Genomics最新文献

{"title":"Co-regulatory crosstalk between m5C, m7G, and o8G RNA modifications via QKI/YBX1 axis in myocardial ischemia-reperfusion injury","authors":"Ziqiang Yang ,&nbsp;Suyun Chen ,&nbsp;Siman Shen ,&nbsp;Wanglong Liu ,&nbsp;Kun Ding ,&nbsp;Fangni Cao ,&nbsp;Simeng Li ,&nbsp;Minjuan Zeng ,&nbsp;Jianning Chen ,&nbsp;Li Xu ,&nbsp;Liangqing Zhang","doi":"10.1016/j.ygeno.2026.111193","DOIUrl":"10.1016/j.ygeno.2026.111193","url":null,"abstract":"<div><h3>Background</h3><div>Ischemia–reperfusion (I/R) injury in the heart triggers oxidative stress and alters post-transcriptional gene regulation. Reactive oxygen species (ROS) generated during oxidative stress induce RNA modifications such as 8-oxo-guanosine (o8G). Other modifications including 5-methylcytosine (m5C) and 7-methylguanosine (m7G) may also contribute to cardiac dysfunction. While the roles of individual RNA modifications in I/R injury are increasingly recognized, the global dynamics and crosstalk among these modifications under oxidative stress remain largely unexplored.</div></div><div><h3>Methods</h3><div>We performed high-throughput sequencing specific to each modification, integrated with mRNA transcriptome profiling of an IR injury mouse model. Differentially modified transcripts were subjected to GO and KEGG enrichment analyses to elucidate their functional relevance. Mechanistically, we demonstrated that RNA modification regulators with distinct functional roles can physically interact with each other, as shown by co-immunoprecipitation and immunofluorescence assays. Global changes in RNA modification levels under the model conditions were assessed using dot blot analysis. Furthermore, the regulatory effects of these enzymes on target mRNA stability were evaluated via Actinomycin D transcriptional inhibition assays.</div></div><div><h3>Results</h3><div>We found that the levels of all three modifications, m5C, m7G, and o8G were increased in IR by dot blot and observed a significant upregulation of three modification peaks under I/R by MeRIP-seq. Both m5C and o8G were predominantly enriched in CDS, while m7G displayed a dynamic redistribution. Our study focuses on the co-regulation crosstalk among three modifications. Functionally, singly or combinatorially modified transcripts were enriched in actin cytoskeleton regulation. Mechanistically, the transcripts of the regulators can be modified by each other and QKI can modulate the global modification level of o8G. QKI and YBX1 interact with each other to cooperatively stabilize ACTN4 mRNA, thereby maintaining cytoskeletal integrity.</div></div><div><h3>Conclusion</h3><div>Our results establish that QKI and YBX1 modulate the actin cytoskeleton via a coordinated network of m5C, m7G, and o8G in I/R injury.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111193"},"PeriodicalIF":3.0,"publicationDate":"2026-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145911189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism of lead resistance in Wickerhamomyces anomalus: Insights from whole genome sequencing","authors":"Lijie Li,&nbsp;Ganqiqige Cha,&nbsp;Fengsheng Zhang","doi":"10.1016/j.ygeno.2025.111192","DOIUrl":"10.1016/j.ygeno.2025.111192","url":null,"abstract":"<div><div>Lead contamination in air, water, and soil has infiltrated foods and feeds, posing severe health risks to humans and animals and remaining a tough challenge. Yeast is a safe and efficient biosorbent for lead removal. This study explored <em>W. anomalus QF-11</em> lead resistance via whole-genome sequencing, finding it tolerates up to 7000 mg/L Pb²⁺. Under 4000 mg/L Pb²⁺ stress, it enhances resistance by scavenging ROS, increasing soluble protein, boosting SOD, POD and CAT activities, and elevating glutathione and trehalose levels. Its genome annotates 63 ABC transporters and antioxidant genes involved in lead adsorption, transportation and compartmentalization, with SODC, SODM, VAN1, TSL1 and others significantly upregulated. This study provides a theoretical basis for <em>W. anomalus QF-11</em> application as a Pb²⁺ biosorbent and data support for novel heavy metal adsorbent development.</div></div>","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111192"},"PeriodicalIF":3.0,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111208"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146656574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111198"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146656582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111202"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146656583","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 2","pages":"Article 111191"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146656586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111186"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146670738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111180"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146670745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111160"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146670750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":12521,"journal":{"name":"Genomics","volume":"118 1","pages":"Article 111159"},"PeriodicalIF":3.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146670751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}