Genes to Cells最新文献

Polished Rice Regulates Maturation but Not Survival of Secondary Cells in Drosophila Male Accessory Gland 精米调节果蝇雄性副腺次生细胞成熟但不影响其存活

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-05-10 DOI: 10.1111/gtc.70025

Shinichi Otsune, Mirai Matsuka, Chisato Shirakashi, Xuanshuo Zhang, Hideki Nakagoshi

引用次数: 0

Profiling of RBM20-Regulated CaMKIIδ Splice Variants Across the Heart, Skeletal Muscle, and Olfactory Bulbs 心脏、骨骼肌和嗅球中rbm20调控的CaMKIIδ剪接变异的分析

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-05-08 DOI: 10.1111/gtc.70021

Yui Maeda, Yuri Yamasu, Hidehito Kuroyanagi

{"title":"Profiling of RBM20-Regulated CaMKIIδ Splice Variants Across the Heart, Skeletal Muscle, and Olfactory Bulbs","authors":"Yui Maeda, Yuri Yamasu, Hidehito Kuroyanagi","doi":"10.1111/gtc.70021","DOIUrl":"https://doi.org/10.1111/gtc.70021","url":null,"abstract":"<p>Calcium/calmodulin-dependent protein kinase IIδ (CaMKIIδ), encoded by the <i>Camk2d</i> gene, plays key regulatory roles in various Ca<sup>2+</sup>-regulated cellular processes. Extensive alternative splicing of the <i>Camk2d</i> gene generates multiple CaMKIIδ splice variants that exhibit differential roles. Despite significant advances in understanding the functions of CaMKIIδ, the full repertoire of <i>Camk2d</i> splice variants in a variety of tissues and their distinct roles in physiological and pathological contexts remain incompletely characterized due to the complex nature of multiple alternative splicing events. Here, we conducted long-read amplicon sequencing to investigate the murine <i>Camk2d</i> splice variants in the heart, skeletal muscle, and olfactory bulbs and show that mRNAs in the heart and skeletal muscle have shorter 3'UTRs. Our results in this study suggest that a key regulator of <i>Camk2d</i> splicing, RNA-binding motif protein 20 (RBM20), whose <i>gain-of-function</i> mutations cause dilated cardiomyopathy, is crucial for the expression of heart-specific splice variants. Olfactory bulbs specifically express novel splice variants that utilize a mutually exclusive exon 6B and/or an alternative polyadenylation site in a novel exon 17.5 in an RBM20-independent manner. The tissue-specific repertoire of CaMKIIδ splice variants and their aberrant expression in disease model animals will help in understanding their roles in physiological and pathological contexts.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70021","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143919398","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

Characteristics of Global Methylation Changes in F1 Mice Sperm DNA Induced by Gestational Arsenic Exposure Are Re-Established in F2 Somatic Cells but Not in F2 Germ Cells 妊娠期砷暴露诱导的F1小鼠精子DNA整体甲基化变化特征在F2体细胞中重新建立，而在F2生殖细胞中没有

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-04-29 DOI: 10.1111/gtc.70022

Takehiro Suzuki, Kazuyuki Okamura, Keiko Nohara

{"title":"Characteristics of Global Methylation Changes in F1 Mice Sperm DNA Induced by Gestational Arsenic Exposure Are Re-Established in F2 Somatic Cells but Not in F2 Germ Cells","authors":"Takehiro Suzuki, Kazuyuki Okamura, Keiko Nohara","doi":"10.1111/gtc.70022","DOIUrl":"https://doi.org/10.1111/gtc.70022","url":null,"abstract":"<div>\u0000 \u0000 <p>Gestational exposure to chemicals has been reported to transmit epigenetic modifications of germ cells not only to somatic cells but also to the germ cells of the next generation, resulting in adverse effects. Arsenic is one of the environmental chemicals of greatest concern, but it is not precisely clarified whether and how epigenetic modifications of F1 sperm caused by gestational exposure are transmitted to the next generation of somatic cells and germ cells. In the present study, we examined the effects of arsenic exposure during gestation on DNA methylation in germ line and somatic cells of the F2. The DNA methylome of F2 sperm was analyzed by reduced representation bisulfite sequencing (RRBS) and compared to that of F2 liver and testis. We found that F2 liver and testis DNA from the arsenic group exhibited the decrease in global DNA methylation levels and bias of DMC distribution toward hypoDMC observed in F1 sperm DNA which we have previously reported, but F2 sperm DNA did not exhibit those characteristics. These studies suggest that the characteristics of epigenetic modifications in F1 sperm induced by gestational arsenic exposure are reestablished in F2 somatic cells but not in F2 germ cells.</p>\u0000 </div>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143888992","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

