Article(id=1305135956571476850, tenantId=1146029695717560320, journalId=1303687221787852879, issueId=1305135915303723476, articleNumber=null, orderNo=null, doi=10.7606/j.issn.1009-1041.2026.07.06, pmid=null, cstr=null, oa=null, hot=null, price=null, onlineType=0, articleFormat=0, articleType=null, articleTypeStr=null, receivedDate=1768924800000, receivedDateStr=2026-01-21, revisedDate=1773936000000, revisedDateStr=2026-03-20, acceptedDate=null, acceptedDateStr=null, onlineDate=1789098260300, onlineDateStr=2026-09-11, pubDate=1784044800000, pubDateStr=2026-07-15, doiRegisterDate=null, doiRegisterDateStr=null, onlineIssueDate=1789098260300, onlineIssueDateStr=2026-09-11, onlineJustAcceptDate=null, onlineJustAcceptDateStr=null, onlineFirstDate=null, onlineFirstDateStr=null, sourceXml=null, magXml=null, createTime=1789098260300, creator=13701087609, updateTime=1789098260300, updator=13701087609, issue=Issue{id=1305135915303723476, tenantId=1146029695717560320, journalId=1303687221787852879, year='2026', volume='46', issue='7', pageStart='F2', pageEnd='990', issueExtLink='null', onlineDate='null', pubDate='1784044800000', pubDateStr='2026-07-15', beforeIssueId=null, nextIssueId=null, price=null, status=1, issueComplete=1, articleOrder=1, issueType=-1, specialIssue=null, createTime=1789098250461, creator='13701087609', updateTime=1789103040607, updator='13701087609', preIssue=null, nextIssue=null, articleTotal=null, ext={EN=IssueExt(id=1305156006661608318, tenantId=1146029695717560320, journalId=1303687221787852879, issueId=1305135915303723476, language=EN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=), CN=IssueExt(id=1305156006661608319, tenantId=1146029695717560320, journalId=1303687221787852879, issueId=1305135915303723476, language=CN, specialIssueTitle=, coverIllustrator=null, specialIssueEditor=, specialIssueAbout=)}, issueFiles=null, downloadFileDto=null}, startPage=897, endPage=908, ext={EN=ArticleExt(id=1305135958035288949, articleId=1305135956571476850, tenantId=1146029695717560320, journalId=1303687221787852879, language=EN, title=Three-Dimensional Chromatin Remodeling and Transcriptional Regulation in a Subgenome of the Wheat 1B/1R Translocation Line, columnId=1305133119129023428, journalTitle=Journal of Triticeae Crops, columnName=Genetics & Breeding, runingTitle=null, highlight=null, articleAbstract=

Wheat lines carrying the 1B/1R translocation have been widely utilized in breeding due to their enhanced disease resistance and yield stability. However, its impact on the three-dimensional (3D) chromatin architecture and transcriptional regulation of non-translocated subgenomes remains largely unexplored. Here, we used a 1B/1R translocation line, Wanmai 270, and its corresponding near-isogenic line lacking the 1B/1R segment to investigate chromatin spatial remodeling in the wheat A subgenome and its relationship with gene expression. By integrating Hi-C, RNA-seq, and qRT-PCR, we systematically characterized the effects of the 1B/1R translocation on 3D genome organization. A substantial number of A/B compartment switching regions were identified in the A subgenome, with a predominance of B-to-A transitions. Notably, compartment reorganization exhibited pronounced heterogeneity across chromosomes. To assess the association between compartment switching and transcriptional changes, 20 differentially expressed genes located within translocation regions were selected for qRT-PCR. Genes in A-to-B regions showed reduced expression in Wanmai 270 relative to those in the near-isogenic line, whereas genes in B-to-A regions exhibited increased expression, consistent with the direction of compartment transitions. Subcompartment analysis revealed a genome-wide decrease in A1/A2 proportions and an increase in B1/B2 proportions in the A subgenome of Wanmai 270, with the most prominent reorganization observed on chromosomes 1A and 3A. Topologically associating domains (TAD) analysis showed that the overall TAD framework was largely conserved between the two lines, although local TAD merging and boundary reorganization occurred in specific regions of Wanmai 270. Integration with transcriptome data further indicated that compartment-translocation regions were enriched for differentially expressed genes involved in chromatin organization, DNA replication, carbohydrate metabolism, and amino acid metabolism. GO, KEGG, and GSEA analyses revealed that transcriptional differences in Wanmai 270 were not characterized by global activation of basal metabolic pathways, but rather by fine-tuned regulation within specific pathways. In summary, the 1B/1R translocation preserves the overall 3D chromatin framework of the A subgenome while inducing multiscale spatial remodeling at the levels of compartments, subcompartments, and local TADs, thereby modulating transcriptional responses through changes in the chromatin regulatory landscape.

