Genes to Cells最新文献

Cryo-EM Structures of Native Chromatin Units From Human Cells 人类细胞原生染色质单位的冷冻电镜结构

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-04-14 DOI: 10.1111/gtc.70019

Suguru Hatazawa, Yoshiyuki Fukuda, Yuki Kobayashi, Lumi Negishi, Masahide Kikkawa, Yoshimasa Takizawa, Hitoshi Kurumizaka

{"title":"Cryo-EM Structures of Native Chromatin Units From Human Cells","authors":"Suguru Hatazawa, Yoshiyuki Fukuda, Yuki Kobayashi, Lumi Negishi, Masahide Kikkawa, Yoshimasa Takizawa, Hitoshi Kurumizaka","doi":"10.1111/gtc.70019","DOIUrl":"https://doi.org/10.1111/gtc.70019","url":null,"abstract":"<p>In eukaryotic cells, genomic DNA is compacted by nucleosomes, as basic repeating units, into chromatin. The nucleosome arrangement in chromatin fibers could be an important determinant for chromatin folding, by which genomic DNA is regulated in the nucleus. To study the structures of chromatin units in cells, we have established a method for the structural analysis of native mono- and poly-nucleosomes prepared from HeLa cells. In this method, the chromatin in isolated nuclei was crosslinked to preserve the proximity information between nucleosomes, followed by chromatin fragmentation by micrococcal nuclease treatment. The mono- and poly-nucleosomes were then fractionated by sucrose gradient ultracentrifugation, and their structures were analyzed by cryo-electron microscopy. Cryo-electron microscopy single particle analysis and cryo-electron tomography visualized a native nucleosome structure and secondary nucleosome arrangements in cellular chromatin. This method provides a complementary strategy to fill the gap between in vitro and in situ analyses of chromatin structure.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143826698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

The 12th 3R + 3C International Symposium: A Meeting for Research Into DNA Replication, Repair, and Recombination, as Well as Chromatin, Chromosomes, and the Cell Cycle

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-04-10 DOI: 10.1111/gtc.70018

Tsutomu Katayama, Masatoshi Fujita, Tatsuro S. Takahashi

{"title":"The 12th 3R + 3C International Symposium: A Meeting for Research Into DNA Replication, Repair, and Recombination, as Well as Chromatin, Chromosomes, and the Cell Cycle","authors":"Tsutomu Katayama, Masatoshi Fujita, Tatsuro S. Takahashi","doi":"10.1111/gtc.70018","DOIUrl":"https://doi.org/10.1111/gtc.70018","url":null,"abstract":"<div>\u0000 \u0000 <p>The 12th 3R + 3C international symposium focused on cutting-edge research into the molecular mechanisms and regulatory systems of DNA replication, repair, and recombination (3R) as well as those of chromatin dynamics, chromosome architecture, and the cell cycle (3C). It also covered pioneering research into how these processes control cell growth, cell homeostasis, differentiation, development, and aging, in addition to how they contribute to diseases such as cancer, chromosomal abnormalities, and evolution of organisms. In terms of methodology, the symposium highlighted new trends in single-molecule/single-cell analysis, cryo-electron microscopy analysis, kinetic analysis of higher-order protein complexes, informatic analysis of genome dynamics, and new mathematical and theoretical analyses. Held in Fukuoka City center from November 18 to 22, 2024, this symposium attracted about 250 participants, including approximately 150 from Japan and nearly 100 from overseas. To foster mutual understanding and exchange between different fields, all the oral presentations took place in a single conference hall throughout the symposium. This format facilitated active and in-depth discussions among participants, including young researchers, graduate students, and postdoctoral fellows.</p>\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143818501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

INTS15, A Subunit of the Integrator Complex, Plays a Key Regulatory Role in Cell Cycle and Differentiation

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-04-07 DOI: 10.1111/gtc.70015

Noriyuki Azuma, Yuki Yamaguchi, Taku Tanaka, Emiko Matsuzaka, Yuki Saida, Tadashi Yokoi, Hiroshi Handa, Jun Hirayama, Hiroshi Nishina

