Histochemistry and Cell Biology最新文献_第8页

CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced. CCAT1 lncRNA具有染色质保留和转录后剪接功能。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-05-19 DOI: 10.1007/s00418-024-02294-w

Chaya Bohrer, Eli Varon, Eldar Peretz, Gita Reinitz, Noa Kinor, David Halle, Aviram Nissan, Yaron Shav-Tal

{"title":"CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced.","authors":"Chaya Bohrer, Eli Varon, Eldar Peretz, Gita Reinitz, Noa Kinor, David Halle, Aviram Nissan, Yaron Shav-Tal","doi":"10.1007/s00418-024-02294-w","DOIUrl":"10.1007/s00418-024-02294-w","url":null,"abstract":"Super-enhancers are unique gene expression regulators widely involved in cancer development. Spread over large DNA segments, they tend to be found next to oncogenes. The super-enhancer c-MYC locus forms long-range chromatin looping with nearby genes, which brings the enhancer and the genes into proximity, to promote gene activation. The colon cancer-associated transcript 1 (CCAT1) gene, which is part of the MYC locus, transcribes a lncRNA that is overexpressed in colon cancer cells through activation by MYC. Comparing different types of cancer cell lines using RNA fluorescence in situ hybridization (RNA FISH), we detected very prominent CCAT1 expression in HeLa cells, observed as several large CCAT1 nuclear foci. We found that dozens of CCAT1 transcripts accumulate on the gene locus, in addition to active transcription occurring from the gene. The accumulating transcripts are released from the chromatin during cell division. Examination of CCAT1 lncRNA expression patterns on the single-RNA level showed that unspliced CCAT1 transcripts are released from the gene into the nucleoplasm. Most of these unspliced transcripts were observed in proximity to the active gene but were not associated with nuclear speckles in which unspliced RNAs usually accumulate. At larger distances from the gene, the CCAT1 transcripts appeared spliced, implying that most CCAT1 transcripts undergo post-transcriptional splicing in the zone of the active gene. Finally, we show that unspliced CCAT1 transcripts can be detected in the cytoplasm during splicing inhibition, which suggests that there are several CCAT1 variants, spliced and unspliced, that the cell can recognize as suitable for export.","PeriodicalId":13107,"journal":{"name":"Histochemistry and Cell Biology","volume":" ","pages":"91-107"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064993","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

Sustained inactivation of the Polycomb PRC1 complex induces DNA repair defects and genomic instability in epigenetic tumors. 多聚胞 PRC1 复合物的持续失活会诱发表观遗传肿瘤中的 DNA 修复缺陷和基因组不稳定性。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-06-18 DOI: 10.1007/s00418-024-02302-z

Chetan C Rawal, Vincent Loubiere, Nadejda L Butova, Juliette Gracia, Victoria Parreno, Chiara Merigliano, Anne-Marie Martinez, Giacomo Cavalli, Irene Chiolo

{"title":"Sustained inactivation of the Polycomb PRC1 complex induces DNA repair defects and genomic instability in epigenetic tumors.","authors":"Chetan C Rawal, Vincent Loubiere, Nadejda L Butova, Juliette Gracia, Victoria Parreno, Chiara Merigliano, Anne-Marie Martinez, Giacomo Cavalli, Irene Chiolo","doi":"10.1007/s00418-024-02302-z","DOIUrl":"10.1007/s00418-024-02302-z","url":null,"abstract":"Cancer initiation and progression are typically associated with the accumulation of driver mutations and genomic instability. However, recent studies demonstrated that cancer can also be driven purely by epigenetic alterations, without driver mutations. Specifically, a 24-h transient downregulation of polyhomeotic (ph-KD), a core component of the Polycomb complex PRC1, is sufficient to induce epigenetically initiated cancers (EICs) in Drosophila, which are proficient in DNA repair and characterized by a stable genome. Whether genomic instability eventually occurs when PRC1 downregulation is performed for extended periods of time remains unclear. Here, we show that prolonged depletion of PH, which mimics cancer initiating events, results in broad dysregulation of DNA replication and repair genes, along with the accumulation of DNA breaks, defective repair, and widespread genomic instability in the cancer tissue. A broad misregulation of H2AK118 ubiquitylation and to a lesser extent of H3K27 trimethylation also occurs and might contribute to these phenotypes. Together, this study supports a model where DNA repair and replication defects accumulate during the tumorigenic transformation epigenetically induced by PRC1 loss, resulting in genomic instability and cancer progression.","PeriodicalId":13107,"journal":{"name":"Histochemistry and Cell Biology","volume":" ","pages":"133-147"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227471/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141418698","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

