Cell Research最新文献

{"title":"Structural basis for linker histone H5–nucleosome binding and chromatin fiber compaction","authors":"Wenyan Li, Jie Hu, Feng Song, Juan Yu, Xin Peng, Shuming Zhang, Lin Wang, Mingli Hu, Jia-Cheng Liu, Yu Wei, Xue Xiao, Yan Li, Dongyu Li, Hui Wang, Bing-Rui Zhou, Linchang Dai, Zongjun Mou, Min Zhou, Haonan Zhang, Zheng Zhou, Huidong Zhang, Yawen Bai, Jin-Qiu Zhou, Wei Li, Guohong Li, Ping Zhu","doi":"10.1038/s41422-024-01009-z","DOIUrl":"10.1038/s41422-024-01009-z","url":null,"abstract":"The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin fiber play a crucial role in biological processes related to DNA. Here, we report a 3.6-angstrom resolution cryogenic electron microscopy structure of H5-bound dodecanucleosome, i.e., the chromatin fiber reconstituted in the presence of linker histone H5, which shows a two-start left-handed double helical structure twisted by tetranucleosomal units. An atomic structural model of the H5-bound chromatin fiber, including an intact chromatosome, is built, which provides structural details of the full-length linker histone H5, including its N-terminal domain and an HMG-motif-like C-terminal domain. The chromatosome structure shows that H5 binds the nucleosome off-dyad through a three-contact mode in the chromatin fiber. More importantly, the H5-chromatin structure provides a fine molecular basis for the intra-tetranucleosomal and inter-tetranucleosomal interactions. In addition, we systematically validated the physiological functions and structural characteristics of the tetranucleosomal unit through a series of genetic and genomic studies in Saccharomyces cerevisiae and in vitro biophysical experiments. Furthermore, our structure reveals that multiple structural asymmetries of histone tails confer a polarity to the chromatin fiber. These findings provide structural and mechanistic insights into how a nucleosomal array folds into a higher-order chromatin fiber with a polarity in vitro and in vivo.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 10","pages":"707-724"},"PeriodicalIF":28.1,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01009-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141892991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synergizing sequence and structure representations to predict protein variants","authors":"Tong Chen, Pranam Chatterjee","doi":"10.1038/s41422-024-01010-6","DOIUrl":"10.1038/s41422-024-01010-6","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 9","pages":"597-598"},"PeriodicalIF":28.1,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01010-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141862135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the role of immune system in the obesity-cancer relationship.","authors":"Camille Blériot, Gerasimos Anagnostopoulos, Florent Ginhoux","doi":"10.1038/s41422-024-01008-0","DOIUrl":"https://doi.org/10.1038/s41422-024-01008-0","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":" ","pages":""},"PeriodicalIF":28.1,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141854989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: Structural and functional evidence that GPR30 is not a direct estrogen receptor","authors":"Heng Liu, Shimeng Guo, Antao Dai, Peiyu Xu, Xin Li, Sijie Huang, Xinheng He, Kai Wu, Xinyue Zhang, Dehua Yang, Xin Xie, H. Eric Xu","doi":"10.1038/s41422-024-00998-1","DOIUrl":"10.1038/s41422-024-00998-1","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 9","pages":"669-669"},"PeriodicalIF":28.1,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00998-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141792079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Yin and Yang of innate immune cell death.","authors":"Yaqiu Wang, Thirumala-Devi Kanneganti","doi":"10.1038/s41422-024-01007-1","DOIUrl":"https://doi.org/10.1038/s41422-024-01007-1","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":" ","pages":""},"PeriodicalIF":28.1,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141765635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coding, or non-coding, that is the question","authors":"Laura Poliseno, Martina Lanza, Pier Paolo Pandolfi","doi":"10.1038/s41422-024-00975-8","DOIUrl":"10.1038/s41422-024-00975-8","url":null,"abstract":"The advent of high-throughput sequencing uncovered that our genome is pervasively transcribed into RNAs that are seemingly not translated into proteins. It was also found that non-coding RNA transcripts outnumber canonical protein-coding genes. This mindboggling discovery prompted a surge in non-coding RNA research that started unraveling the functional relevance of these new genetic units, shaking the classic definition of “gene”. While the non-coding RNA revolution was still taking place, polysome/ribosome profiling and mass spectrometry analyses revealed that peptides can be translated from non-canonical open reading frames. Therefore, it is becoming evident that the coding vs non-coding dichotomy is way blurrier than anticipated. In this review, we focus on several examples in which the binary classification of coding vs non-coding genes is outdated, since the same bifunctional gene expresses both coding and non-coding products. We discuss the implications of this intricate usage of transcripts in terms of molecular mechanisms of gene expression and biological outputs, which are often concordant, but can also surprisingly be discordant. Finally, we discuss the methodological caveats that are associated with the study of bifunctional genes, and we highlight the opportunities and challenges of therapeutic exploitation of this intricacy towards the development of anticancer therapies.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 9","pages":"609-629"},"PeriodicalIF":28.1,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00975-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs","authors":"Kuan Ren, Fengxia Zhou, Fan Zhang, Mingyu Yin, Yuwei Zhu, Shouyu Wang, Yan Chen, Tengjin Huang, Zixuan Wu, Jiale He, Anqi Zhang, Changyou Guo, Zhiwei Huang","doi":"10.1038/s41422-024-00999-0","DOIUrl":"10.1038/s41422-024-00999-0","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 11","pages":"814-814"},"PeriodicalIF":28.1,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-00999-0.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rejuvenating immunity through a balancing stem cell act.","authors":"Sten Eirik W Jacobsen","doi":"10.1038/s41422-024-01005-3","DOIUrl":"https://doi.org/10.1038/s41422-024-01005-3","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":" ","pages":""},"PeriodicalIF":28.1,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141751215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deletion of V483 in the spike confers evolutionary advantage on SARS-CoV-2 for human adaptation and host-range expansion after a prolonged pandemic","authors":"Can Yue, Shuo Liu, Bo Meng, Kaiyue Fan, Sijie Yang, Pan Liu, Qianhui Zhu, Xin Mao, Yuanling Yu, Fei Shao, Peng Wang, Youchun Wang, Ravindra Kumar Gupta, Yunlong Cao, Xiangxi Wang","doi":"10.1038/s41422-024-01000-8","DOIUrl":"10.1038/s41422-024-01000-8","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 10","pages":"739-742"},"PeriodicalIF":28.1,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01000-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141726114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Painful memories boost protective immunity","authors":"Tri Giang Phan, Elissa K. Deenick","doi":"10.1038/s41422-024-01002-6","DOIUrl":"10.1038/s41422-024-01002-6","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"34 11","pages":"751-752"},"PeriodicalIF":28.1,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41422-024-01002-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}