ArticleG3 (Bethesda, Md.)2021
Leveraging histone modifications to improve genome annotations.
Article in G3 (Bethesda, Md.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 15 citations in OpenAlex.
- Lineage-specific evolution of regulatory landscapes in a polyploid plant and its diploid progenitors.bioRxiv : the preprint server for biology · 2026Article
- Two independent origins of XY sex chromosomes in Asparagus.Molecular biology and evolution · 2026Article
- Tick genomics through a Nanopore: a low-cost approach for tick genomics.BMC genomics · 2025Article
- From GWAS signal to function: targeted CRISPR activation enables functional characterization of non-coding SNPs in chickens.Frontiers in genome editing · 2025Article
- MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.Nature communications · 2024Article
- Enhancers associated with unstable RNAs are rare in plants.bioRxiv : the preprint server for biology · 2023Article
- Simple and accurate transcriptional start site identification using Smar2C2 and examination of conserved promoter features.The Plant journal : for cell and molecular biology · 2022Article
- Epigenome guided crop improvement: current progress and future opportunities.Emerging topics in life sciences · 2022Review
- Small RNAs mediate transgenerational inheritance of genome-wide trans-acting epialleles in maize.Genome biology · 2022Article
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
- Green plant genomes: What we know in an era of rapidly expanding opportunities.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Quality control and evaluation of plant epigenomics data.The Plant cell · 2022Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Accurate genome annotations are essential to modern biology; however, they remain challenging to produce. Variation in gene structure and expression across species, as well as within an organism, make correctly annotating genes arduous; an issue exacerbated by pitfalls in current in silico methods. These issues necessitate complementary approaches to add additional confidence and rectify potential misannotations. Integration of epigenomic data into genome annotation is one such approach. In this study, we utilized sets of histone modification data, which are precisely distributed at either gene bodies or promoters to evaluate the annotation of the Zea mays genome. We leveraged these data genome wide, allowing for identification of annotations discordant with empirical data. In total, 13,159 annotation discrepancies were found in Z. mays upon integrating data across three different tissues, which were corroborated using RNA-based approaches. Upon correction, genes were extended by an average of 2128 base pairs, and we identified 2529 novel genes. Application of this method to five additional plant genomes identified a series of misannotations, as well as identified novel genes, including 13,836 in Asparagus officinalis, 2724 in Setaria viridis, 2446 in Sorghum bicolor, 8631 in Glycine max, and 2585 in Phaseolous vulgaris. This study demonstrates that histone modification data can be leveraged to rapidly improve current genome annotations across diverse plant lineages.
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Registered trials
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