Nucleic Acids Research最新文献

The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-20 DOI: 10.1093/nar/gkaf094

Shivlee Nirwal, Ritika Jha, Naveen Narayanan, Minakshi Sharma, Dhananjaya S Kulkarni, Dalchand Sharma, Amith S Babu, Dhiraj K Suthar, Desirazu N Rao, Deepak T Nair

{"title":"The structure of the MutL-CTD:processivity-clamp complex provides insight regarding strand discrimination in non-methyl-directed DNA mismatch repair","authors":"Shivlee Nirwal, Ritika Jha, Naveen Narayanan, Minakshi Sharma, Dhananjaya S Kulkarni, Dalchand Sharma, Amith S Babu, Dhiraj K Suthar, Desirazu N Rao, Deepak T Nair","doi":"10.1093/nar/gkaf094","DOIUrl":"https://doi.org/10.1093/nar/gkaf094","url":null,"abstract":"Many prokaryotes, including members of the Neisseria species, lack MutH and cannot employ methyl-directed DNA mismatch repair (MMR). The nick on the daughter strand is created by the endonuclease activity present in the C-terminal domain (CTD) of the MutL homodimer. MutL-CTD is known to interact with the processivity-clamp. The crystal structure of the homodimeric MutL-CTD from Neisseria (NgoL-CTD) in complex with homodimeric processivity-clamp (Nβ-Clamp) shows that each NgoL-CTD monomer binds to a Nβ-Clamp monomer through the conserved motif III (517QHLLIP522). The structure and allied biochemical studies plus in vivo growth assays conducted with wild-type (wt) plus mutant proteins shows that the endonuclease dimer sits transversely across the C-terminal face of the Nβ-Clamp ring. The comparison of the structure with that of the partial prokaryotic replisome suggests that the relative orientation of DNA, Nβ-Clamp, and NgoL-CTD may direct the daughter strand towards one of the active sites in endonuclease homodimer. Nicking assays conducted with wt and mutant NgoL-CTD in the presence and absence of Nβ-Clamp support this inference. Overall, our studies posit that strand discrimination in non-methyl-directed MMR is achieved through a structural strategy involving the β-Clamp which is distinct from the chemical strategy employed in prokaryotes like Escherichia coli.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"25 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462866","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}

引用次数: 0

The NEXT complex regulates H3K27me3 levels to affect cancer progression by degrading G4/U-rich lncRNAs

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-20 DOI: 10.1093/nar/gkaf107

Qianqian Yang, Zihan Zhou, Lian Li, Runhui Lu, Guofang Hou, Caihu Huang, Jiayi Huang, Hongyan Li, Yafan Zhang, Junya Li, Yixin Zhang, Anan Xu, Ran Chen, Yanli Wang, Xian Zhao, Jian Huang, Yiwei Wang, Xiaojing Zhao, Jianxiu Yu

{"title":"The NEXT complex regulates H3K27me3 levels to affect cancer progression by degrading G4/U-rich lncRNAs","authors":"Qianqian Yang, Zihan Zhou, Lian Li, Runhui Lu, Guofang Hou, Caihu Huang, Jiayi Huang, Hongyan Li, Yafan Zhang, Junya Li, Yixin Zhang, Anan Xu, Ran Chen, Yanli Wang, Xian Zhao, Jian Huang, Yiwei Wang, Xiaojing Zhao, Jianxiu Yu","doi":"10.1093/nar/gkaf107","DOIUrl":"https://doi.org/10.1093/nar/gkaf107","url":null,"abstract":"Polycomb repressive complex 2 (PRC2) is responsible for depositing H3K27me3 and plays essential roles in gene silencing during development and cancer. Meanwhile, the nuclear exosome targeting (NEXT) complex facilitates the degradation of numerous noncoding RNAs in the nucleoplasm. Here we find that the functional deficiency of the NEXT complex leads to an overall decrease in H3K27me3 levels. Specifically, ZCCHC8 depletion results in significant upregulation of nascent long noncoding RNAs (lncRNAs) containing G-quadruplex (G4) and U-Rich motifs (G4/U-Rich lncRNAs). The G4 motif binds to EZH2, blocking the chromatin recruitment of PRC2, while the U-Rich motif is specifically recognized by the NEXT complex for RNA exosome-mediated degradation. In tumor tissues with high ZCCHC8 expression in clear cell renal cell carcinoma (ccRCC) and lung adenocarcinoma (LUAD) patients, the NEXT complex excessively degrades nascent G4/U-Rich lncRNAs. Consequently, PRC2 core subunits are released and recruited to neighboring genomic loci, resulting in increased H3K27me3 levels and downregulation of adjacent genes, including tumor suppressors like SEMA5A and ARID1A. Notably, the EZH2 inhibitor Tazemetostat (EPZ-6438) exhibits greater sensitivity in cells with higher ZCCHC8 expression. Altogether, our findings demonstrate a novel mechanism that the NEXT complex regulates H3K27me3 levels by degrading nascent G4/U-Rich lncRNAs in cancer cells.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"50 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462867","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}

