Pub Date : 2024-10-09DOI: 10.1016/j.molcel.2024.09.016
Chiara Grelloni, Raffaele Garraffo, Adriano Setti, Francesca Rossi, Giovanna Peruzzi, Mario Cinquanta, Maria Carmela Di Rosa, Marco Alessandro Pierotti, Manuel Beltran, Irene Bozzoni
Circular RNAs (circRNAs) are covalently closed RNA molecules widely expressed in eukaryotes and deregulated in several pathologies, including cancer. Many studies point to their activity as microRNAs (miRNAs) and protein sponges; however, we propose a function based on circRNA-mRNA interaction to regulate mRNA fate. We show that the widely tumor-associated circHIPK3 directly interacts in vivo with the BRCA1 mRNA through the back-splicing region in human cancer cells. This interaction increases BRCA1 translation by competing for the binding of the fragile-X mental retardation 1 protein (FMRP) protein, which we identified as a BRCA1 translational repressor. CircHIPK3 depletion or disruption of the circRNA-mRNA interaction decreases BRCA1 protein levels and increases DNA damage, sensitizing several cancer cells to DNA-damage-inducing agents and rendering them susceptible to synthetic lethality. Additionally, blocking FMRP interaction with BRCA1 mRNA with locked nucleic acid (LNA) restores physiological protein levels in BRCA1 hemizygous breast cancer cells, underscoring the importance of this circRNA-mRNA interaction in regulating DNA-damage response.
{"title":"BRCA1 levels and DNA-damage response are controlled by the competitive binding of circHIPK3 or FMRP to the BRCA1 mRNA","authors":"Chiara Grelloni, Raffaele Garraffo, Adriano Setti, Francesca Rossi, Giovanna Peruzzi, Mario Cinquanta, Maria Carmela Di Rosa, Marco Alessandro Pierotti, Manuel Beltran, Irene Bozzoni","doi":"10.1016/j.molcel.2024.09.016","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.09.016","url":null,"abstract":"Circular RNAs (circRNAs) are covalently closed RNA molecules widely expressed in eukaryotes and deregulated in several pathologies, including cancer. Many studies point to their activity as microRNAs (miRNAs) and protein sponges; however, we propose a function based on circRNA-mRNA interaction to regulate mRNA fate. We show that the widely tumor-associated <em>circHIPK3</em> directly interacts <em>in vivo</em> with the <em>BRCA1</em> mRNA through the back-splicing region in human cancer cells. This interaction increases <em>BRCA1</em> translation by competing for the binding of the fragile-X mental retardation 1 protein (FMRP) protein, which we identified as a <em>BRCA1</em> translational repressor. <em>CircHIPK3</em> depletion or disruption of the circRNA-mRNA interaction decreases BRCA1 protein levels and increases DNA damage, sensitizing several cancer cells to DNA-damage-inducing agents and rendering them susceptible to synthetic lethality. Additionally, blocking FMRP interaction with <em>BRCA1</em> mRNA with locked nucleic acid (LNA) restores physiological protein levels in BRCA1 hemizygous breast cancer cells, underscoring the importance of this circRNA-mRNA interaction in regulating DNA-damage response.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"57 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142385959","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}
Pub Date : 2024-10-08DOI: 10.1016/j.molcel.2024.09.018
Evgeny Deforzh, Prakash Kharel, Yanhong Zhang, Anton Karelin, Abdellatif El Khayari, Pavel Ivanov, Anna M. Krichevsky
The role of long non-coding RNAs (lncRNAs) in malignant cell transformation remains elusive. We previously identified an enhancer-associated lncRNA, LINC01116 (named HOXDeRNA), as a transformative factor converting human astrocytes into glioma-like cells. Employing a combination of CRISPR editing, chromatin isolation by RNA purification coupled with sequencing (ChIRP-seq), in situ mapping RNA-genome interactions (iMARGI), chromatin immunoprecipitation sequencing (ChIP-seq), HiC, and RNA/DNA FISH, we found that HOXDeRNA directly binds to CpG islands within the promoters of 35 glioma-specific transcription factors (TFs) distributed throughout the genome, including key stem cell TFs SOX2, OLIG2, POU3F2, and ASCL1, liberating them from PRC2 repression. This process requires a distinct RNA quadruplex structure and other segments of HOXDeRNA, interacting with EZH2 and CpGs, respectively. Subsequent transformation activates multiple oncogenes (e.g., EGFR, miR-21, and WEE1), driven by the SOX2- and OLIG2-dependent glioma-specific super enhancers. These results help reconstruct the sequence of events underlying the process of astrocyte transformation, highlighting HOXDeRNA’s central genome-wide activity and suggesting a shared RNA-dependent mechanism in otherwise heterogeneous and multifactorial gliomagenesis.
