ArticleGenome biology2013
Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
66 citing papers in PubMed, 122 citations in OpenAlex.
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- Chromatin Immunoprecipitation in Crops.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Conservation and variability of long-range interactions in structurally diverse maize genomes.Nature communications · 2025Article
- Epigenetics in the modern era of crop improvements.Science China. Life sciences · 2025Review
- Transgenerational epigenetic inheritance during plant evolution and breeding.Trends in plant science · 2024Review
- Insights into heterosis from histone modifications in the flag leaf of inter-subspecific hybrid rice.BMC plant biology · 2024Article
- Heritable changes of epialleles near genes in maize can be triggered in the absence of CHH methylation.Plant physiology · 2024Article
- Review
- Dynamic patterns of gene expressional and regulatory variations in cotton heterosis.Frontiers in plant science · 2024Article
- A complete telomere-to-telomere assembly of the maize genome.Nature genetics · 2023Article
- Epigenetic Changes Occurring in Plant Inbreeding.International journal of molecular sciences · 2023Review
- Characterization of Genes That Exhibit Genotype-Dependent Allele-Specific Expression and Its Implications for the Development of Maize Kernel.International journal of molecular sciences · 2023Article
- Contribution of RdDM to the ecotype-specific differential methylation on conserved as well as highly variable regions between Arabidopsis ecotypes.BMC genomics · 2023Article
- Genome-wide analysis of transcriptome and histone modifications inFrontiers in plant science · 2023Article
- Conservation Study of Imprinted Genes in Maize Triparental Heterozygotic Kernels.International journal of molecular sciences · 2022Article
- Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heteroticiScience · 2022Article
- Comprehensive molecular evaluation of the histone methyltransferase gene family and their important roles in two-line hybrid wheat.BMC plant biology · 2022Article
- Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates.Plant biotechnology journal · 2022Article
- High Stability of the Epigenome in Drosophila Interspecific Hybrids.Genome biology and evolution · 2022Article
- Dynamic Transcriptome Analysis Reveals Complex Regulatory Pathway Underlying Induction and Dose Effect by Different Exogenous Auxin IAA and 2,4-D DuringFrontiers in plant science · 2022Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent genome-wide studies suggested that in addition to genetic variations, epigenetic variations may also be associated with differential gene expression and growth vigor in plant hybrids. Maize is an ideal model system for the study of epigenetic variations in hybrids given the significant heterotic performance, the well-known complexity of the genome, and the rich history in epigenetic studies. However, integrated comparative transcriptomic and epigenomic analyses in different organs of maize hybrids remain largely unexplored.
resultsHere, we generated integrated maps of transcriptomes and epigenomes of shoots and roots of two maize inbred lines and their reciprocal hybrids, and globally surveyed the epigenetic variations and their relationships with transcriptional divergence between different organs and genotypes. We observed that whereas histone modifications vary both between organs and between genotypes, DNA methylation patterns are more distinguishable between genotypes than between organs. Histone modifications were associated with transcriptomic divergence between organs and between hybrids and parents. Further, we show that genes up-regulated in both shoots and roots of hybrids were significantly enriched in the nucleosome assembly pathway. Interestingly, 22- and 24-nt siRNAs were shown to be derived from distinct transposable elements, and for different transposable elements in both shoots and roots, the differences in siRNA activity between hybrids and patents were primarily driven by different siRNA species.
conclusionsThese results suggest that despite variations in specific genes or genomic loci, similar mechanisms may account for the genome-wide epigenetic regulation of gene activity and transposon stability in different organs of maize hybrids.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.