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Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize

https://doi.org/10.1093/jxb/erab074
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Analysis of nonadditive protein accumulation in young primary roots of a maize ( Zea mays L.) F 1 ‐hybrid compared to its parental inbred lines
inferredcites →https://doi.org/10.1002/tpg2.20018openalex-snapshot
Global profiling of N 6 ‐methyladenosine methylation in maize callus induction
inferredcites →https://doi.org/10.1007/s00122-009-1190-3openalex-snapshot
Heterotic patterns of sugar and amino acid components in developing maize kernels
inferredcites →https://doi.org/10.1007/s11103-008-9290-zopenalex-snapshot
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
inferredcites →https://doi.org/10.1016/j.bbagrm.2018.10.006openalex-snapshot
m6A-mediated translation regulation
inferredcites →https://doi.org/10.1016/j.cell.2012.05.003openalex-snapshot
Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons
inferredcites →https://doi.org/10.1016/j.cell.2015.05.014openalex-snapshot
N6-methyladenosine Modulates Messenger RNA Translation Efficiency
inferredcites →https://doi.org/10.1016/j.cell.2015.10.012openalex-snapshot
5′ UTR m6A Promotes Cap-Independent Translation
inferredcites →https://doi.org/10.1016/j.cell.2017.03.031openalex-snapshot
Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation
inferredcites →https://doi.org/10.1016/j.cell.2017.05.003openalex-snapshot
The U6 snRNA m 6 A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention
inferredcites →https://doi.org/10.1016/j.cell.2017.05.045openalex-snapshot
Dynamic RNA Modifications in Gene Expression Regulation
inferredcites →https://doi.org/10.1016/j.celrep.2018.10.020openalex-snapshot
N6-Methyladenosine Inhibits Local Ribonucleolytic Cleavage to Stabilize mRNAs in Arabidopsis
inferredcites →https://doi.org/10.1016/j.copbio.2010.03.002openalex-snapshot
More from less: plant growth under limited water
inferredcites →https://doi.org/10.1016/j.cub.2018.06.041openalex-snapshot
Heterosis in plants
inferredcites →https://doi.org/10.1016/j.devcel.2016.06.008openalex-snapshot
N6-Methyladenosine RNA Modification Regulates Shoot Stem Cell Fate in Arabidopsis
inferredcites →https://doi.org/10.1016/j.molcel.2012.10.015openalex-snapshot
ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility
inferredcites →https://doi.org/10.1016/j.molcel.2016.01.012openalex-snapshot
Nuclear m6A Reader YTHDC1 Regulates mRNA Splicing
inferredcites →https://doi.org/10.1016/j.tig.2006.12.006openalex-snapshot
Heterosis: revisiting the magic
inferredcites →https://doi.org/10.1016/j.tig.2017.04.003openalex-snapshot
m 6 A in mRNA: An Ancient Mechanism for Fine-Tuning Gene Expression
inferredcites →https://doi.org/10.1016/j.tplants.2019.01.005openalex-snapshot
Messenger RNA Modifications in Plants
inferredcites →https://doi.org/10.1038/cr.2014.151openalex-snapshot
FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis
inferredcites →https://doi.org/10.1038/cr.2017.10openalex-snapshot
Cytoplasmic m6A reader YTHDF3 promotes mRNA translation
inferredcites →https://doi.org/10.1038/cr.2017.15openalex-snapshot
YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA
inferredcites →https://doi.org/10.1038/nature11112openalex-snapshot
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq
inferredcites →https://doi.org/10.1038/nature12730openalex-snapshot
N6-methyladenosine-dependent regulation of messenger RNA stability
inferredcites →https://doi.org/10.1038/nature14234openalex-snapshot
N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions
inferredcites →https://doi.org/10.1038/nature20568openalex-snapshot
m6A modulates neuronal functions and sex determination in Drosophila
inferredcites →https://doi.org/10.1038/nature20577openalex-snapshot
m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination
inferredcites →https://doi.org/10.1038/nature22971openalex-snapshot
Improved maize reference genome with single-molecule technologies
inferredcites →https://doi.org/10.1038/nbt.3122openalex-snapshot
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
inferredcites →https://doi.org/10.1038/ncomms11194openalex-snapshot
Genome-wide assessment of differential translations with ribosome profiling data
inferredcites →https://doi.org/10.1038/ncomms7258openalex-snapshot
Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis
inferredcites →https://doi.org/10.1038/ncomms8309openalex-snapshot
Salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in Arabidopsis hybrids
inferredcites →https://doi.org/10.1038/ng.3974openalex-snapshot
A quantitative genetic framework highlights the role of epistatic effects for grain-yield heterosis in bread wheat
inferredcites →https://doi.org/10.1038/nmeth.3317openalex-snapshot
HISAT: a fast spliced aligner with low memory requirements
inferredcites →https://doi.org/10.1038/nrg3185openalex-snapshot