, authors=Zhen WANG¹, Bin ZHANG¹, Lichao SHI¹, Rui LIU¹, Jinxiu LI¹, Jinbang LI¹, Jun CHEN², authorsList=Zhen WANG, Bin ZHANG, Lichao SHI, Rui LIU, Jinxiu LI, Jinbang LI, Jun CHEN, authorCompany=null, correspAuthors=Jinbang LI, authorNote=null, correspAuthorsNote=null, copyrightStatement=null, copyrightOwner=null, extLink=null, articleAbsUrl=null, sourceXml=null, magXml=null, pdfUrl=null, pdf=null, pdfFileSize=null, pdfExtLink=null, richHtmlUrl=null, mobilePdfUrl=null, reviewReport=null, pdfFirstPage=null, abstractGraph=null, abstractGraphContent=null, abstractVideo=null, citation=null, cebUrl=null, magXmlContent=null, mapNumber=null, fund=null), CN=ArticleExt(id=1305135958320501622, articleId=1305135956571476850, tenantId=1146029695717560320, journalId=1303687221787852879, language=CN, title=1B/1R易位下小麦A亚基因组三维染色质重塑与转录调控, columnId=1305133119284212678, journalTitle=麦类作物学报, columnName=遗传育种, runingTitle=null, highlight=null, articleAbstract=

1B/1R易位系小麦因兼具抗病性和产量稳定性而在育种中得到广泛应用，但其对非易位亚基因组三维染色质结构及转录调控的影响仍缺乏系统认识。本研究以1B/1R易位系品种宛麦270及其不含1B/1R易位片段的近等基因系为试验材料，综合利用Hi-C技术、转录组测序及qRT-PCR，从三维基因组层面系统解析1B/1R易位背景下小麦A亚基因组染色质空间结构的重塑特征及其与基因表达调控之间的关系。在A亚基因组中鉴定到大量A/B区室状态转换区段，且整体以B→A转换为主，但区室重排在不同染色体间呈现明显的非均一分布特征。为验证区室转换与基因表达变化之间的关联性，对位于区室转换区段内的20个差异表达基因进行qRT-PCR分析。结果表明，A→B转换区段内基因在宛麦270中的表达量整体低于其近等基因系，而B→A转换区段内基因则整体表现为表达量升高，其表达量变化与区室状态转换趋势一致。亚区室分析显示，宛麦270在A亚基因组整体上表现为A1/A2亚区室比例降低、B1/B2亚区室比例升高，其中1A和3A染色体的亚区室重构最为显著。经TAD（拓扑关联结构域）分析，两种材料在A亚基因组尺度上维持相对稳定的TAD结构框架，但在部分染色体局部区域中，宛麦270出现了TAD合并和边界重组现象。通过进一步结合转录组分析，A/B区室转换区段内富集了大量差异表达基因，这些基因主要涉及染色质组织、DNA复制、碳水化合物代谢及氨基酸代谢等功能过程。经GO、KEGG及GSEA分析，宛麦270的转录差异并非表现为基础代谢通路的整体激活，而更多体现为特定通路内基因的精细化调控。综上，1B/1R易位在保持A亚基因组整体三维结构稳定的同时，引发了区室、亚区室及局部TAD层级的空间重塑，并通过改变基因所处的空间调控环境影响其转录响应。

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