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Cis-regulatory elements within TEs can influence expression of nearby maize genes

View ORCID ProfileJaclyn M Noshay, Alexandre P Marand, View ORCID ProfileSarah N Anderson, View ORCID ProfilePeng Zhou, Maria Katherine Mejia Guerra, Zefu Lu, Christine O’Connor, Peter A Crisp, Candice N. Hirsch, Robert J Schmitz, View ORCID ProfileNathan M Springer
doi: https://doi.org/10.1101/2020.05.20.107169
Jaclyn M Noshay
*Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
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Alexandre P Marand
†Department of Genetics, University of Georgia, Athens, 30602, USA
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Sarah N Anderson
‡Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
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Peng Zhou
*Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
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Maria Katherine Mejia Guerra
§Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14850, USA
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Zefu Lu
†Department of Genetics, University of Georgia, Athens, 30602, USA
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Christine O’Connor
**Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
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Peter A Crisp
††School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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Candice N. Hirsch
**Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
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Robert J Schmitz
†Department of Genetics, University of Georgia, Athens, 30602, USA
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Nathan M Springer
*Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
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Abstract

Transposable elements (TEs) have the potential to create regulatory variation both through disruption of existing DNA regulatory elements and through creation of novel DNA regulatory elements. In a species with a large genome, such as maize, the many TEs interspersed with genes creates opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22 or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. TEs that carry ACRs exhibit an enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may create novel regulatory elements. These analyses highlight the potential for TEs to rewire transcriptional responses in eukaryotic genomes.

Data Availability In this study we utilize previously published datasets that are available through the following accessions: SRX4727413, SRR8738272, and SRR8740852.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 22, 2020.
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Cis-regulatory elements within TEs can influence expression of nearby maize genes
Jaclyn M Noshay, Alexandre P Marand, Sarah N Anderson, Peng Zhou, Maria Katherine Mejia Guerra, Zefu Lu, Christine O’Connor, Peter A Crisp, Candice N. Hirsch, Robert J Schmitz, Nathan M Springer
bioRxiv 2020.05.20.107169; doi: https://doi.org/10.1101/2020.05.20.107169
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Cis-regulatory elements within TEs can influence expression of nearby maize genes
Jaclyn M Noshay, Alexandre P Marand, Sarah N Anderson, Peng Zhou, Maria Katherine Mejia Guerra, Zefu Lu, Christine O’Connor, Peter A Crisp, Candice N. Hirsch, Robert J Schmitz, Nathan M Springer
bioRxiv 2020.05.20.107169; doi: https://doi.org/10.1101/2020.05.20.107169

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