{"title":"HOXDeRNA activates a cancerous transcription program and super enhancers via genome-wide binding","authors":"Evgeny Deforzh, Prakash Kharel, Yanhong Zhang, Anton Karelin, Abdellatif El Khayari, Pavel Ivanov, Anna M. Krichevsky","doi":"10.1016/j.molcel.2024.09.018","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.09.018","url":null,"abstract":"The role of long non-coding RNAs (lncRNAs) in malignant cell transformation remains elusive. We previously identified an enhancer-associated lncRNA, LINC01116 (named HOXDeRNA), as a transformative factor converting human astrocytes into glioma-like cells. Employing a combination of CRISPR editing, chromatin isolation by RNA purification coupled with sequencing (ChIRP-seq), <em>in situ</em> mapping RNA-genome interactions (iMARGI), chromatin immunoprecipitation sequencing (ChIP-seq), HiC, and RNA/DNA FISH, we found that HOXDeRNA directly binds to CpG islands within the promoters of 35 glioma-specific transcription factors (TFs) distributed throughout the genome, including key stem cell TFs SOX2, OLIG2, POU3F2, and ASCL1, liberating them from PRC2 repression. This process requires a distinct RNA quadruplex structure and other segments of HOXDeRNA, interacting with EZH2 and CpGs, respectively. Subsequent transformation activates multiple oncogenes (e.g., EGFR, miR-21, and WEE1), driven by the SOX2- and OLIG2-dependent glioma-specific super enhancers. These results help reconstruct the sequence of events underlying the process of astrocyte transformation, highlighting HOXDeRNA’s central genome-wide activity and suggesting a shared RNA-dependent mechanism in otherwise heterogeneous and multifactorial gliomagenesis.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"51 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142384292","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}
Pub Date : 2024-10-08DOI: 10.1016/j.molcel.2024.09.020
Xiaohui Lin, Dipika Gupta, Alina Vaitsiankova, Seema Khattri Bhandari, Kay Sze Karina Leung, Demis Menolfi, Brian J. Lee, Helen R. Russell, Steven Gershik, Xiaoyu Huang, Wei Gu, Peter J. McKinnon, Françoise Dantzer, Eli Rothenberg, Alan E. Tomkinson, Shan Zha
Poly (ADP-ribose) polymerase (PARP) 1 and 2 enzymatic inhibitors (PARPi) are promising cancer treatments. But recently, their use has been hindered by unexplained severe anemia and treatment-related leukemia. In addition to enzymatic inhibition, PARPi also trap PARP1 and 2 at DNA lesions. Here we report that, unlike Parp2−/− mice, which develop normally, mice expressing catalytically inactive Parp2 (E534A and Parp2EA/EA) succumb to Tp53- and Chk2-dependent erythropoietic failure in utero, mirroring Lig1−/− mice. While DNA damage mainly activates PARP1, we demonstrate that DNA replication activates PARP2 robustly. PARP2 is selectively recruited and activated by 5′-phosphorylated nicks (5′p-nicks), including those between Okazaki fragments, resolved by ligase 1 (Lig1) and Lig3. Inactive PARP2, but not its active form or absence, impedes Lig1- and Lig3-mediated ligation, causing dose-dependent replication fork collapse, which is detrimental to erythroblasts with ultra-fast forks. This PARylation-dependent structural function of PARP2 at 5′p-nicks explains the detrimental effects of PARP2 inactivation on erythropoiesis, shedding light on PARPi-induced anemia and the selection for TP53/CHK2 loss.
