Abstract
Transposable elements can be highly mutagenic because when they transpose they can insert into genes and disrupt their function, a propensity which has been exploited in many organisms to generate tagged mutant alleles. The Mutator (Mu) family transposon is a family of DNA-type transposons in maize with a particularly high duplication frequency, which results in large numbers of new mutations in lineages that carry active Mu elements. Here we describe a rapid and cost-effective Miseq-based Mu transposon profiling pipeline. This method can also be used for identifying flanking sequences of other types of long insertions such as T-DNAs.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet 41:331–368
Lisch D (2013) How important are transposons for plant evolution? Nat Rev Genet 14:49–61
Hedges DJ, Deininger PL (2007) Inviting instability: transposable elements, double-strand breaks, and the maintenance of genome integrity. Mutat Res 616:46–59
Liu K, Wessler SR (2017) Transposition of Mutator-like transposable elements (MULEs) resembles hAT and Transib elements and V(D)J recombination. Nucleic Acids Res 45:6644–6655
Robertson DS (1978) Characterization of a mutator system in maize. Mutation Res 51:21–28
Benito MI, Walbot V (1997) Characterization of the maize mutator transposable element MURA transposase as a DNA-binding protein. Mol Cell Biol 17:5165–5175
Lisch D (2002) Mutator transposons. Trends Plant Sci 7:498–504
Candela H, Hake S (2008) The art and design of genetic screens: maize. Nat Rev Genet 9:192–203
McCarty DR, Settles AM, Suzuki M et al (2005) Steady-state transposon mutagenesis in inbred maize. Plant J 44:52–61
Williams-Carrier R, Stiffler N, Belcher S et al (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy mutator lines of maize. Plant J 63:167–177
McCarty DR, Latshaw S, Wu S et al (2013) Mu-seq: sequence-based mapping and identification of transposon induced mutations. PLoS One 8(10):e77172
O'Malley RC, Alonso JM, Kim CJ et al (2007) An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. Nat Protoc 2:2910–2917
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359
Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079
Robinson JT, Thorvaldsdottir H, Winckler W et al (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842
Acknowledgments
This work was supported by the National Science Foundation Grant DBI-1237931 and Purdue Startup Funds to D.L.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Zhang, X., Zhao, M., Lisch, D. (2020). Cost-Effective Profiling of Mutator Transposon Insertions in Maize by Next-Generation Sequencing. In: Vaschetto, L. (eds) Cereal Genomics. Methods in Molecular Biology, vol 2072. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9865-4_5
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9865-4_5
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-9864-7
Online ISBN: 978-1-4939-9865-4
eBook Packages: Springer Protocols