Dataset Information

Developmental dynamics of endogenous peptides in maize

ABSTRACT: In this study, we present a comprehensive peptidomic atlas of 13 tissues in maize spanning the vegetative and reproductive phases. Using 3-frame translation of canonical coding sequences (CDSs), we identified 6,100 non-redundant endogenous peptides, significantly expanding the known repertoire of peptides in plants. By integrating the peptidomic coexpression profiles with previously reported proteomic profiles, we found that the peptide abundance did not consistently correlate with the abundance of their source proteins, suggesting complex regulatory mechanisms. This integrated peptidomic and proteomic map not only provides a valuable resource for exploring the functional roles of endogenous peptides in maize development, but will also enable researchers to explore the functional relationship among genes, peptides, and proteins in various biological contexts.

INSTRUMENT(S):

ORGANISM(S): Zea Mays (maize)

TISSUE(S): Leaf

SUBMITTER: Shunxi Wang

LAB HEAD: Liuji Wu

PROVIDER: PXD055863 | Pride | 2025-05-07

REPOSITORIES: Pride

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A comprehensive atlas of endogenous peptides in maize.

Ali Usman U Tian Lei L Tang Ruihong R Wang Shunxi S Luo Weiwei W Liu Shanshan S Zhang Jinghua J Wu Liuji L

iMeta 20241111 6

In this study, we present a comprehensive peptidomic atlas of 13 maize tissues, covering both vegetative and reproductive phases. Using a three-frame translation of canonical coding sequences, we identified 6100 nonredundant endogenous peptides, significantly expanding the known plant peptide repertoire. By integrating peptidomic coexpression profiles with previously reported proteomic profiles, we found that the peptide abundance did not consistently correlate with the abundance of their source ...[more]

PMID: 39742302

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Project description:Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues. Examination of DNA methylated modifications in 2 maize tissues.

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