引用次数: 0

Evolving a terminal deoxynucleotidyl transferase for commercial enzymatic DNA synthesis

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-20 DOI: 10.1093/nar/gkaf115

Stephanie M Forget, Mikayla J Krawczyk, Anders M Knight, Charlene Ching, Rachelle A Copeland, Niusha Mahmoodi, Melissa A Mayo, James Nguyen, Amanda Tan, Mathew Miller, Jonathan Vroom, Stefan Lutz

{"title":"Evolving a terminal deoxynucleotidyl transferase for commercial enzymatic DNA synthesis","authors":"Stephanie M Forget, Mikayla J Krawczyk, Anders M Knight, Charlene Ching, Rachelle A Copeland, Niusha Mahmoodi, Melissa A Mayo, James Nguyen, Amanda Tan, Mathew Miller, Jonathan Vroom, Stefan Lutz","doi":"10.1093/nar/gkaf115","DOIUrl":"https://doi.org/10.1093/nar/gkaf115","url":null,"abstract":"Enzymatic DNA synthesis, using stepwise nucleotide addition catalyzed by template-independent polymerases, promises higher efficiency, quality, and sustainability than today’s industry-standard phosphoramidite-based processes. We report the directed evolution of a terminal deoxynucleotidyl transferase that uses 3′-phosphate-blocked 2′-deoxynucleoside triphosphates (dNTPs) to control the polymerization reaction. Over 32 iterative rounds of laboratory evolution, 80 amino acid substitutions—constituting ∼20% of the coding protein sequence—were introduced. The engineered polymerase exhibits uniformly high catalytic activity, raising incorporation efficiency by 200-fold to &gt;99% for dNTPs with a 3′-reversible terminator while reducing extension times by &gt;600-fold to 90 s. The same enzyme variant displays improved enzyme robustness, as reflected in the 20°C increase in thermostability. Based on these performance characteristics, the engineered polymerase represents an operational prototype for biocatalytic DNA synthesis at a commercial scale.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"65 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462865","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}

引用次数: 0

Virus-derived siRNA: Coronavirus and influenza virus trigger antiviral RNAi immunity in birds

IF 14.9 2区生物学

Nucleic Acids Research Pub Date : 2025-02-20 DOI: 10.1093/nar/gkaf116

Yaotang Wu, Peng Liu, Jie Zhou, Mei Fu, Chenlu Wang, Ningna Xiong, Wenxin Ji, Zhisheng Wang, Jian Lin, Qian Yang

{"title":"Virus-derived siRNA: Coronavirus and influenza virus trigger antiviral RNAi immunity in birds","authors":"Yaotang Wu, Peng Liu, Jie Zhou, Mei Fu, Chenlu Wang, Ningna Xiong, Wenxin Ji, Zhisheng Wang, Jian Lin, Qian Yang","doi":"10.1093/nar/gkaf116","DOIUrl":"https://doi.org/10.1093/nar/gkaf116","url":null,"abstract":"RNA interference (RNAi) is a key antiviral immune mechanism in eukaryotes. However, antiviral RNAi in vertebrates has only been observed in cells with poor interferon systems or in viral suppressors of RNAi (VSR) deficiency virus infections. Our research discovered that infecting macrophages with wild-type coronavirus (Infectious bronchitis virus, IBV) and influenza viruses (Avian influenza virus, AIV) can trigger RNAi antiviral immunity and produce a certain amount of virus-derived siRNA (vsiRNA). These vsiRNAs have an inhibitory effect on the virus and carry out targeted silencing along the Dicer-Ago2-vsiRNA axis. Notably, these vsiRNAs are distributed throughout the virus's entire genome, with a predilection for A/U at the 5′ and 3′ termini of vsiRNA. In addition, Dicer cleavage produces vsiRNA based on the RWM motif, where R represents A/G, W represents A/C, and M represents A/U. We also discovered that avian LGP2 and MDA5 proteins positively impact the expression of the Dicer protein and the Dicer subtype “DicerM.” Most importantly, the PS-vsiRNA plasmid combined with nanomaterial polyetherimide (PEI) showed excellent anti-virus activity in specific-pathogen-free (SPF) chickens. These findings show that RNA viruses trigger the production of the vsiRNA in avian somatic cells, which is of great significance for the application of therapeutic vaccines.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"3 1","pages":""},"PeriodicalIF":14.9,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462873","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}