{"title":"INTS15, A Subunit of the Integrator Complex, Plays a Key Regulatory Role in Cell Cycle and Differentiation","authors":"Noriyuki Azuma, Yuki Yamaguchi, Taku Tanaka, Emiko Matsuzaka, Yuki Saida, Tadashi Yokoi, Hiroshi Handa, Jun Hirayama, Hiroshi Nishina","doi":"10.1111/gtc.70015","DOIUrl":"https://doi.org/10.1111/gtc.70015","url":null,"abstract":"<div>\u0000 \u0000 <p>We previously reported that <i>Integrator complex subunit 15</i> (<i>INTS15</i>) is a causative gene for an autosomal-dominant eye disease named variable panocular malformations (VPMs) and that INTS15 stably interacts with the Integrator complex to support snRNA 3′ end processing, thereby controlling mRNA splicing. Here we report another critical function of INTS15 in cell cycle control. HeLa cells and human iPS cells were engineered to overexpress INTS15 expression in a cumate-responsive manner and used to study its role in the regulation of cell cycle and differentiation. INTS15 activates the expression of <i>p53</i> and <i>p21</i> to induce G1 arrest when overexpressed. In in vitro differentiation of iPS cells, INTS15 promotes the formation of the three germ layers as well as differentiation into late retinal tissues. Meanwhile, INTS15 knockdown results in defects in G2/M progression and apoptosis. Moreover, INTS15 expression levels vary substantially by cell type and flactuate during the cell cycle. Thus, this study reveals a novel biological aspect of the Integrator complex and demonstrates its potential practical applications.</p>\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143793710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Cryo-EM Analysis of a Unique Subnucleosome Containing Centromere-Specific Histone Variant CENP-A

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-24 DOI: 10.1111/gtc.70016

Osamu Kawasaki, Yoshimasa Takizawa, Iori Kiyokawa, Hitoshi Kurumizaka, Kayo Nozawa

{"title":"Cryo-EM Analysis of a Unique Subnucleosome Containing Centromere-Specific Histone Variant CENP-A","authors":"Osamu Kawasaki, Yoshimasa Takizawa, Iori Kiyokawa, Hitoshi Kurumizaka, Kayo Nozawa","doi":"10.1111/gtc.70016","DOIUrl":"https://doi.org/10.1111/gtc.70016","url":null,"abstract":"<p>In eukaryotes, genomic DNA is stored in the nucleus as nucleosomes, in which a DNA segment is wrapped around a protein octamer consisting of two each of the four histones, H2A, H2B, H3, and H4. The core histones can be replaced by histone variants or altered with covalent modifications, contributing to the regulation of chromosome structure and nuclear activities. The formation of an octameric histone core in nucleosomes is widely accepted. Recently, the H3–H4 octasome, a novel nucleosome-like structure with a histone octamer consisting solely of H3 and H4, has been reported. CENP-A is the centromere-specific histone H3 variant and determines the position of kinetochore assembly during mitosis. CENP-A is a distant H3 variant sharing approximately 50% amino acid sequence with H3. In this study, we found that CENP-A and H4 also formed an octamer without H2A and H2B in vitro. We determined the structure of the CENP-A–H4 octasome at 3.66 Å resolution. In the CENP-A–H4 octasome, an approximately 120-base pair DNA segment was wrapped around the CENP-A–H4 octameric core and displayed the four CENP-A RG-loops, which are the direct binding sites for another centromeric protein, CENP-N.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689876","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

The Impact of the DNA Topoisomerase IIβ C-Terminal Region on the Selective Degradation Induced by ICRF-193 Treatment