{"title":"Inactive Parp2 causes Tp53-dependent lethal anemia by blocking replication-associated nick ligation in erythroblasts","authors":"Xiaohui Lin, Dipika Gupta, Alina Vaitsiankova, Seema Khattri Bhandari, Kay Sze Karina Leung, Demis Menolfi, Brian J. Lee, Helen R. Russell, Steven Gershik, Xiaoyu Huang, Wei Gu, Peter J. McKinnon, Françoise Dantzer, Eli Rothenberg, Alan E. Tomkinson, Shan Zha","doi":"10.1016/j.molcel.2024.09.020","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.09.020","url":null,"abstract":"Poly (ADP-ribose) polymerase (PARP) 1 and 2 enzymatic inhibitors (PARPi) are promising cancer treatments. But recently, their use has been hindered by unexplained severe anemia and treatment-related leukemia. In addition to enzymatic inhibition, PARPi also trap PARP1 and 2 at DNA lesions. Here we report that, unlike <em>Parp2</em><sup><em>−/−</em></sup> mice, which develop normally, mice expressing catalytically inactive Parp2 (E534A and <em>Parp2</em><sup><em>EA/EA</em></sup>) succumb to <em>Tp53</em>- and <em>Chk2</em>-dependent erythropoietic failure <em>in utero</em>, mirroring <em>Lig1</em><sup><em>−/−</em></sup> mice. While DNA damage mainly activates PARP1, we demonstrate that DNA replication activates PARP2 robustly. PARP2 is selectively recruited and activated by 5′-phosphorylated nicks (5′p-nicks), including those between Okazaki fragments, resolved by ligase 1 (Lig1) and Lig3. Inactive PARP2, but not its active form or absence, impedes Lig1- and Lig3-mediated ligation, causing dose-dependent replication fork collapse, which is detrimental to erythroblasts with ultra-fast forks. This PARylation-dependent structural function of PARP2 at 5′p-nicks explains the detrimental effects of PARP2 inactivation on erythropoiesis, shedding light on PARPi-induced anemia and the selection for TP53/CHK2 loss.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"14 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142384289","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}
Pub Date : 2024-10-04DOI: 10.1016/j.molcel.2024.09.015
Joydeb Sinha, Jan F. Nickels, Abby R. Thurm, Connor H. Ludwig, Bella N. Archibald, Michaela M. Hinks, Jun Wan, Dong Fang, Lacramioara Bintu
Histone H3.3 is frequently mutated in tumors, with the lysine 36 to methionine mutation (K36M) being a hallmark of chondroblastomas. While it is known that H3.3K36M changes the epigenetic landscape, its effects on gene expression dynamics remain unclear. Here, we use a synthetic reporter to measure the effects of H3.3K36M on silencing and epigenetic memory after recruitment of the ZNF10 Krüppel-associated box (KRAB) domain, part of the largest class of human repressors and associated with H3K9me3 deposition. We find that H3.3K36M, which decreases H3K36 methylation and increases histone acetylation, leads to a decrease in epigenetic memory and promoter methylation weeks after KRAB release. We propose a model for establishment and maintenance of epigenetic memory, where the H3K36 methylation pathway is necessary to maintain histone deacetylation and convert H3K9me3 domains into DNA methylation for stable epigenetic memory. Our quantitative model can inform oncogenic mechanisms and guide development of epigenetic editing tools.