引用次数: 0

DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-02-08 DOI: 10.1093/nar/gkaf068

Valentina Frezza, Lidia Chellini, Veronica Riccioni, Davide Bonvissuto, Ramona Palombo, Maria Paola Paronetto

{"title":"DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells.","authors":"Valentina Frezza, Lidia Chellini, Veronica Riccioni, Davide Bonvissuto, Ramona Palombo, Maria Paola Paronetto","doi":"10.1093/nar/gkaf068","DOIUrl":"10.1093/nar/gkaf068","url":null,"abstract":"Ewing sarcomas (ESs) are biologically aggressive tumours of bone and soft tissues caused by chromosomal translocations yielding in-frame fusion proteins driving the neoplastic transformation. The DNA/RNA helicase DHX9 is an important regulator of cellular processes often deregulated in cancer. Using transcriptome profiling, our study reveals cancer-relevant genes whose splicing is modulated by DHX9. Immunodepletion experiments demonstrate that DHX9 impacts on the recruitment of U2 small nuclear RNP (snRNP) onto the pre-mRNA. Analysis of structure and sequence features of DHX9 target exons reveal that DHX9-sensitive exons display shorter flanking introns and contain HNRNPC and TIA1 consensus motifs. A prominent target of DHX9 is exon 11 in the Cortactin (CTTN) gene, which is alternatively spliced to generate isoforms with different activities in cell migration and tumour invasion. Alternative inclusion of the exon 11 in CTTN gene is one of the most recurrent isoform switches in multiple cancer types, thus highlighting the pivotal role of DHX9 in defining the tumour phenotype. Biochemical analyses reveal that DHX9 binding promotes the recruitment of U2snRNP, SF3B1, and SF3A2 to the splice sites flanking exon 11. These findings uncover a new role of DHX9 in the control of co-transcriptional splicing in ES, which may represent a new druggable target to counteract ES malignancy.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 4","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11826090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-02-08 DOI: 10.1093/nar/gkaf092

Lingjie Liu, Yixin Zhao, Rebecca Hassett, Shushan Toneyan, Peter K Koo, Adam Siepel

{"title":"Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.","authors":"Lingjie Liu, Yixin Zhao, Rebecca Hassett, Shushan Toneyan, Peter K Koo, Adam Siepel","doi":"10.1093/nar/gkaf092","DOIUrl":"10.1093/nar/gkaf092","url":null,"abstract":"Rates of transcription elongation vary within and across eukaryotic gene bodies. Here, we introduce new methods for predicting elongation rates from nascent RNA sequencing data. First, we devise a probabilistic model that predicts nucleotide-specific elongation rates as a generalized linear function of nearby genomic and epigenomic features. We validate this model with simulations and apply it to public PRO-seq (Precision Run-On Sequencing) and epigenomic data for four cell types, finding that reductions in local elongation rate are associated with cytosine nucleotides, DNA methylation, splice sites, RNA stem-loops, CTCF (CCCTC-binding factor) binding sites, and several histone marks, including H3K36me3 and H4K20me1. By contrast, increases in local elongation rate are associated with thymines, A+T-rich and low-complexity sequences, and H3K79me2 marks. We then introduce a convolutional neural network that improves our local rate predictions. Our analysis is the first to permit genome-wide predictions of relative nucleotide-specific elongation rates.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 4","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11833694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-02-08 DOI: 10.1093/nar/gkaf068

Valentina Frezza, Lidia Chellini, Veronica Riccioni, Davide Bonvissuto, Ramona Palombo, Maria Paola Paronetto