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-24 DOI: 10.1111/gtc.70017

Shinji Kawano, Shogo Ikeda

{"title":"The Impact of the DNA Topoisomerase IIβ C-Terminal Region on the Selective Degradation Induced by ICRF-193 Treatment","authors":"Shinji Kawano, Shogo Ikeda","doi":"10.1111/gtc.70017","DOIUrl":"https://doi.org/10.1111/gtc.70017","url":null,"abstract":"<div>\u0000 \u0000 <p>ICRF-193, a catalytic inhibitor of DNA topoisomerase II (TOP2), induces the formation of the TOP2 closed-clamp intermediate. Only the ICRF-193-induced topoisomerase IIβ (TOP2B) closed clamp is known to be selectively and rapidly degraded in vertebrates, but the details are unknown. In this study, we focused on the C-terminal domain (CTD) of TOP2B, which regulates its nuclear dynamics, and sought the region that affects the ICRF-193-induced TOP2B closed-clamp degradation. Using a CTD-swapping mutant between topoisomerase IIα (TOP2A) and TOP2B, we found that the CTD of TOP2B, but not that of TOP2A, is involved in the TOP2B closed-clamp degradation. Furthermore, we identified the C-terminal region (CTR) of TOP2B (amino acids 1570-1621) as a domain that affects TOP2B closed-clamp degradation using a CTR truncation mutant (ΔCTR). A transcription inhibitor inhibited the ICRF-193-induced TOP2B closed-clamp degradation, but the TOP2B ΔCTR closed-clamp degradation was not. In addition, the results of co-immunoprecipitation and immunofluorescence staining showed that the proximity of TOP2B and RNA polymerase II on chromatin in the presence of ICRF-193 tended to be reduced by the lack of TOP2B CTR. Taken together, our data indicate that the TOP2B CTR is involved in the transcription-dependent TOP2B closed-clamp degradation induced by ICRF-193.</p>\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143689744","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Correction to “DNA Double-Strand Breaks Induce the Expression of Flavin-Containing Monooxygenase and Reduce Root Meristem Size in Arabidopsis thaliana”

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-21 DOI: 10.1111/gtc.70014

引用次数: 0

Improvement of Targeting Efficiency by Promoter Replacement of Markers in Integration Vectors

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-20 DOI: 10.1111/gtc.70013

Akihisa Matsuyama, Atsushi Hashimoto, Manabu Arioka, Minoru Yoshida

{"title":"Improvement of Targeting Efficiency by Promoter Replacement of Markers in Integration Vectors","authors":"Akihisa Matsuyama, Atsushi Hashimoto, Manabu Arioka, Minoru Yoshida","doi":"10.1111/gtc.70013","DOIUrl":"10.1111/gtc.70013","url":null,"abstract":"<div>\u0000 \u0000 <p>To establish a gene expression system that reflects physiological conditions, we developed a series of vectors that can be integrated into the chromosome. Compared with the integration vectors employing double-crossover recombination, single-crossover integration vectors have the advantage of high transformation efficiency. However, because single-crossover recombination generates repeat sequences upstream and downstream of the integrated fragment, this strategy is often associated with a risk that an integrated fragment may pop out from the chromosome during cultivation. Here, we assessed the frequency of pop-out using a fission yeast single-crossover integration vector, pDUAL. We also examined the effect of shortening the repeats on pop-out by employing a strategy involving heterologous replacement of the promoter for the <i>leu1</i> marker in the vector. Due to the intrinsic low frequency of pop-out, the effect of promoter conversion on pop-out was negligible, if any. However, a clear ameliorative effect was observed in obtaining the desirable transformants in which a vector fragment was correctly inserted at the targeted locus, a result that may be driven by the limited potential for recombination in the promoter replacement construct.</p>\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143663209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Heterochromatin Protein Swi6 Suppresses Aberrant Gene Conversion at mat Loci by Adjusting the Balance Between the Two Pathways of Swi2 and Rad57

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-13 DOI: 10.1111/gtc.70012

Takumi Fujioka, Yota Murakami, Shinya Takahata

{"title":"Heterochromatin Protein Swi6 Suppresses Aberrant Gene Conversion at mat Loci by Adjusting the Balance Between the Two Pathways of Swi2 and Rad57","authors":"Takumi Fujioka, Yota Murakami, Shinya Takahata","doi":"10.1111/gtc.70012","DOIUrl":"https://doi.org/10.1111/gtc.70012","url":null,"abstract":"<div>\u0000 \u0000 <p>Heterochromatin protein 1 (HP1) is a highly conserved, canonical factor involved in heterochromatin formation. HP1 has been shown to interact with proteins other than silencing factors and heterochromatin effectors. In fission yeast, the loss of the HP1 homolog Swi6 disrupts heterochromatin structure and affects mating type switching at the <i>mat</i> locus, where heterochromatin exists; however, cell growth is unaffected. In this study, we focused on the Swi6 dimerization domain, which provides a binding surface for various interactors. We isolated a distinctive <i>swi6H321Q</i> mutant that does not affect heterochromatin structure but causes variegation in growth defects and abnormal recombination at the <i>mat</i> locus. This mutation disrupts the interaction between Swi6 and Swi2, a <i>mat</i> locus-specific recombination protein. The AT-hook motif of Swi2, which is also required for chromatin localization at the <i>mat</i> locus, is necessary for growth inhibition, suggesting that mislocalization of Swi2 at the <i>mat</i> locus induces growth inhibition. Genetic analysis revealed that abnormal recombination at the <i>mat</i> region was independent of Swi2 but dependent on the Rad57-dependent homologous recombination pathway. These results suggest that Swi6 plays an important role in gene conversion at the <i>mat</i> locus by producing an appropriate selection of homologous recombination factors.</p>\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Advantages of Mutant Generation by Genome Rearrangements of Non-Conventional Yeast via Direct Nuclease Transfection

