Pub Date : 2024-10-04DOI: 10.1038/s41594-024-01385-5
Zuhui Wang, Bo Wang, Di Niu, Chao Yin, Ying Bi, Claudia Cattoglio, Kyle M. Loh, Luke D. Lavis, Hao Ge, Wulan Deng
Pioneer transcription factors (PTFs) possess the unique capability to access closed chromatin regions and initiate cell fate changes, yet the underlying mechanisms remain elusive. Here, we characterized the single-molecule dynamics of PTFs targeting chromatin in living cells, revealing a notable ‘confined target search’ mechanism. PTFs such as FOXA1, FOXA2, SOX2, OCT4 and KLF4 sampled chromatin more frequently than non-PTF MYC, alternating between fast free diffusion in the nucleus and slower confined diffusion within mesoscale zones. Super-resolved microscopy showed closed chromatin organized as mesoscale nucleosome-dense domains, confining FOXA2 diffusion locally and enriching its binding. We pinpointed specific histone-interacting disordered regions, distinct from DNA-binding domains, crucial for confined target search kinetics and pioneer activity within closed chromatin. Fusion to other factors enhanced pioneer activity. Kinetic simulations suggested that transient confinement could increase target association rate by shortening search time and binding repeatedly. Our findings illuminate how PTFs recognize and exploit closed chromatin organization to access targets, revealing a pivotal aspect of gene regulation.
{"title":"Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells","authors":"Zuhui Wang, Bo Wang, Di Niu, Chao Yin, Ying Bi, Claudia Cattoglio, Kyle M. Loh, Luke D. Lavis, Hao Ge, Wulan Deng","doi":"10.1038/s41594-024-01385-5","DOIUrl":"https://doi.org/10.1038/s41594-024-01385-5","url":null,"abstract":"<p>Pioneer transcription factors (PTFs) possess the unique capability to access closed chromatin regions and initiate cell fate changes, yet the underlying mechanisms remain elusive. Here, we characterized the single-molecule dynamics of PTFs targeting chromatin in living cells, revealing a notable ‘confined target search’ mechanism. PTFs such as FOXA1, FOXA2, SOX2, OCT4 and KLF4 sampled chromatin more frequently than non-PTF MYC, alternating between fast free diffusion in the nucleus and slower confined diffusion within mesoscale zones. Super-resolved microscopy showed closed chromatin organized as mesoscale nucleosome-dense domains, confining FOXA2 diffusion locally and enriching its binding. We pinpointed specific histone-interacting disordered regions, distinct from DNA-binding domains, crucial for confined target search kinetics and pioneer activity within closed chromatin. Fusion to other factors enhanced pioneer activity. Kinetic simulations suggested that transient confinement could increase target association rate by shortening search time and binding repeatedly. Our findings illuminate how PTFs recognize and exploit closed chromatin organization to access targets, revealing a pivotal aspect of gene regulation.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-01DOI: 10.1038/s41594-024-01394-4
Richard D. Schargel, M. Zuhaib Qayyum, Ajay Singh Tanwar, Ravi C. Kalathur, Elizabeth H. Kellogg
RNA-guided endonucleases, once thought to be exclusive to prokaryotes, have been recently identified in eukaryotes and are called Fanzors. They are classified into two clades, Fanzor1 and Fanzor2. Here we present the cryo-electron microscopy structure of Acanthamoeba polyphaga mimivirus Fanzor2, revealing its ωRNA architecture, active site and features involved in transposon-adjacent motif recognition. A comparison to Fanzor1 and TnpB structures highlights divergent evolutionary paths, advancing our understanding of RNA-guided endonucleases.
{"title":"Structure of Fanzor2 reveals insights into the evolution of the TnpB superfamily","authors":"Richard D. Schargel, M. Zuhaib Qayyum, Ajay Singh Tanwar, Ravi C. Kalathur, Elizabeth H. Kellogg","doi":"10.1038/s41594-024-01394-4","DOIUrl":"https://doi.org/10.1038/s41594-024-01394-4","url":null,"abstract":"<p>RNA-guided endonucleases, once thought to be exclusive to prokaryotes, have been recently identified in eukaryotes and are called Fanzors. They are classified into two clades, Fanzor1 and Fanzor2. Here we present the cryo-electron microscopy structure of <i>Acanthamoeba polyphaga</i> mimivirus Fanzor2, revealing its ωRNA architecture, active site and features involved in transposon-adjacent motif recognition. A comparison to Fanzor1 and TnpB structures highlights divergent evolutionary paths, advancing our understanding of RNA-guided endonucleases.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142360099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-27DOI: 10.1038/s41594-024-01383-7
Inga V. Hochheiser, Matthias Geyer
An understudied subset of NOD-like receptors are involved in the reproductive system, and their dysfunction can cause infertility. The recently obtained structures of the core subcortical maternal complex assembled around one of them, NLRP5, provide important insight into this building block of early embryo cytoplasmic lattices.
