Zhixiang Luo

Huazhong Agricultural University

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Nathan M. Springer

University of Minnesota

Qing Li

Huazhong Agricultural University

Qiang Xu

Huazhong Agricultural University

Jinsheng Lai

China Agricultural University

Mei Zhang

State Key Laboratory of Oral Diseases

Leiming Wu

Anhui Agricultural University

Lin Li

Chinese Academy of Sciences

Lin Li

Huazhong Agricultural University

Ruilin Wang

Chinese PLA General Hospital

David Paez‐Espino

Joint Genome Institute

Cooperative Institutions

Ocean University of China

Huazhong Agricultural University

Chinese Academy of Sciences

Shanghai Zhangjiang Laboratory

Qingdao National Laboratory for Marine Science and Technology

Laoshan Laboratory

Sun Yat-sen University

China Agricultural University

Ministry of Agriculture and Rural Affairs

Huazhong University of Science and Technology

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Virioplankton assemblages from challenger deep, the deepest place in the oceans

iScience (2022)

Gao Chen Yantao Liang Yong Jiang David Paez‐Espino Meiaoxue Han

Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.

10.1016/j.isci.2022.104680

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An epiallele of a gene encoding a PfkB-type carbohydrate kinase affects plant architecture in maize

The Plant Cell (2025)

Ruonan Li Yue Xu Qiang Xu Jing Tang Wenqing Chen

Abstract Plant architecture greatly contributes to grain yield, but the epigenetic regulation of plant architecture remains elusive. Here, we identified the maize (Zea mays L.) mutant plant architecture 1 (par1), which shows reduced plant height, shorter and narrower leaves, and larger leaf angles than the wild type. Interestingly, par1 is an epiallele harboring a de novo CACTA insertion in the intron of the Par1 gene. High DNA methylation levels of the CACTA insertion are associated with strong Par1 expression and normal phenotypes. In contrast, low DNA methylation levels of this insertion are associated with weak Par1 expression and a mutant-like phenotype. The Par1 gene encodes a PfkB-type carbohydrate kinase that converts nucleosides to nucleoside monophosphates both in vitro and in vivo. Additional analyses showed that genes differentially expressed in the par1 mutant are enriched in jasmonic acid (JA) metabolism, and levels of JA metabolites were significantly higher in the mutant than in the wild type. Treatment with either nucleoside monophosphates or a synthetic inhibitor of JA biosynthesis reduced JA levels and partially rescued the mutant phenotype. In summary, we identified an epiallele of a gene encoding a PfkB-type carbohydrate kinase that might affect nucleoside monophosphate and JA levels, thus affecting maize growth.

10.1093/plcell/koaf017

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Additional file 6 of DNA demethylation affects imprinted gene expression in maize endosperm

Figshare (2022)

Qiang Xu Leiming Wu Zhixiang Luo Mei Zhang Jinsheng Lai

Additional file 6. List of genes that are related with ZmROS1ab-sensitive DMRs.

DNA demethylation

Demethylation

Genomic Imprinting

10.6084/m9.figshare.19336257

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Additional file 5 of DNA demethylation affects imprinted gene expression in maize endosperm

Figshare (2022)

Qiang Xu Leiming Wu Zhixiang Luo Mei Zhang Jinsheng Lai

Additional file 5. Imprinted genes from literatures and this study.

DNA demethylation

Demethylation

Genomic Imprinting

10.6084/m9.figshare.19336254

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Additional file 2 of DNA demethylation affects imprinted gene expression in maize endosperm

Figshare (2022)

Qiang Xu Leiming Wu Zhixiang Luo Mei Zhang Jinsheng Lai

Additional file 2. Summary of data generated in this study.

DNA demethylation

Demethylation

Genomic Imprinting

10.6084/m9.figshare.19336245

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Additional file 4 of DNA demethylation affects imprinted gene expression in maize endosperm

Figshare (2022)

Qiang Xu Leiming Wu Zhixiang Luo Mei Zhang Jinsheng Lai

Additional file 4. List of DEGs between zmros1 and WT.

DNA demethylation

Demethylation

Genomic Imprinting

10.6084/m9.figshare.19336251

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Additional file 3 of DNA demethylation affects imprinted gene expression in maize endosperm

Figshare (2022)

Qiang Xu Leiming Wu Zhixiang Luo Mei Zhang Jinsheng Lai

Additional file 3. List of DMRs between zmros1 and WT.

DNA demethylation

Demethylation

Genomic Imprinting

10.6084/m9.figshare.19336248

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A novel active transposon creates allelic variation through altered translation rate to influence protein abundance

Nucleic Acids Research (2023)

Guo Chen Ruilin Wang Yizhe Jiang Xiaoxiao Dong Jing Xu

Abstract Protein translation is tightly and precisely controlled by multiple mechanisms including upstream open reading frames (uORFs), but the origins of uORFs and their role in maize are largely unexplored. In this study, an active transposition event was identified during the propagation of maize inbred line B73. The transposon, which was named BTA for ‘B73 active transposable element hAT’, creates a novel dosage-dependent hypomorphic allele of the hexose transporter gene ZmSWEET4c through insertion within the coding sequence in the first exon, and results in reduced kernel size. The BTA insertion does not affect transcript abundance but reduces protein abundance of ZmSWEET4c, probably through the introduction of a uORF. Furthermore, the introduction of BTA sequence in the exon of other genes can regulate translation efficiency without affecting their mRNA levels. A transposon capture assay revealed 79 novel insertions for BTA and BTA-like elements. These insertion sites have typical euchromatin features, including low levels of DNA methylation and high levels of H3K27ac. A putative autonomous element that mobilizes BTA and BTA-like elements was identified. Together, our results suggest a transposon-based origin of uORFs and document a new role for transposable elements to influence protein abundance and phenotypic diversity by affecting the translation rate.

10.1093/nar/gkac1195

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DNA demethylation affects imprinted gene expression in maize endosperm

Genome biology (2022)

Qiang Xu Leiming Wu Zhixiang Luo Mei Zhang Jinsheng Lai

Abstract Background DNA demethylation occurs in many species and is involved in diverse biological processes. However, the occurrence and role of DNA demethylation in maize remain unknown. Results We analyze loss-of-function mutants of two major genes encoding DNA demethylases. No significant change in DNA methylation has been detected in these mutants. However, we detect increased DNA methylation levels in the mutants around genes and some transposons. The increase in DNA methylation is accompanied by alteration in gene expression, with a tendency to show downregulation, especially for the genes that are preferentially expressed in endosperm. Imprinted expression of both maternally and paternally expressed genes changes in F 1 hybrid with the mutant as female and the wild-type as male parental line, but not in the reciprocal hybrid. This alteration in gene expression is accompanied by allele-specific DNA methylation differences, suggesting that removal of DNA methylation of the maternal allele is required for the proper expression of these imprinted genes. Finally, we demonstrate that hypermethylation in the double mutant is associated with reduced binding of transcription factor to its target, and altered gene expression. Conclusions Our results suggest that active removal of DNA methylation is important for transcription factor binding and proper gene expression in maize endosperm.

Genomic Imprinting

DNA demethylation

Demethylation

Human genetics

10.1186/s13059-022-02641-x

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Citations (32)