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-11 DOI: 10.1111/gtc.70010

Arisa H. Oda, Taishi Yasukawa, Miki Tamura, Ayumu Sano, Naohisa Masuo, Kunihiro Ohta

{"title":"Advantages of Mutant Generation by Genome Rearrangements of Non-Conventional Yeast via Direct Nuclease Transfection","authors":"Arisa H. Oda, Taishi Yasukawa, Miki Tamura, Ayumu Sano, Naohisa Masuo, Kunihiro Ohta","doi":"10.1111/gtc.70010","DOIUrl":"https://doi.org/10.1111/gtc.70010","url":null,"abstract":"<p>We previously developed a genome engineering method (TAQing2.0) based on the direct delivery of DNA endonucleases into living cells, which induces genome rearrangements even in non-sporulating nonconventional yeasts without introducing foreign DNA. Using TAQing2.0 and conventional mutagenesis (by nitrosoguanidine), we obtained mutant asexual <i>Candida utilis</i> strains capable of growing under highly acidic conditions (pH 1.8). Whole genome resequencing revealed that the genomic sequences of mutants generated by both methods contain a negligible small population of unmappable sequences, suggesting that both types of mutants can be regarded as equivalent to naturally occurring mutants. TAQing2.0 mutants exhibit multiple genome rearrangements with few point mutations, whereas conventional mutagenesis produces numerous point mutations. This feature enabled us to easily identify candidate genes (e.g., <i>LYP</i><i>1</i> homolog) responsible for acid resistance. TAQing2.0 is a powerful and versatile tool for mutant production and gene hunting without invasion of foreign DNA.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Potential Role of Trap Clone Accumulation Areas (TCAAs) in Sustaining Pluripotency in Mouse Embryonic Stem Cells

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-03-09 DOI: 10.1111/gtc.70011

Masatake Araki, Luna Ikeda, Takumi Yonemori, Kumiko Yoshinobu, Mariko Yamane, Takumi Ichikawa, Kimi Araki

{"title":"Potential Role of Trap Clone Accumulation Areas (TCAAs) in Sustaining Pluripotency in Mouse Embryonic Stem Cells","authors":"Masatake Araki, Luna Ikeda, Takumi Yonemori, Kumiko Yoshinobu, Mariko Yamane, Takumi Ichikawa, Kimi Araki","doi":"10.1111/gtc.70011","DOIUrl":"https://doi.org/10.1111/gtc.70011","url":null,"abstract":"<div>\u0000 \u0000 <p>Analysis of gene trap clones (TCs) revealed the existence of regions where TCs accumulate in the absence of genes. These regions were designated as trap clone accumulation areas (TCAAs). To ascertain the physiological function of TCAAs, negative control regions devoid of genes and TCs (NC1 and NC11), two randomly selected known gene sets (G1 and G11), and a set of genes presumed to be involved in maintaining pluripotency in embryonic stem (ES) cells (GP) were generated and compared with TCAAs. The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) results indicated that TCAAs exhibited characteristics comparable to G1, G11, and GP, suggesting an open chromatin structure. Oct4-chromatin immunoprecipitation-sequencing (ChIP-seq) demonstrated that TCAAs had markedly elevated signals compared to G1 and 11, and a comparable level to that of GP. With regard to H3K4me1 and H3K27ac, which are associated with enhancer activity, TCAAs were observed to exhibit significantly higher levels than G1 and 11 and a comparable level to that of GP. Furthermore, approximately half of the super-enhancers overlapped with TCAAs in an ES cell-specific manner. These findings suggest that TCAAs are involved in maintaining the pluripotency of mouse ES cells.</p>\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 2","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143581866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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