{"title":"Insights into reproduction-regulating NOD-like receptors","authors":"Inga V. Hochheiser, Matthias Geyer","doi":"10.1038/s41594-024-01383-7","DOIUrl":"https://doi.org/10.1038/s41594-024-01383-7","url":null,"abstract":"An understudied subset of NOD-like receptors are involved in the reproductive system, and their dysfunction can cause infertility. The recently obtained structures of the core subcortical maternal complex assembled around one of them, NLRP5, provide important insight into this building block of early embryo cytoplasmic lattices.","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-26DOI: 10.1038/s41594-024-01393-5
Svetlana Farberov, Omer Ziv, Jian You Lau, Rotem Ben-Tov Perry, Yoav Lubelsky, Eric Miska, Grzegorz Kudla, Igor Ulitsky
Long noncoding RNAs (lncRNAs) are increasingly appreciated for their important functions in mammalian cells. However, how their functional capacities are encoded in their sequences and manifested in their structures remains largely unknown. Some lncRNAs bind to and modulate the availability of RNA-binding proteins, but the structural principles that underlie this mode of regulation are unknown. The NORAD lncRNA is a known decoy for Pumilio proteins, which modulate the translation and stability of hundreds of messenger RNAs and, consequently, a regulator of genomic stability and aging. Here we probed the RNA structure and long-range RNA–RNA interactions formed by human NORAD inside cells under different stressful conditions. We discovered a highly modular structure consisting of well-defined domains that contribute independently to NORAD function. Following arsenite stress, most structural domains undergo relaxation and form interactions with other RNAs that are targeted to stress granules. We further revealed a unique structural organization that spatially clusters the multiple Pumilio binding sites along NORAD and consequently contributes to the derepression of Pumilio targets. We then applied these structural principles to design an effective artificial decoy for the let-7 microRNA. Our work demonstrates how the sequence of a lncRNA spatially clusters its function into separated domains and how structural principles can be employed for the rational design of lncRNAs with desired activities.
{"title":"Structural features within the NORAD long noncoding RNA underlie efficient repression of Pumilio activity","authors":"Svetlana Farberov, Omer Ziv, Jian You Lau, Rotem Ben-Tov Perry, Yoav Lubelsky, Eric Miska, Grzegorz Kudla, Igor Ulitsky","doi":"10.1038/s41594-024-01393-5","DOIUrl":"https://doi.org/10.1038/s41594-024-01393-5","url":null,"abstract":"<p>Long noncoding RNAs (lncRNAs) are increasingly appreciated for their important functions in mammalian cells. However, how their functional capacities are encoded in their sequences and manifested in their structures remains largely unknown. Some lncRNAs bind to and modulate the availability of RNA-binding proteins, but the structural principles that underlie this mode of regulation are unknown. The NORAD lncRNA is a known decoy for Pumilio proteins, which modulate the translation and stability of hundreds of messenger RNAs and, consequently, a regulator of genomic stability and aging. Here we probed the RNA structure and long-range RNA–RNA interactions formed by human NORAD inside cells under different stressful conditions. We discovered a highly modular structure consisting of well-defined domains that contribute independently to NORAD function. Following arsenite stress, most structural domains undergo relaxation and form interactions with other RNAs that are targeted to stress granules. We further revealed a unique structural organization that spatially clusters the multiple Pumilio binding sites along NORAD and consequently contributes to the derepression of Pumilio targets. We then applied these structural principles to design an effective artificial decoy for the let-7 microRNA. Our work demonstrates how the sequence of a lncRNA spatially clusters its function into separated domains and how structural principles can be employed for the rational design of lncRNAs with desired activities.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142321494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-25DOI: 10.1038/s41594-024-01389-1
Ireneusz Górniak, Zachery Stephens, Satchal K. Erramilli, Tomasz Gawda, Anthony A. Kossiakoff, Jochen Zimmer
Hyaluronan (HA) is an essential component of the vertebrate extracellular matrix. It is a heteropolysaccharide of N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA) reaching several megadaltons in healthy tissues. HA is synthesized and translocated in a coupled reaction by HA synthase (HAS). Here, structural snapshots of HAS provide insights into HA biosynthesis, from substrate recognition to HA elongation and translocation. We monitor the extension of a GlcNAc primer with GlcA, reveal the coordination of the uridine diphosphate product by a conserved gating loop and capture the opening of a translocation channel to coordinate a translocating HA polymer. Furthermore, we identify channel-lining residues that modulate HA product lengths. Integrating structural and biochemical analyses suggests an avenue for polysaccharide engineering based on finely tuned enzymatic activity and HA coordination.
