ArticlePlant molecular biology2008
Genome-wide allele-specific expression analysis using Massively Parallel Signature Sequencing (MPSS) reveals cis- and trans-effects on gene expression in maize hybrid meristem tissue.
Article in Plant molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers, 1 of them a synthesis that pooled it.
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Who cites it
53 citing papers in PubMed, 1 synthesis or guideline pooled it, 104 citations in OpenAlex.
- Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci.BMC plant biology · 2014Pooled it
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- Non-Additive and Asymmetric Allelic Expression ofAnimals : an open access journal from MDPI · 2024Article
- Study on Allele Specific Expression of Long-Term Residents in High Altitude Areas.Evolutionary bioinformatics online · 2024Article
- Integrated analysis of DNA methylation, transcriptome, and global metabolites in interspecific heteroticiScience · 2022Article
- Comprehensive silk gland multi-omics comparison illuminates two alternative mechanisms in silkworm heterosis.Zoological research · 2022Article
- Transposon insertions regulate genome-wide allele-specific expression and underpin flower colour variations in apple (Malus spp.).Plant biotechnology journal · 2022Article
- Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis.BMC plant biology · 2022Article
- Power calculator for detecting allelic imbalance using hierarchical Bayesian model.BMC research notes · 2021Article
- Phasing analysis of the transcriptome and epigenome in a rice hybrid reveals the inheritance and difference in DNA methylation and allelic transcription regulation.Plant communications · 2021Article
- Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera).Plant molecular biology · 2021Article
- Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize.Journal of experimental botany · 2021Article
- Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids.Microorganisms · 2020Article
- Functional Identification ofFrontiers in plant science · 2020Article
- Integrative Omics Analysis Reveals a Limited Transcriptional Shock After Yeast Interspecies Hybridization.Frontiers in genetics · 2020Article
- Unraveling cis and trans regulatory evolution during cotton domestication.Nature communications · 2019Article
- Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Allelic differences in expression are important genetic factors contributing to quantitative trait variation in various organisms. However, the extent of genome-wide allele-specific expression by different modes of gene regulation has not been well characterized in plants. In this study we developed a new methodology for allele-specific expression analysis by applying Massively Parallel Signature Sequencing (MPSS), an open ended and sequencing based mRNA profiling technology. This methodology enabled a genome-wide evaluation of cis- and trans-effects on allelic expression in six meristem stages of the maize hybrid. Summarization of data from nearly 400 pairs of MPSS allelic signature tags showed that 60% of the genes in the hybrid meristems exhibited differential allelic expression. Because both alleles are subjected to the same trans-acting factors in the hybrid, the data suggest the abundance of cis-regulatory differences in the genome. Comparing the same allele expressed in the hybrid versus its inbred parents showed that 40% of the genes were differentially expressed, suggesting different trans-acting effects present in different genotypes. Such trans-acting effects may result in gene expression in the hybrid different from allelic additive expression. With this approach we quantified gene expression in the hybrid relative to its inbred parents at the allele-specific level. As compared to measuring total transcript levels, this study provides a new level of understanding of different modes of gene regulation in the hybrid and the molecular basis of heterosis.
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