{"title":"DHX9 helicase impacts on splicing decisions by modulating U2 snRNP recruitment in Ewing sarcoma cells.","authors":"Valentina Frezza, Lidia Chellini, Veronica Riccioni, Davide Bonvissuto, Ramona Palombo, Maria Paola Paronetto","doi":"10.1093/nar/gkaf068","DOIUrl":"https://doi.org/10.1093/nar/gkaf068","url":null,"abstract":"Ewing sarcomas (ESs) are biologically aggressive tumours of bone and soft tissues caused by chromosomal translocations yielding in-frame fusion proteins driving the neoplastic transformation. The DNA/RNA helicase DHX9 is an important regulator of cellular processes often deregulated in cancer. Using transcriptome profiling, our study reveals cancer-relevant genes whose splicing is modulated by DHX9. Immunodepletion experiments demonstrate that DHX9 impacts on the recruitment of U2 small nuclear RNP (snRNP) onto the pre-mRNA. Analysis of structure and sequence features of DHX9 target exons reveal that DHX9-sensitive exons display shorter flanking introns and contain HNRNPC and TIA1 consensus motifs. A prominent target of DHX9 is exon 11 in the Cortactin (CTTN) gene, which is alternatively spliced to generate isoforms with different activities in cell migration and tumour invasion. Alternative inclusion of the exon 11 in CTTN gene is one of the most recurrent isoform switches in multiple cancer types, thus highlighting the pivotal role of DHX9 in defining the tumour phenotype. Biochemical analyses reveal that DHX9 binding promotes the recruitment of U2snRNP, SF3B1, and SF3A2 to the splice sites flanking exon 11. These findings uncover a new role of DHX9 in the control of co-transcriptional splicing in ES, which may represent a new druggable target to counteract ES malignancy.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 4","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458953","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}

引用次数: 0

Discovery of reversing enzymes for RNA ADP-ribosylation reveals a possible defence module against toxic attack.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-02-08 DOI: 10.1093/nar/gkaf069

Yang Lu, Marion Schuller, Nathan P Bullen, Petra Mikolcevic, Iva Zonjic, Roberto Raggiaschi, Andreja Mikoc, John C Whitney, Ivan Ahel

{"title":"Discovery of reversing enzymes for RNA ADP-ribosylation reveals a possible defence module against toxic attack.","authors":"Yang Lu, Marion Schuller, Nathan P Bullen, Petra Mikolcevic, Iva Zonjic, Roberto Raggiaschi, Andreja Mikoc, John C Whitney, Ivan Ahel","doi":"10.1093/nar/gkaf069","DOIUrl":"https://doi.org/10.1093/nar/gkaf069","url":null,"abstract":"Nucleic acid ADP-ribosylation and its associated enzymes involved in catalysis and hydrolysis are widespread among all kingdoms of life. Yet, its roles in mammalian and bacterial physiology including inter-/intraspecies conflicts are currently underexplored. Recently, several examples of enzymatic systems for RNA ADP-ribosylation have been identified, showing that all major types of RNA species, including messenger RNA, ribosomal RNA, and transfer RNA, can be targeted by ADP-ribosyltransferases (ARTs) which attach ADP-ribose modifications either to nucleobases, the backbone ribose, or phosphate ends. Yet little is known about the reversibility of RNA ADP-ribosylation by ADP-ribosylhydrolases belonging to the macrodomain, ARH, or NADAR superfamilies. Here, we characterize the hydrolytic activity of ADP-ribosylhydrolases on RNA species ADP-ribosylated by mammalian and bacterial ARTs. We demonstrate that NADAR ADP-ribosylhydrolases are the only hydrolase family able to reverse guanosine RNA base ADP-ribosylation while they are inactive on phosphate-end RNA ADP-ribosylation. Furthermore, we reveal that macrodomain-containing PARG enzymes are the only hydrolase type with the ability for specific and efficient reversal of 2'-hydroxyl group RNA ADP-ribosylation catalysed by Pseudomonas aeruginosa effector toxin RhsP2. Moreover, using the RhsP2/bacterial PARG system as an example, we demonstrate that PARG enzymes can act as protective immunity enzymes against antibacterial RNA-targeting ART toxins.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 4","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458958","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}