透明质酸(HA)是脊椎动物细胞外基质的重要组成部分。它是一种由 N-乙酰葡糖胺(GlcNAc)和葡萄糖醛酸(GlcA)组成的杂多糖,在健康组织中可达数个百万吨。HA 通过 HA 合成酶(HAS)的耦合反应合成并转运。在这里,HAS 的结构快照提供了对 HA 生物合成(从底物识别到 HA 延伸和转运)的深入了解。我们用 GlcA 监测了 GlcNAc 引物的延伸,揭示了尿苷二磷酸产物通过一个保守的门控环的配位,并捕捉到了转位通道的打开以配位转位的 HA 聚合物。此外,我们还发现了可调节 HA 产物长度的通道衬里残基。将结构分析与生化分析相结合,为基于酶活性和 HA 协调的多糖工程提供了一条途径。
{"title":"Structural insights into translocation and tailored synthesis of hyaluronan","authors":"Ireneusz Górniak, Zachery Stephens, Satchal K. Erramilli, Tomasz Gawda, Anthony A. Kossiakoff, Jochen Zimmer","doi":"10.1038/s41594-024-01389-1","DOIUrl":"https://doi.org/10.1038/s41594-024-01389-1","url":null,"abstract":"<p>Hyaluronan (HA) is an essential component of the vertebrate extracellular matrix. It is a heteropolysaccharide of <i>N</i>-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA) reaching several megadaltons in healthy tissues. HA is synthesized and translocated in a coupled reaction by HA synthase (HAS). Here, structural snapshots of HAS provide insights into HA biosynthesis, from substrate recognition to HA elongation and translocation. We monitor the extension of a GlcNAc primer with GlcA, reveal the coordination of the uridine diphosphate product by a conserved gating loop and capture the opening of a translocation channel to coordinate a translocating HA polymer. Furthermore, we identify channel-lining residues that modulate HA product lengths. Integrating structural and biochemical analyses suggests an avenue for polysaccharide engineering based on finely tuned enzymatic activity and HA coordination.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142317257","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-23DOI: 10.1038/s41594-024-01397-1
Kei Saotome, Luke L. McGoldrick, Jo-Hao Ho, Trudy F. Ramlall, Sweta Shah, Michael J. Moore, Jee Hae Kim, Raymond Leidich, William C. Olson, Matthew C. Franklin
Activation of the chemokine receptor CXCR4 by its chemokine ligand CXCL12 regulates diverse cellular processes. Previously reported crystal structures of CXCR4 revealed the architecture of an inactive, homodimeric receptor. However, many structural aspects of CXCR4 remain poorly understood. Here, we use cryo-electron microscopy to investigate various modes of human CXCR4 regulation. CXCL12 activates CXCR4 by inserting its N terminus deep into the CXCR4 orthosteric pocket. The binding of US Food and Drug Administration-approved antagonist AMD3100 is stabilized by electrostatic interactions with acidic residues in the seven-transmembrane-helix bundle. A potent antibody blocker, REGN7663, binds across the extracellular face of CXCR4 and inserts its complementarity-determining region H3 loop into the orthosteric pocket. Trimeric and tetrameric structures of CXCR4 reveal modes of G-protein-coupled receptor oligomerization. We show that CXCR4 adopts distinct subunit conformations in trimeric and tetrameric assemblies, highlighting how oligomerization could allosterically regulate chemokine receptor function.
