ArticleGenetics2007
Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes.
Article in Genetics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 108 citations in OpenAlex.
- DNA Methylation and Alternative Splicing Safeguard Genome and Transcriptome After a Retrotransposition Burst inInternational journal of molecular sciences · 2025Article
- Exploring the Effect of High-Energy Heavy Ion Beam on Rice Genome: Transposon Activation.Genes · 2023Article
- DNA methylation and histone modifications induced by abiotic stressors in plants.Genes & genomics · 2022Review
- Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions.Frontiers in cell and developmental biology · 2022Review
- High genetic and epigenetic variation of transposable elements: Potential drivers to rapid adaptive evolution for the noxious invasive weedEcology and evolution · 2021Article
- DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems.BMC genomics · 2020Article
- Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome.GigaScience · 2019Article
- Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes.Molecular genetics and genomics : MGG · 2018Article
- Analysis of somaclonal variation in transgenic and regenerated plants of Arabidopsis thaliana using methylation related metAFLP and TMD markers.Plant cell reports · 2018Article
- Insertion of a solo LTR retrotransposon associates with spur mutations in 'Red Delicious' apple (Malus × domestica).Plant cell reports · 2017Article
- Laser Irradiation-Induced DNA Methylation Changes Are Heritable and Accompanied with Transpositional Activation ofFrontiers in plant science · 2017Article
- Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions.BMC genomics · 2016Article
- Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum.Molecular genetics and genomics : MGG · 2016Article
- The Role of DNA Methylation in Xylogenesis in Different Tissues of Poplar.Frontiers in plant science · 2016Article
- Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations.BMC plant biology · 2015Article
- Article
- Differential regulation of genes by retrotransposons in rice promoters.Plant molecular biology · 2015Article
- Genome-wide analysis of DNA methylation in photoperiod- and thermo-sensitive male sterile rice Peiai 64S.BMC genomics · 2015Article
- Tissue culture-induced heritable genomic variation in rice, and their phenotypic implications.PloS one · 2014Article
- Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants.Journal of genetics · 2013Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) represent approximately 45% of the human genome and 50-90% of some grass genomes. While most elements contain inactivating mutations, others are reversibly inactivated (silenced) by epigenetic mechanisms, including cytosine methylation. Previous studies have shown that retrotransposons can influence the expression of adjacent host genes. In this study, the methylation patterns of TEs and their flanking sequences in different tissues were undertaken using a novel technique called transposon methylation display (TMD). TMD was successfully applied on a highly copied (approximately 1000 copies), newly amplified LTR retrotransposon family in rice called Dasheng. We determined that the methylation status of a subset of LTRs varies in leaves vs. roots. In addition, we determined that tissue-specific LTR methylation correlated with tissue-specific expression of the flanking rice gene. Genes showing tissue-specific expression were in opposite orientation relative to the LTR. Antisense transcripts were detected in the tissue where the sense transcripts from that gene were not detected. Comparative analysis of Dasheng LTR methylation in the two subspecies, japonica vs. indica revealed LTR-mediated differences in subspecies gene expression. Subspecies-specific expression was due either to polymorphic Dasheng insertion sites between the two subspecies or to subspecies-specific methylation of LTRs at the same locus accounted for observed differences in the expression of adjacent genes.
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