{"title":"The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation","authors":"Joydeb Sinha, Jan F. Nickels, Abby R. Thurm, Connor H. Ludwig, Bella N. Archibald, Michaela M. Hinks, Jun Wan, Dong Fang, Lacramioara Bintu","doi":"10.1016/j.molcel.2024.09.015","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.09.015","url":null,"abstract":"Histone H3.3 is frequently mutated in tumors, with the lysine 36 to methionine mutation (K36M) being a hallmark of chondroblastomas. While it is known that H3.3K36M changes the epigenetic landscape, its effects on gene expression dynamics remain unclear. Here, we use a synthetic reporter to measure the effects of H3.3K36M on silencing and epigenetic memory after recruitment of the ZNF10 Krüppel-associated box (KRAB) domain, part of the largest class of human repressors and associated with H3K9me3 deposition. We find that H3.3K36M, which decreases H3K36 methylation and increases histone acetylation, leads to a decrease in epigenetic memory and promoter methylation weeks after KRAB release. We propose a model for establishment and maintenance of epigenetic memory, where the H3K36 methylation pathway is necessary to maintain histone deacetylation and convert H3K9me3 domains into DNA methylation for stable epigenetic memory. Our quantitative model can inform oncogenic mechanisms and guide development of epigenetic editing tools.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"51 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374104","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}
Pub Date : 2024-10-04DOI: 10.1016/j.molcel.2024.09.008
Ankur Garg, Renfu Shang, Todor Cvetanovic, Eric C. Lai, Leemor Joshua-Tor
MicroRNA (miRNA) biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by the Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryoelectron microscopy (cryo-EM) and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has the structural plasticity to accommodate a range of pri-miRNAs. These structures revealed key features of the 5′ UG sequence motif, more comprehensively represented as the “flipped U with paired N” (fUN) motif. Our analysis explains how cleavage of class-II pri-let-7 members harboring a bulged nucleotide generates a non-canonical precursor with a 1-nt 3′ overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 contributes to MP fidelity by interacting with the CNNC motif and Drosha’s Piwi/Argonaute/Zwille (PAZ)-like domain. Overall, this study sheds light on the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.
由 Drosha RNase III 酶及其伙伴 DGCR8 组成的微处理器（MP）对初级 miRNA（pri-miRNA）发夹进行切割后，就开始了微 RNA（miRNA）的生物生成。多种 pri-miRNA 序列基序会影响 MP 的识别、保真度和效率。在这里，我们对几种与人类 MP 复合的 let-7 家族 pri-miRNA 进行了冷冻电子显微镜（cryo-EM）和生化研究。我们发现 MP 具有结构可塑性，可以容纳一系列 pri-miRNA。这些结构揭示了 5′ UG 序列基序的关键特征，更全面地表述为 "带成对 N 的翻转 U"（fUN）基序。我们的分析解释了携带凸起核苷酸的 II 类 pri-let-7 成员如何通过裂解产生具有 1-nt 3′ 悬垂的非经典前体。最后，MP-SRSF3-pri-let-7f1结构揭示了SRSF3如何通过与CNNC基序和Drosha的Piwi/Argonaute/Zwille（PAZ）样结构域相互作用来促进MP的保真度。总之，这项研究揭示了 MP 灵活识别、准确切割和调控处理不同 pri-miRNA 的机制。
{"title":"The structural landscape of Microprocessor-mediated processing of pri-let-7 miRNAs","authors":"Ankur Garg, Renfu Shang, Todor Cvetanovic, Eric C. Lai, Leemor Joshua-Tor","doi":"10.1016/j.molcel.2024.09.008","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.09.008","url":null,"abstract":"MicroRNA (miRNA) biogenesis is initiated upon cleavage of a primary miRNA (pri-miRNA) hairpin by the Microprocessor (MP), composed of the Drosha RNase III enzyme and its partner DGCR8. Multiple pri-miRNA sequence motifs affect MP recognition, fidelity, and efficiency. Here, we performed cryoelectron microscopy (cryo-EM) and biochemical studies of several let-7 family pri-miRNAs in complex with human MP. We show that MP has the structural plasticity to accommodate a range of pri-miRNAs. These structures revealed key features of the 5′ UG sequence motif, more comprehensively represented as the “flipped U with paired N” (fUN) motif. Our analysis explains how cleavage of class-II pri-let-7 members harboring a bulged nucleotide generates a non-canonical precursor with a 1-nt 3′ overhang. Finally, the MP-SRSF3-pri-let-7f1 structure reveals how SRSF3 contributes to MP fidelity by interacting with the CNNC motif and Drosha’s Piwi/Argonaute/Zwille (PAZ)-like domain. Overall, this study sheds light on the mechanisms for flexible recognition, accurate cleavage, and regulated processing of different pri-miRNAs by MP.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"9 8 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374106","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}