{"title":"Structural insights into CXCR4 modulation and oligomerization","authors":"Kei Saotome, Luke L. McGoldrick, Jo-Hao Ho, Trudy F. Ramlall, Sweta Shah, Michael J. Moore, Jee Hae Kim, Raymond Leidich, William C. Olson, Matthew C. Franklin","doi":"10.1038/s41594-024-01397-1","DOIUrl":"https://doi.org/10.1038/s41594-024-01397-1","url":null,"abstract":"<p>Activation of the chemokine receptor CXCR4 by its chemokine ligand CXCL12 regulates diverse cellular processes. Previously reported crystal structures of CXCR4 revealed the architecture of an inactive, homodimeric receptor. However, many structural aspects of CXCR4 remain poorly understood. Here, we use cryo-electron microscopy to investigate various modes of human CXCR4 regulation. CXCL12 activates CXCR4 by inserting its N terminus deep into the CXCR4 orthosteric pocket. The binding of US Food and Drug Administration-approved antagonist AMD3100 is stabilized by electrostatic interactions with acidic residues in the seven-transmembrane-helix bundle. A potent antibody blocker, REGN7663, binds across the extracellular face of CXCR4 and inserts its complementarity-determining region H3 loop into the orthosteric pocket. Trimeric and tetrameric structures of CXCR4 reveal modes of G-protein-coupled receptor oligomerization. We show that CXCR4 adopts distinct subunit conformations in trimeric and tetrameric assemblies, highlighting how oligomerization could allosterically regulate chemokine receptor function.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-20DOI: 10.1038/s41594-024-01382-8
You Yu, Juncheng Wang, Kaixian Liu, Zhi Zheng, Meret Arter, Corentin Claeys Bouuaert, Stephen Pu, Dinshaw J. Patel, Scott Keeney
DNA double-strand breaks that initiate meiotic recombination are formed by the topoisomerase-relative enzyme Spo11, supported by conserved auxiliary factors. Because high-resolution structural data have not been available, many questions remain about the architecture of Spo11 and its partners and how they engage with DNA. We report cryo-electron microscopy structures at up to 3.3-Å resolution of DNA-bound core complexes of Saccharomyces cerevisiae Spo11 with Rec102, Rec104 and Ski8. In these structures, monomeric core complexes make extensive contacts with the DNA backbone and with the recessed 3′-OH and first 5′ overhanging nucleotide, establishing the molecular determinants of DNA end-binding specificity and providing insight into DNA cleavage preferences in vivo. The structures of individual subunits and their interfaces, supported by functional data in yeast, provide insight into the role of metal ions in DNA binding and uncover unexpected structural variation in homologs of the Top6BL component of the core complex.
启动减数分裂重组的 DNA 双链断裂是由拓扑异构酶相关酶 Spo11 在保守辅助因子的支持下形成的。由于尚未获得高分辨率的结构数据,有关 Spo11 及其伙伴的结构以及它们如何与 DNA 结合的许多问题依然存在。我们报告了酿酒酵母 Spo11 与 Rec102、Rec104 和 Ski8 的 DNA 结合核心复合物的高达 3.3 Å 分辨率的低温电子显微镜结构。在这些结构中,单体核心复合物与 DNA 主干以及凹陷的 3′-OH和第一个 5′悬垂核苷酸广泛接触,从而确定了 DNA 末端结合特异性的分子决定因素,并深入了解了体内 DNA 的裂解偏好。单个亚基及其界面的结构得到了酵母中功能数据的支持,使人们深入了解了金属离子在 DNA 结合中的作用,并发现了核心复合物 Top6BL 组成部分同源物中意想不到的结构变异。
{"title":"Cryo-EM structures of the Spo11 core complex bound to DNA","authors":"You Yu, Juncheng Wang, Kaixian Liu, Zhi Zheng, Meret Arter, Corentin Claeys Bouuaert, Stephen Pu, Dinshaw J. Patel, Scott Keeney","doi":"10.1038/s41594-024-01382-8","DOIUrl":"https://doi.org/10.1038/s41594-024-01382-8","url":null,"abstract":"<p>DNA double-strand breaks that initiate meiotic recombination are formed by the topoisomerase-relative enzyme Spo11, supported by conserved auxiliary factors. Because high-resolution structural data have not been available, many questions remain about the architecture of Spo11 and its partners and how they engage with DNA. We report cryo-electron microscopy structures at up to 3.3-Å resolution of DNA-bound core complexes of <i>Saccharomyces cerevisiae</i> Spo11 with Rec102, Rec104 and Ski8. In these structures, monomeric core complexes make extensive contacts with the DNA backbone and with the recessed 3′-OH and first 5′ overhanging nucleotide, establishing the molecular determinants of DNA end-binding specificity and providing insight into DNA cleavage preferences in vivo. The structures of individual subunits and their interfaces, supported by functional data in yeast, provide insight into the role of metal ions in DNA binding and uncover unexpected structural variation in homologs of the Top6BL component of the core complex.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-20DOI: 10.1038/s41594-024-01391-7
Ying Zhang, Kaijing Chen, Seng Chuan Tang, Yichao Cai, Akiko Nambu, Yi Xiang See, Chaoyu Fu, Anandhkumar Raju, Benjamin Lebeau, Zixun Ling, Jia Jia Chan, Yvonne Tay, Marek Mutwil, Manikandan Lakshmanan, Greg Tucker-Kellogg, Wee Joo Chng, Daniel G. Tenen, Motomi Osato, Vinay Tergaonkar, Melissa Jane Fullwood