引用次数: 0

NEAT1-mediated regulation of proteostasis and mRNA localization impacts autophagy dysregulation in Rett syndrome.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-02-08 DOI: 10.1093/nar/gkaf074

Edilene Siqueira, Cecilia D Velasco, Ariadna Tarrasón, Marta Soler, Tara Srinivas, Fernando Setién, Cristina Oliveira-Mateos, Marta Casado-Pelaez, Laura Martinez-Verbo, Judith Armstrong, Manel Esteller, Letícia F Alves, Artur Llobet, Sonia Guil

{"title":"NEAT1-mediated regulation of proteostasis and mRNA localization impacts autophagy dysregulation in Rett syndrome.","authors":"Edilene Siqueira, Cecilia D Velasco, Ariadna Tarrasón, Marta Soler, Tara Srinivas, Fernando Setién, Cristina Oliveira-Mateos, Marta Casado-Pelaez, Laura Martinez-Verbo, Judith Armstrong, Manel Esteller, Letícia F Alves, Artur Llobet, Sonia Guil","doi":"10.1093/nar/gkaf074","DOIUrl":"10.1093/nar/gkaf074","url":null,"abstract":"Rett syndrome (RTT) is a severe neurodevelopmental disorder primarily caused by loss-of-function mutations in the MECP2 gene, resulting in diverse cellular dysfunctions. Here, we investigated the role of the long noncoding RNA (lncRNA) NEAT1 in the context of MeCP2 deficiency using human neural cells and RTT patient samples. Through single-cell RNA sequencing and molecular analyses, we found that NEAT1 is markedly downregulated in MECP2 knockout (KO) cells at various stages of neural differentiation. NEAT1 downregulation correlated with aberrant activation of the mTOR pathway, abnormal protein metabolism, and dysregulated autophagy, contributing to the accumulation of protein aggregates and impaired mitochondrial function. Reactivation of NEAT1 in MECP2-KO cells rescued these phenotypes, indicating its critical role downstream of MECP2. Furthermore, direct RNA-RNA interaction was revealed as the key process for NEAT1 influence on autophagy genes, leading to altered subcellular localization of specific autophagy-related messenger RNAs and impaired biogenesis of autophagic complexes. Importantly, NEAT1 restoration rescued the morphological defects observed in MECP2-KO neurons, highlighting its crucial role in neuronal maturation. Overall, our findings elucidate lncRNA NEAT1 as a key mediator of MeCP2 function, regulating essential pathways involved in protein metabolism, autophagy, and neuronal morphology.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 4","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Crossovers are regulated by a conserved and disordered synaptonemal complex domain.

IF 16.6 2区生物学

Nucleic Acids Research Pub Date : 2025-02-08 DOI: 10.1093/nar/gkaf095

Ana Rita Rodrigues Neves, Ivana Čavka, Tobias Rausch, Simone Köhler

{"title":"Crossovers are regulated by a conserved and disordered synaptonemal complex domain.","authors":"Ana Rita Rodrigues Neves, Ivana Čavka, Tobias Rausch, Simone Köhler","doi":"10.1093/nar/gkaf095","DOIUrl":"10.1093/nar/gkaf095","url":null,"abstract":"During meiosis, the number and distribution of crossovers (COs) must be precisely regulated through CO assurance and interference to prevent chromosome missegregation and genomic instability in the progeny. Here we show that this regulation of COs depends on a disordered and conserved domain within the synaptonemal complex (SC). This domain is located at the C-terminus of the central element protein SYP-4 in Caenorhabditis elegans. While not necessary for synapsis, the C-terminus of SYP-4 is crucial for both CO assurance and interference. Although the SYP-4 C-terminus contains many potential phosphorylation sites, we found that phosphorylation is not the primary regulator of CO events. Instead, we discovered that nine conserved phenylalanines are required to recruit a pro-CO factor predicted to be an E3 ligase and regulate the physical properties of the SC. We propose that this conserved and disordered domain plays a crucial role in maintaining the SC in a state that allows transmitting signals to regulate CO formation. While the underlying mechanisms remain to be fully understood, our findings align with existing models suggesting that the SC plays a critical role in determining the number and distribution of COs along chromosomes, thereby safeguarding the genome for future generations.","PeriodicalId":19471,"journal":{"name":"Nucleic Acids Research","volume":"53 4","pages":""},"PeriodicalIF":16.6,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11833701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0