Pub Date : 2024-10-04DOI: 10.1016/j.molcel.2024.09.011
Adham Safieddine, Marie-Noëlle Benassy, Thomas Bonte, Floric Slimani, Oriane Pourcelot, Michel Kress, Michèle Ernoult-Lange, Maïté Courel, Emeline Coleno, Arthur Imbert, Antoine Laine, Annie Munier Godebert, Angelique Vinit, Corinne Blugeon, Guillaume Chevreux, Daniel Gautheret, Thomas Walter, Edouard Bertrand, Marianne Bénard, Dominique Weil
Understanding the dynamics of RNA targeting to membraneless organelles is essential to disentangle their functions. Here, we investigate how P-bodies (PBs) evolve during cell-cycle progression in HEK293 cells. PB purification across the cell cycle uncovers widespread changes in their RNA content, partly uncoupled from cell-cycle-dependent changes in RNA expression. Single-molecule fluorescence in situ hybridization (FISH) shows various mRNA localization patterns in PBs peaking in G1, S, or G2, with examples illustrating the timely capture of mRNAs in PBs when their encoded protein becomes dispensable. Rather than directly reflecting absence of translation, cyclic mRNA localization in PBs can be controlled by RBPs, such as HuR in G2, and by RNA features. Indeed, while PB mRNAs are AU rich at all cell-cycle phases, they are specifically longer in G1, possibly related to post-mitotic PB reassembly. Altogether, our study supports a model where PBs are more than a default location for excess untranslated mRNAs.
{"title":"Cell-cycle-dependent mRNA localization in P-bodies","authors":"Adham Safieddine, Marie-Noëlle Benassy, Thomas Bonte, Floric Slimani, Oriane Pourcelot, Michel Kress, Michèle Ernoult-Lange, Maïté Courel, Emeline Coleno, Arthur Imbert, Antoine Laine, Annie Munier Godebert, Angelique Vinit, Corinne Blugeon, Guillaume Chevreux, Daniel Gautheret, Thomas Walter, Edouard Bertrand, Marianne Bénard, Dominique Weil","doi":"10.1016/j.molcel.2024.09.011","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.09.011","url":null,"abstract":"Understanding the dynamics of RNA targeting to membraneless organelles is essential to disentangle their functions. Here, we investigate how P-bodies (PBs) evolve during cell-cycle progression in HEK293 cells. PB purification across the cell cycle uncovers widespread changes in their RNA content, partly uncoupled from cell-cycle-dependent changes in RNA expression. Single-molecule fluorescence <em>in situ</em> hybridization (FISH) shows various mRNA localization patterns in PBs peaking in G1, S, or G2, with examples illustrating the timely capture of mRNAs in PBs when their encoded protein becomes dispensable. Rather than directly reflecting absence of translation, cyclic mRNA localization in PBs can be controlled by RBPs, such as HuR in G2, and by RNA features. Indeed, while PB mRNAs are AU rich at all cell-cycle phases, they are specifically longer in G1, possibly related to post-mitotic PB reassembly. Altogether, our study supports a model where PBs are more than a default location for excess untranslated mRNAs.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"207 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142374105","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}
Pub Date : 2024-10-03DOI: 10.1016/j.molcel.2024.08.019
Li Yang, Igor Ulitsky, Wendy V. Gilbert, Chengqi Yi, Jernej Ule, Maïwen Caudron-Herger
High-throughput sequencing methods have led to the discovery of many non-coding RNAs, RNA modifications, and protein-RNA interactions. While the list keeps growing, the challenge of determining their functions remains. For our focus issue on RNA biology, we spoke with several researchers about their perspective on investigating the functions of RNA.