Human silencers have been shown to regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form ‘super-silencers’ and whether they are linked to cancer progression. Here, we show two silencer components of the FGF18 gene can cooperate through compensatory chromatin interactions to form a super-silencer. Double knockout of two silencers exhibited synergistic upregulation of FGF18 expression and changes in cell identity. To perturb the super-silencers, we applied combinational treatment of an enhancer of zeste homolog 2 inhibitor GSK343, and a repressor element 1-silencing transcription factor inhibitor, X5050 (‘GR’). Interestingly, GR led to severe loss of topologically associated domains and loops, which were associated with reduced CTCF and TOP2A mRNA levels. Moreover, GR synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects in vivo. Overall, our data demonstrated a super-silencer example and showed that GR can disrupt super-silencers, potentially leading to cancer ablation.
{"title":"Super-silencer perturbation by EZH2 and REST inhibition leads to large loss of chromatin interactions and reduction in cancer growth","authors":"Ying Zhang, Kaijing Chen, Seng Chuan Tang, Yichao Cai, Akiko Nambu, Yi Xiang See, Chaoyu Fu, Anandhkumar Raju, Benjamin Lebeau, Zixun Ling, Jia Jia Chan, Yvonne Tay, Marek Mutwil, Manikandan Lakshmanan, Greg Tucker-Kellogg, Wee Joo Chng, Daniel G. Tenen, Motomi Osato, Vinay Tergaonkar, Melissa Jane Fullwood","doi":"10.1038/s41594-024-01391-7","DOIUrl":"https://doi.org/10.1038/s41594-024-01391-7","url":null,"abstract":"<p>Human silencers have been shown to regulate developmental gene expression. However, the functional importance of human silencers needs to be elucidated, such as whether they can form ‘super-silencers’ and whether they are linked to cancer progression. Here, we show two silencer components of the <i>FGF18</i> gene can cooperate through compensatory chromatin interactions to form a super-silencer. Double knockout of two silencers exhibited synergistic upregulation of <i>FGF18</i> expression and changes in cell identity. To perturb the super-silencers, we applied combinational treatment of an enhancer of zeste homolog 2 inhibitor GSK343, and a repressor element 1-silencing transcription factor inhibitor, X5050 (‘GR’). Interestingly, GR led to severe loss of topologically associated domains and loops, which were associated with reduced <i>CTCF</i> and <i>TOP2A</i> mRNA levels. Moreover, GR synergistically upregulated super-silencer-controlled genes related to cell cycle, apoptosis and DNA damage, leading to anticancer effects in vivo. Overall, our data demonstrated a super-silencer example and showed that GR can disrupt super-silencers, potentially leading to cancer ablation.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142276078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-19DOI: 10.1038/s41594-024-01395-3
Selene Sellés-Baiget, Sara M. Ambjørn, Alberto Carli, Ivo A. Hendriks, Irene Gallina, Norman E. Davey, Bente Benedict, Alessandra Zarantonello, Sampath A. Gadi, Bob Meeusen, Emil P. T. Hertz, Laura Slappendel, Daniel Semlow, Shana Sturla, Michael L. Nielsen, Jakob Nilsson, Thomas C. R. Miller, Julien P. Duxin
Translesion DNA synthesis (TLS) is a cellular process that enables the bypass of DNA lesions encountered during DNA replication and is emerging as a primary target of chemotherapy. Among vertebrate DNA polymerases, polymerase κ (Polκ) has the distinctive ability to bypass minor groove DNA adducts in vitro. However, Polκ is also required for cells to overcome major groove DNA adducts but the basis of this requirement is unclear. Here, we combine CRISPR base-editor screening technology in human cells with TLS analysis of defined DNA lesions in Xenopus egg extracts to unravel the functions and regulations of Polκ during lesion bypass. Strikingly, we show that Polκ has two main functions during TLS, which are differentially regulated by Rev1 binding. On the one hand, Polκ is essential to replicate across a minor groove DNA lesion in a process that depends on PCNA ubiquitylation but is independent of Rev1. On the other hand, through its cooperative interaction with Rev1 and ubiquitylated PCNA, Polκ appears to stabilize the Rev1–Polζ extension complex on DNA to allow extension past major groove DNA lesions and abasic sites, in a process that is independent of Polκ’s catalytic activity. Together, our work identifies catalytic and noncatalytic functions of Polκ in TLS and reveals important regulatory mechanisms underlying the unique domain architecture present at the C-terminal end of Y-family TLS polymerases.