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
inferredcites →https://doi.org/10.1038/s41422-018-0040-8openalex-snapshot
Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism
inferredcites →https://doi.org/10.1038/s41467-019-13386-wopenalex-snapshot
Unraveling cis and trans regulatory evolution during cotton domestication
inferredcites →https://doi.org/10.1038/s41556-018-0045-zopenalex-snapshot
Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation
inferredcites →https://doi.org/10.1038/s41586-019-1016-7openalex-snapshot
Histone H3 trimethylation at lysine 36 guides m6A RNA modification co-transcriptionally
inferredcites →https://doi.org/10.1038/s41588-018-0182-0openalex-snapshot
Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes
inferredcites →https://doi.org/10.1039/b908315dopenalex-snapshot
Global signatures of protein and mRNA expression levels
inferredcites →https://doi.org/10.1073/pnas.0510430103openalex-snapshot
All possible modes of gene action are observed in a global comparison of gene expression in a maize F 1 hybrid and its inbred parents
inferredcites →https://doi.org/10.1073/pnas.1019217108openalex-snapshot
Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor
inferredcites →https://doi.org/10.1073/pnas.1317811111openalex-snapshot
Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis
inferredcites →https://doi.org/10.1073/pnas.1519926112openalex-snapshot
Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids
inferredcites →https://doi.org/10.1073/pnas.1613372113openalex-snapshot
Role of DNA methylation in hybrid vigor in Arabidopsis thaliana
inferredcites →https://doi.org/10.1073/pnas.1613623113openalex-snapshot
Twenty-four–nucleotide siRNAs produce heritable trans-chromosomal methylation in F1 Arabidopsis hybrids
inferredcites →https://doi.org/10.1073/pnas.1703139114openalex-snapshot
Arabidopsis m 6 A demethylase activity modulates viral infection of a plant virus and the m 6 A abundance in its genomic RNAs
inferredcites →https://doi.org/10.1073/pnas.1820513116openalex-snapshot
Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis
inferredcites →https://doi.org/10.1073/pnas.1919086117openalex-snapshot
Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice
inferredcites →https://doi.org/10.1074/mcp.mr118.001246openalex-snapshot
Exploiting Interdata Relationships in Next-generation Proteomics Analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btp498openalex-snapshot
Next generation software for functional trend analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/nar/gkx141openalex-snapshot
N 6-methyladenosine alters RNA structure to regulate binding of a low-complexity protein
inferredcites →https://doi.org/10.1093/nar/gkx778openalex-snapshot
N6-methyladenosine demethylase FTO targets pre-mRNAs and regulates alternative splicing and 3′-end processing
inferredcites →https://doi.org/10.1101/gr.138461.112openalex-snapshot
Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents
inferredcites →https://doi.org/10.1101/gr.5347007openalex-snapshot
Allelic variation and heterosis in maize: How do two halves make more than a whole?
inferredcites →https://doi.org/10.1104/pp.109.148965openalex-snapshot
Developmental Stage Specificity and the Role of Mitochondrial Metabolism in the Response of Arabidopsis Leaves to Prolonged Mild Osmotic Stress
inferredcites →https://doi.org/10.1104/pp.16.00262openalex-snapshot
Nonsyntenic genes drive tissue-specific dynamics of differential, nonadditive and allelic expression patterns in maize hybrids
inferredcites →https://doi.org/10.1104/pp.17.01054openalex-snapshot
Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids
inferredcites →https://doi.org/10.1104/pp.19.00323openalex-snapshot
Evolution of the RNA N6-Methyladenosine Methylome Mediated by Genomic Duplication
inferredcites →https://doi.org/10.1104/pp.19.00817openalex-snapshot
Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids
inferredcites →https://doi.org/10.1104/pp.19.00987openalex-snapshot
Natural Variation in RNA m 6 A Methylation and Its Relationship with Translational Status
inferredcites →https://doi.org/10.1105/tpc.108.058883openalex-snapshot
MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor
inferredcites →https://doi.org/10.1105/tpc.110.076133openalex-snapshot
Heterosis
inferredcites →https://doi.org/10.1105/tpc.111.094870openalex-snapshot
Genome-Wide Analysis of DNA Methylation and Gene Expression Changes in Two Arabidopsis Ecotypes and Their Reciprocal Hybrids
inferredcites →https://doi.org/10.1105/tpc.151030openalex-snapshot
In Search of the Molecular Basis of Heterosis
inferredcites →https://doi.org/10.1105/tpc.16.00808openalex-snapshot
Mutations in eIF5B Confer Thermosensitive and Pleiotropic Phenotypes via Translation Defects in Arabidopsis thaliana
inferredcites →https://doi.org/10.1105/tpc.16.00912openalex-snapshot
ALKBH10B Is an RNA N 6 -Methyladenosine Demethylase Affecting Arabidopsis Floral Transition