{"title":"The challenges of investigating RNA function","authors":"Li Yang, Igor Ulitsky, Wendy V. Gilbert, Chengqi Yi, Jernej Ule, Maïwen Caudron-Herger","doi":"10.1016/j.molcel.2024.08.019","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.08.019","url":null,"abstract":"High-throughput sequencing methods have led to the discovery of many non-coding RNAs, RNA modifications, and protein-RNA interactions. While the list keeps growing, the challenge of determining their functions remains. For our <span><span>focus issue on RNA biology</span><svg aria-label=\"Opens in new window\" focusable=\"false\" height=\"20\" viewbox=\"0 0 8 8\"><path d=\"M1.12949 2.1072V1H7V6.85795H5.89111V2.90281L0.784057 8L0 7.21635L5.11902 2.1072H1.12949Z\"></path></svg></span>, we spoke with several researchers about their perspective on investigating the functions of RNA.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"54 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142369134","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}
Pub Date : 2024-10-03DOI: 10.1016/j.molcel.2024.09.010
Thomas R. Cech, Chen Davidovich, Richard G. Jenner
Diverse biochemical, structural, and in vivo data support models for the regulation of polycomb repressive complex 2 (PRC2) activity by RNAs, which may contribute to the maintenance of epigenetic states. Here, we summarize this research and also suggest why it can be difficult to capture biologically relevant PRC2-RNA interactions in living cells.
{"title":"PRC2-RNA interactions: Viewpoint from Tom Cech, Chen Davidovich, and Richard Jenner","authors":"Thomas R. Cech, Chen Davidovich, Richard G. Jenner","doi":"10.1016/j.molcel.2024.09.010","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.09.010","url":null,"abstract":"Diverse biochemical, structural, and <em>in vivo</em> data support models for the regulation of polycomb repressive complex 2 (PRC2) activity by RNAs, which may contribute to the maintenance of epigenetic states. Here, we summarize this research and also suggest why it can be difficult to capture biologically relevant PRC2-RNA interactions in living cells.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"77 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142369140","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}
Pub Date : 2024-10-03DOI: 10.1016/j.molcel.2024.09.005
Gable M. Wadsworth, Sukanya Srinivasan, Lien B. Lai, Moulisubhro Datta, Venkat Gopalan, Priya R. Banerjee
RNAs and RNA-binding proteins can undergo spontaneous or active condensation into phase-separated liquid-like droplets. These condensates are cellular hubs for various physiological processes, and their dysregulation leads to diseases. Although RNAs are core components of many cellular condensates, the underlying molecular determinants for the formation, regulation, and function of ribonucleoprotein condensates have largely been studied from a protein-centric perspective. Here, we highlight recent developments in ribonucleoprotein condensate biology with a particular emphasis on RNA-driven phase transitions. We also present emerging future directions that might shed light on the role of RNA condensates in spatiotemporal regulation of cellular processes and inspire bioengineering of RNA-based therapeutics.
{"title":"RNA-driven phase transitions in biomolecular condensates","authors":"Gable M. Wadsworth, Sukanya Srinivasan, Lien B. Lai, Moulisubhro Datta, Venkat Gopalan, Priya R. Banerjee","doi":"10.1016/j.molcel.2024.09.005","DOIUrl":"https://doi.org/10.1016/j.molcel.2024.09.005","url":null,"abstract":"RNAs and RNA-binding proteins can undergo spontaneous or active condensation into phase-separated liquid-like droplets. These condensates are cellular hubs for various physiological processes, and their dysregulation leads to diseases. Although RNAs are core components of many cellular condensates, the underlying molecular determinants for the formation, regulation, and function of ribonucleoprotein condensates have largely been studied from a protein-centric perspective. Here, we highlight recent developments in ribonucleoprotein condensate biology with a particular emphasis on RNA-driven phase transitions. We also present emerging future directions that might shed light on the role of RNA condensates in spatiotemporal regulation of cellular processes and inspire bioengineering of RNA-based therapeutics.","PeriodicalId":18950,"journal":{"name":"Molecular Cell","volume":"12 1","pages":""},"PeriodicalIF":16.0,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142369674","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}
Pub Date : 2024-10-03DOI: 10.1016/j.molcel.2024.09.012
David Dierks, Schraga Schwartz
In this issue of Molecular Cell, Tang et al. suggest that m6A deposition is predominantly post-transcriptional.1 They further propose that nuclear dwell time dictates the post-transcriptional accumulation of m6A. These findings have important implications for m6A biogenesis and function.
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