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Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize

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...

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Autores principales: Barbaglia, Allison M., Klusman, Katarina M., Higgins, John, Shaw, Janine R., Hannah, L. Curtis, Lal, Shailesh K.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296258/
https://www.ncbi.nlm.nih.gov/pubmed/22174072
http://dx.doi.org/10.1534/genetics.111.136176
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author Barbaglia, Allison M.
Klusman, Katarina M.
Higgins, John
Shaw, Janine R.
Hannah, L. Curtis
Lal, Shailesh K.
author_facet Barbaglia, Allison M.
Klusman, Katarina M.
Higgins, John
Shaw, Janine R.
Hannah, L. Curtis
Lal, Shailesh K.
author_sort Barbaglia, Allison M.
collection PubMed
description 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.
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spelling pubmed-32962582012-03-20 Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize Barbaglia, Allison M. Klusman, Katarina M. Higgins, John Shaw, Janine R. Hannah, L. Curtis Lal, Shailesh K. Genetics Investigations 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. Genetics Society of America 2012-03 /pmc/articles/PMC3296258/ /pubmed/22174072 http://dx.doi.org/10.1534/genetics.111.136176 Text en Copyright © 2012 by the Genetics Society of America Available freely online through the author-supported open access option.
spellingShingle Investigations
Barbaglia, Allison M.
Klusman, Katarina M.
Higgins, John
Shaw, Janine R.
Hannah, L. Curtis
Lal, Shailesh K.
Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize
title Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize
title_full Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize
title_fullStr Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize
title_full_unstemmed Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize
title_short Gene Capture by Helitron Transposons Reshuffles the Transcriptome of Maize
title_sort gene capture by helitron transposons reshuffles the transcriptome of maize
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296258/
https://www.ncbi.nlm.nih.gov/pubmed/22174072
http://dx.doi.org/10.1534/genetics.111.136176
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