Dataset Information

Large-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipelineLarge-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline

ABSTRACT: Non-canonical peptides (NCPs) have been shown to play critical roles in fundamental biological processes. Despite their importance, NCPs have been rarely identified and characterized in plants. Here we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe customized six-frame translation database and for the first time applied this pipeline to large-scale identification of NCPs in both monocot and dicot plants. Altogether, 1,993 and 1,860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. The NCPs showed distinct characteristics compared to canonical peptides and can be derived from introns, 3’UTRs, 5’UTRs, junctions and intergenic regions. These results revealed that non-canonical translation or cryptic translation events occur more universally than previously thought. In addition, maize NCPs were found enriched within the regions associated with phenotypic variation or regions under domestication selection, indicating their potential function in plant genetic regulations of complex traits and evolution. Summarily, this study provides the first unbiased and global view of plant NCPs. The identification of large-scale NCPs in both monocot and dicot plants reveals that a much larger portion of the plant genome can be translated biologically functional molecules, which has important implications in functional genomic studies. The present study also provides a useful resource for the characterization of more hidden NCPs in other plants.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Zea Mays (maize)

TISSUE(S): Leaf

SUBMITTER: Shunxi Wang

LAB HEAD: Liuji Wu

PROVIDER: PXD017081 | Pride | 2020-08-11

REPOSITORIES: Pride

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Publications

Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline.

Wang Shunxi S Tian Lei L Liu Haijun H Li Xiang X Zhang Jinghua J Chen Xueyan X Jia Xingmeng X Zheng Xu X Wu Shubiao S Chen Yanhui Y Yan Jianbing J Wu Liuji L

Molecular plant 20200521 7

Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. In this study, we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants.A total of 1993 and 1860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. These NCPs showed distinct characte ...[more]

PMID: 32445888

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Project description:Genomic instability associated with DNA replication stress is linked to cancer and genetic pathologies in humans. If not properly regulated, replication stress, such as fork stalling and collapse, can be induced at natural replication impediments present throughout the genome. The fork protection complex (FPC) is thought to play a critical role in stabilizing stalled replication forks at several known replication barriers including eukaryotic rDNA genes and the fission yeast mating-type locus. However, little is known about the role of the FPC at other natural impediments including telomeres. Telomeres are considered to be difficult to replicate due to the presence of repetitive GT-rich sequences and telomere-binding proteins. However, the regulatory mechanism that ensures telomere replication is not fully understood. Here, we report the role of the fission yeast Swi1/Timeless, a subunit of the FPC, in telomere replication. Loss of Swi1 causes telomere shortening in a telomerase-independent manner. Our epistasis analyses suggest that heterochromatin and telomere-binding proteins are not major impediments for telomere replication in the absence of Swi1. Instead, repetitive DNA sequences impair telomere integrity in swi1Î mutant cells, leading to the loss of repeat DNA. In the absence of Swi1, telomere shortening is accompanied with an increased recruitment of Rad52 recombinase and more frequent amplification of telomere/subtelomeres, reminiscent of tumor cells that utilize the alternative lengthening of telomeres pathway (ALT) to maintain telomeres. These results suggest that Swi1 ensures telomere replication by suppressing recombination and repeat instability at telomeres. Our studies may also be relevant in understanding the potential role of the FPC in regulation of telomere stability in cancer cells. Genome-wide distributions of Rad52 in wild type and in swi1 deletion in fission yeast The'SP1173_WT ChIP-seq' is an input sample (non-tagged data).

Dataset Information

Large-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipelineLarge-scale discovery of non-canonical peptides in monocot and dicot plants through an integrated peptidogenomic pipeline

Publications

Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline.

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