment
  • Transcriptome*
  • Zea mays / genetics*


  • DNA Transposable Elements
  • RNA, Messenger

Associated data

  • GENBANK/AC205986
  • GENBANK/AC209160
  • GENBANK/AC211765
  • GENBANK/AC213839
  • GENBANK/AC220956
  • GENBANK/JN417509
  • GENBANK/JN638823
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  • GENBANK/JN638839
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  • GENBANK/JN638841
  • GENBANK/JN638842
  • GENBANK/JN638843
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  • GENBANK/JN638849