转座DNA合成(TLS)是一个细胞过程,它能绕过DNA复制过程中遇到的DNA病变,并逐渐成为化疗的一个主要靶点。在脊椎动物的DNA聚合酶中,聚合酶κ(Polκ)具有绕过体外小沟DNA加合物的独特能力。然而,细胞也需要 Polκ 来克服主沟 DNA 加合物,但这一要求的基础尚不清楚。在这里,我们将人体细胞中的CRISPR碱基编辑器筛选技术与爪蟾卵提取物中定义的DNA病变的TLS分析相结合,揭示了Polκ在病变旁路过程中的功能和调控。令人震惊的是,我们发现 Polκ 在 TLS 期间有两种主要功能,它们受 Rev1 结合的调控不同。一方面,Polκ对于跨越小沟DNA病变的复制至关重要,这一过程依赖于PCNA泛素化,但与Rev1无关。另一方面,通过与 Rev1 和泛素化 PCNA 的合作作用,Polκ 似乎能稳定 DNA 上的 Rev1-Polζ 延伸复合物,使其延伸穿过主沟 DNA 病变和缺失位点,这一过程与 Polκ 的催化活性无关。总之,我们的工作确定了 Polκ 在 TLS 中的催化和非催化功能,并揭示了 Y-家族 TLS 聚合酶 C 端独特结构域的重要调控机制。
{"title":"Catalytic and noncatalytic functions of DNA polymerase κ in translesion DNA synthesis","authors":"Selene Sellés-Baiget, Sara M. Ambjørn, Alberto Carli, Ivo A. Hendriks, Irene Gallina, Norman E. Davey, Bente Benedict, Alessandra Zarantonello, Sampath A. Gadi, Bob Meeusen, Emil P. T. Hertz, Laura Slappendel, Daniel Semlow, Shana Sturla, Michael L. Nielsen, Jakob Nilsson, Thomas C. R. Miller, Julien P. Duxin","doi":"10.1038/s41594-024-01395-3","DOIUrl":"https://doi.org/10.1038/s41594-024-01395-3","url":null,"abstract":"<p>Translesion DNA synthesis (TLS) is a cellular process that enables the bypass of DNA lesions encountered during DNA replication and is emerging as a primary target of chemotherapy. Among vertebrate DNA polymerases, polymerase κ (Polκ) has the distinctive ability to bypass minor groove DNA adducts in vitro. However, Polκ is also required for cells to overcome major groove DNA adducts but the basis of this requirement is unclear. Here, we combine CRISPR base-editor screening technology in human cells with TLS analysis of defined DNA lesions in <i>Xenopus</i> egg extracts to unravel the functions and regulations of Polκ during lesion bypass. Strikingly, we show that Polκ has two main functions during TLS, which are differentially regulated by Rev1 binding. On the one hand, Polκ is essential to replicate across a minor groove DNA lesion in a process that depends on PCNA ubiquitylation but is independent of Rev1. On the other hand, through its cooperative interaction with Rev1 and ubiquitylated PCNA, Polκ appears to stabilize the Rev1–Polζ extension complex on DNA to allow extension past major groove DNA lesions and abasic sites, in a process that is independent of Polκ’s catalytic activity. Together, our work identifies catalytic and noncatalytic functions of Polκ in TLS and reveals important regulatory mechanisms underlying the unique domain architecture present at the C-terminal end of Y-family TLS polymerases.</p>","PeriodicalId":18822,"journal":{"name":"Nature structural & molecular biology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142245303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}