Iron-Dependent JMJD1A-Mediated Demethylation of H3K9me2 Regulates Gene Expression During Adipogenesis in a Spatial Genome Organization-Dependent Manner 铁依赖性jmjd1a介导的H3K9me2去甲基化以空间基因组组织依赖的方式调节脂肪形成过程中的基因表达

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-04-28 DOI: 10.1111/gtc.70023

Shinnosuke Masuda, Tetsuro Komatsu, Safiya Atia, Tomohiro Suzuki, Mayuko Hayashi, Atsushi Toyoda, Hiroshi Kimura, Takeshi Inagaki

{"title":"Iron-Dependent JMJD1A-Mediated Demethylation of H3K9me2 Regulates Gene Expression During Adipogenesis in a Spatial Genome Organization-Dependent Manner","authors":"Shinnosuke Masuda, Tetsuro Komatsu, Safiya Atia, Tomohiro Suzuki, Mayuko Hayashi, Atsushi Toyoda, Hiroshi Kimura, Takeshi Inagaki","doi":"10.1111/gtc.70023","DOIUrl":"https://doi.org/10.1111/gtc.70023","url":null,"abstract":"<p>Chromatin restructuring across multiple hierarchical scales directs lineage-specific gene expression during cell differentiation. Here, we investigated the iron-dependent demethylation of histone H3 lysine 9 dimethylation (H3K9me2) by the demethylase jumonji domain-containing 1A (JMJD1A) in adipocyte differentiation. Using the 3T3-L1 adipocyte differentiation model, we show that JMJD1A knockdown increases H3K9me2 levels, whereas forced expression of wild-type JMJD1A reduces H3K9me2 levels within the A compartment, as defined by megabase scale high-throughput chromosome conformation capture (Hi-C) data. In contrast, a JMJD1A mutant defective in iron coordination was unable to demethylate H3K9me2. Genome-wide analyses of H3K9me2 levels at transcription start sites on a kilobase scale demonstrated that JMJD1A targets genes involved in peroxisome proliferator-activated receptor signaling and lipid metabolism in an iron-dependent manner, supporting a model in which H3K9me2 demethylation facilitates adipogenic transcription networks. Furthermore, we examined the relationship between H3K9me2 and lamin B1 levels within lamina-associated domains (LADs) specifically reorganized during differentiation. Although LADs with higher H3K9me2 exhibited modestly elevated lamin B1 association in preadipocytes, lamin B1 levels declined during differentiation regardless of H3K9me2 status. These findings emphasize the importance of the iron-dependent enzymatic function in JMJD1A and broaden our understanding of how specific H3K9 demethylases coordinate compartmentalized epigenetic programs during adipogenesis.</p>","PeriodicalId":12742,"journal":{"name":"Genes to Cells","volume":"30 3","pages":""},"PeriodicalIF":1.3,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/gtc.70023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880041","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

Correction to “The Impact of SETBP1 Mutations in Neurological Diseases and Cancer” 更正“SETBP1突变对神经系统疾病和癌症的影响”

IF 1.3 4区生物学

Genes to Cells Pub Date : 2025-04-20 DOI: 10.1111/gtc.70020

引用次数: 0

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 第12届3R + 3C国际研讨会：DNA复制、修复和重组，以及染色质、染色体和细胞周期的研究会议

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 INTS15是整合子复合体的一个亚基，在细胞周期和分化中起着关键的调节作用

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 含有着丝粒特异性组蛋白变体CENP-A的独特亚核小体的冷冻电镜分析

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 DNA拓扑异构酶i β c末端区对ICRF-193诱导的选择性降解的影响

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