{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:59:40Z","timestamp":1785419980437,"version":"3.56.0"},"reference-count":38,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T00:00:00Z","timestamp":1781222400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key R&D Program of Shandong Province, China","award":["2025LZGC005"],"award-info":[{"award-number":["2025LZGC005"]}]},{"DOI":"10.13039\/501100007129","name":"Shandong Provincial Natural Science Foundation","doi-asserted-by":"crossref","award":["ZR2023QC239"],"award-info":[{"award-number":["ZR2023QC239"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100007129","name":"Shandong Provincial Natural Science Foundation","doi-asserted-by":"crossref","award":["ZR2023QC249"],"award-info":[{"award-number":["ZR2023QC249"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100007129","name":"Shandong Provincial Natural Science Foundation","doi-asserted-by":"crossref","award":["ZR2023QC217"],"award-info":[{"award-number":["ZR2023QC217"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Innovation Fund of Shandong Academy of Agricultural Sciences","award":["CXGC2026H24"],"award-info":[{"award-number":["CXGC2026H24"]}]},{"award":["CXGC2026H24"],"award-info":[{"award-number":["CXGC2026H24"]}],"id":[{"id":"https:\/\/ror.org\/01fbgjv04","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Postdoctoral Innovation Program of Shandong Province","award":["SDCX-ZG-202503132"],"award-info":[{"award-number":["SDCX-ZG-202503132"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>DNA methylation is a key epigenetic regulator in plant development. However, the changes in methylation patterns between the early and late stages of grape berry development, the two phases with the most pronounced morphological differences, and the respective roles of methylation at these stages remain largely unexplored. To investigate the dynamic DNA methylation changes during this stage and their regulatory role in fruit development, we constructed genome-wide methylation maps of grape at two key time points: the early development stage (7 days after flowering, 7DAF; hereafter referred to as S1) and the late development stages (78 days after flowering, 78DAF; hereafter referred to as S2). Global cytosine methylation increased from 12.57% (S1) to 14.16% (S2), driven primarily by a substantial increase in CHH methylation (from 5.88% to 7.92%; p &lt; 0.001), whereas CG and CHG methylation showed no statistically significant change. Most differentially methylated regions (DMRs) were hypermethylated in S2, predominantly in the CHH context. Integrative methylome and transcriptome analysis revealed that CHH hypermethylation was associated with the downregulation of YABBY5 (a berry size repressor) and upregulation of UGPase (a cell wall biosynthesis gene), suggesting a potential regulatory role in fruit expansion. Because our study compares only two time points, it cannot distinguish between gradual and stage-specific methylation changes, and functional validation of the identified genes is required. Nevertheless, these findings provides a valuable resource for understanding stage-specific DNA methylation dynamics and their association with gene expression during grape berry development.<\/jats:p>","DOI":"10.3390\/plants15121815","type":"journal-article","created":{"date-parts":[[2026,6,12]],"date-time":"2026-06-12T09:49:51Z","timestamp":1781257791000},"page":"1815","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Integrated Analysis of DNA Methylation and Transcriptomic Dynamics in the Grape Variety \u2018Cabernet Franc\u2019 at Early and Late Stages of Fruit Development"],"prefix":"10.3390","volume":"15","author":[{"given":"Qingtian","family":"Zhang","sequence":"first","affiliation":[{"name":"Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shouming","family":"Shan","sequence":"additional","affiliation":[{"name":"College of Enology and Horticulture, Ningxia University, Yinchuan 750021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoyu","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Biological Science and Technology, Jinan University, Jinan 250022, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Wang","sequence":"additional","affiliation":[{"name":"Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhaobo","family":"Lang","sequence":"additional","affiliation":[{"name":"Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0129-0401","authenticated-orcid":false,"given":"Yujing","family":"Lin","sequence":"additional","affiliation":[{"name":"Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2195-3583","authenticated-orcid":false,"given":"Wei","family":"Ji","sequence":"additional","affiliation":[{"name":"College of Horticulture, Shanxi Agricultural University, Jinzhong 030031, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4989-8136","authenticated-orcid":false,"given":"Ao","family":"Li","sequence":"additional","affiliation":[{"name":"Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"uhae285","DOI":"10.1093\/hr\/uhae285","article-title":"CHH hypermethylation contributes to the early ripening of grapes revealed by DNA methylome landscape of \u2018Kyoho\u2019 and its bud mutant","volume":"12","author":"Wei","year":"2025","journal-title":"Hortic. 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