ArticleG3 (Bethesda, Md.)2019
Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.
Article in G3 (Bethesda, Md.), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- MDR1 DNA glycosylase regulates the expression of genomically imprinted genes and Helitrons.The Plant journal : for cell and molecular biology · 2025Article
- Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis.The plant genome · 2025Article
- Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements in Barley (Frontiers in plant science · 2024Article
- The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants.Epigenomes · 2023Review
- Identification of transcriptionally active transposons in Barley.BMC genomic data · 2023Article
- Review
- Genomic imbalance modulates transposable element expression in maize.Plant communications · 2023Article
- Effects of Wolbachia on Transposable Element Expression Vary Between Drosophila melanogaster Host Genotypes.Genome biology and evolution · 2023Article
- Chromosomal-level genome assembly of the high-quality Xian/Indica rice (Oryza sativa L.) Xiangyaxiangzhan.BMC plant biology · 2023Article
- Article
- The maize gene maternal derepression of r1 encodes a DNA glycosylase that demethylates DNA and reduces siRNA expression in the endosperm.The Plant cell · 2022Article
- The genomic ecosystem of transposable elements in maize.PLoS genetics · 2021Article
- Article
- Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize.Plant physiology · 2021Article
- Widespread imprinting of transposable elements and variable genes in the maize endosperm.PLoS genetics · 2021Article
- Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons.Genetics · 2021Article
- Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development.Plants (Basel, Switzerland) · 2020Article
- Genomic and Transcriptomic Survey Provides New Insight into the Organization and Transposition Activity of Highly Expressed LTR Retrotransposons of Sunflower (International journal of molecular sciences · 2020Article
- Long-Read cDNA Sequencing Enables a "Gene-Like" Transcript Annotation of Transposable Elements.The Plant cell · 2020Article
- Small RNA-MediatedGenetics · 2020Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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