inferredcites →https://doi.org/10.1105/tpc.17.00833openalex-snapshot
An m 6 A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.17.00854openalex-snapshot
The YTH Domain Protein ECT2 Is an m 6 A Reader Required for Normal Trichome Branching in Arabidopsis
inferredcites →https://doi.org/10.1105/tpc.17.00934openalex-snapshot
The m 6 A Reader ECT2 Controls Trichome Morphology by Affecting mRNA Stability in Arabidopsis
inferredcites →https://doi.org/10.1111/jipb.12917openalex-snapshot
H3K36me2 is highly correlated with m6A modifications in plants
inferredcites →https://doi.org/10.1111/nph.14102openalex-snapshot
Trait to gene analysis reveals that allelic variation in three genes determines seed vigour
inferredcites →https://doi.org/10.1111/nph.14586openalex-snapshot
Identification of factors required for m 6 A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI
inferredcites →https://doi.org/10.1111/pbi.13149openalex-snapshot
N6‐methyladenosine regulatory machinery in plants: composition, function and evolution
inferredcites →https://doi.org/10.1111/pbi.13186openalex-snapshot
Genome‐wide identification and analysis of heterotic loci in three maize hybrids
inferredcites →https://doi.org/10.1111/pbi.13333openalex-snapshot
Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea
inferredcites →https://doi.org/10.1111/tpj.13073openalex-snapshot
Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress
inferredcites →https://doi.org/10.1111/tpj.13285openalex-snapshot
Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour
inferredcites →https://doi.org/10.1111/tpj.13432openalex-snapshot
Patterns of gene expression in developing embryos of Arabidopsis hybrids
inferredcites →https://doi.org/10.1111/tpj.13605openalex-snapshot
Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNA s
inferredcites →https://doi.org/10.1146/annurev-cellbio-100616-060758openalex-snapshot
Rethinking m6A Readers, Writers, and Erasers
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2013-14-6-r57openalex-snapshot
Conservation and divergence of transcriptomic and epigenomic variation in maize hybrids
inferredcites →https://doi.org/10.1186/s12870-015-0549-7openalex-snapshot
Transposable elements, mRNA expression level and strand-specificity of small RNAs are associated with non-additive inheritance of gene expression in hybrid plants
inferredcites →https://doi.org/10.1186/s12870-019-1878-8openalex-snapshot
Comparative transcriptome analysis reveals important roles of nonadditive genes in maize hybrid An’nong 591 under heat stress
inferredcites →https://doi.org/10.1186/s12985-018-0997-4openalex-snapshot
N 6 -methyl-adenosine level in Nicotiana tabacum is associated with tobacco mosaic virus
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1186/s13059-017-1281-4openalex-snapshot
Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid
inferredcites →https://doi.org/10.1186/s13059-019-1771-7openalex-snapshot
RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening
inferredcites →https://doi.org/10.1186/s40478-020-00941-6openalex-snapshot
RNA modifications in brain tumorigenesis
inferredcites →https://doi.org/10.12688/f1000research.9037.1openalex-snapshot
SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
inferredcites →https://doi.org/10.12688/f1000research.9037.2openalex-snapshot
SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes
inferredcites →https://doi.org/10.1371/journal.pgen.1000734openalex-snapshot
Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
inferredcites →https://doi.org/10.1371/journal.pgen.1008120openalex-snapshot
The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice
inferredcites →https://doi.org/10.1534/genetics.106.060699openalex-snapshot
Cis-transcriptional Variation in Maize Inbred Lines B73 and Mo17 Leads to Additive Expression Patterns in the F1 Hybrid
inferredcites →https://doi.org/10.2307/1311538openalex-snapshot
Integrated Responses of Plants to Stress
inferredcites →https://doi.org/10.3389/fpls.2012.00048openalex-snapshot
Adenosine Methylation in Arabidopsis mRNA is Associated with the 3′ End and Reduced Levels Cause Developmental Defects
inferredcites →https://doi.org/10.7554/elife.31311openalex-snapshot
YTHDC1 mediates nuclear export of N6-methyladenosine methylated mRNAs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population
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Epitranscriptomics: An Additional Regulatory Layer in Plants’ Development and Stress Response
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Transcriptome Analysis Reveals a Major Gene Expression Pattern and Important Metabolic Pathways in the Control of Heterosis in Chinese Cabbage
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Additional file 1 of Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus
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Additional file 2 of Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus
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