Dynamic patterns of transcript abundance of transposable element families in maize

Sarah N. Anderson, Michelle C. Stitzer, Peng Zhou, Jeffrey Ross-Ibarra, Cory D. Hirsch, Nathan M. Springer

Research output: Contribution to journalArticle

Abstract

Transposable Elements (TEs) are mobile elements that contribute the majority of DNA sequences in the maize genome. Due to their repetitive nature, genomic studies of TEs are complicated by the difficulty of properly attributing multi-mapped short reads to specific genomic loci. Here, we utilize a method to attribute RNA-seq reads to TE families rather than particular loci in order to characterize transcript abundance for TE families in the maize genome. We applied this method to assess per-family expression of transposable elements in >800 published RNA-seq libraries representing a range of maize development, genotypes, and hybrids. While a relatively small proportion of TE families are transcribed, expression is highly dynamic with most families exhibiting tissue-specific expression. A large number of TE families were specifically detected in pollen and endosperm, consistent with reproductive dynamics that maintain silencing of TEs in the germ line. We find that B73 transcript abundance is a poor predictor of TE expression in other genotypes and that transcript levels can differ even for shared TEs. Finally, by assessing recombinant inbred line and hybrid transcriptomes, complex patterns of TE transcript abundance across genotypes emerged. Taken together, this study reveals a dynamic contribution of TEs to maize transcriptomes.

Original languageEnglish (US)
Pages (from-to)3673-3682
Number of pages10
JournalG3: Genes, Genomes, Genetics
Volume9
Issue number11
DOIs
StatePublished - Nov 1 2019

Fingerprint

DNA Transposable Elements
Zea mays
Genotype
Transcriptome
Transcriptional Silencer Elements
Genome
RNA
Endosperm
Pollen
Germ Cells
Libraries

Keywords

  • Expression
  • Transposable elements
  • Zea mays

PubMed: MeSH publication types

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

Cite this

Dynamic patterns of transcript abundance of transposable element families in maize. / Anderson, Sarah N.; Stitzer, Michelle C.; Zhou, Peng; Ross-Ibarra, Jeffrey; Hirsch, Cory D.; Springer, Nathan M.

In: G3: Genes, Genomes, Genetics, Vol. 9, No. 11, 01.11.2019, p. 3673-3682.

Research output: Contribution to journalArticle

Anderson, Sarah N. ; Stitzer, Michelle C. ; Zhou, Peng ; Ross-Ibarra, Jeffrey ; Hirsch, Cory D. ; Springer, Nathan M. / Dynamic patterns of transcript abundance of transposable element families in maize. In: G3: Genes, Genomes, Genetics. 2019 ; Vol. 9, No. 11. pp. 3673-3682.
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