Visualizing histone H4K20me1 in knock-in mice expressing the mCherry-tagged modification-specific intracellular antibody. 在表达 mCherry 标记修饰特异性细胞内抗体的基因敲入小鼠中观察组蛋白 H4K20me1。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-05-19 DOI: 10.1007/s00418-024-02296-8

Yuko Sato, Maoko Takenoshita, Miku Ueoka, Jun Ueda, Kazuo Yamagata, Hiroshi Kimura

{"title":"Visualizing histone H4K20me1 in knock-in mice expressing the mCherry-tagged modification-specific intracellular antibody.","authors":"Yuko Sato, Maoko Takenoshita, Miku Ueoka, Jun Ueda, Kazuo Yamagata, Hiroshi Kimura","doi":"10.1007/s00418-024-02296-8","DOIUrl":"10.1007/s00418-024-02296-8","url":null,"abstract":"During development and differentiation, histone modifications dynamically change locally and globally, associated with transcriptional regulation, DNA replication and repair, and chromosome condensation. The level of histone H4 Lys20 monomethylation (H4K20me1) increases during the G2 to M phases of the cell cycle and is enriched in facultative heterochromatin, such as inactive X chromosomes in cycling cells. To track the dynamic changes of H4K20me1 in living cells, we have developed a genetically encoded modification-specific intracellular antibody (mintbody) probe that specifically binds to the modification. Here, we report the generation of knock-in mice in which the coding sequence of the mCherry-tagged version of the H4K20me1-mintbody is inserted into the Rosa26 locus. The knock-in mice, which ubiquitously expressed the H4K20me1-mintbody, developed normally and were fertile, indicating that the expression of the probe does not disturb the cell growth, development, or differentiation. Various tissues isolated from the knock-in mice exhibited nuclear fluorescence without the need for fixation. The H4K20me1-mintbody was enriched in inactive X chromosomes in developing embryos and in XY bodies during spermatogenesis. The knock-in mice will be useful for the histochemical analysis of H4K20me1 in any cell types.","PeriodicalId":13107,"journal":{"name":"Histochemistry and Cell Biology","volume":" ","pages":"41-52"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227479/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140957074","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

Seeing genomes. 看到基因组

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 DOI: 10.1007/s00418-024-02301-0

Tom Misteli

引用次数: 0

Dynamic chromosome association with nuclear organelles in living cells. 活细胞中染色体与核细胞器的动态结合。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-05-30 DOI: 10.1007/s00418-024-02288-8

Lam Minh Uyen Phan, Wei-Hong Yeo, Hao F Zhang, Sui Huang

{"title":"Dynamic chromosome association with nuclear organelles in living cells.","authors":"Lam Minh Uyen Phan, Wei-Hong Yeo, Hao F Zhang, Sui Huang","doi":"10.1007/s00418-024-02288-8","DOIUrl":"10.1007/s00418-024-02288-8","url":null,"abstract":"The development of progressively sophisticated tools complemented by the integration of live cell imaging enhances our understanding of the four-dimensional (4D) nucleome, revealing elaborate molecular interactions and chromatin states. Yet, the dynamics of chromosomes in relation to nuclear organelles or to each other across cell cycle in living cells are underexplored. We have developed photoconvertible GFP H3-Dendra2 stably expressing in PC3M cells. The nuclear lamina and perinucleolar associated heterochromatin or diffuse chromosome regions were photoconverted through a single-point activation using a confocal microscope. The results demonstrated a dynamic nature for both types of chromosomes in the same cell cycle and across mitosis. While some chromosome domains were heritably associated with either nuclear lamina or nucleoli, others changed alliance to different nuclear organelles postmitotically. In addition, co-photoconverted chromosome domains often do not stay together within the same cell cycle and across mitosis, suggesting a transient nature of chromosome neighborhoods. Long-range spreading and movement of chromosomes were also observed. Interestingly, when cells were treated with a low concentration of actinomycin D that inhibits Pol I transcription through intercalating GC-rich DNA, chromosome movement was significantly blocked. Treatment with another Pol I inhibitor, metarrestin, which does not impact DNA, had little effect on the movement, suggesting that the DNA structure itself plays a role in chromosome dynamics. Furthermore, inhibition of Pol II transcription with α-amanitin also reduced the chromosome movement, demonstrating that Pol II, but not Pol I transcription, is important for chromosome dynamics in the nucleus.","PeriodicalId":13107,"journal":{"name":"Histochemistry and Cell Biology","volume":" ","pages":"149-159"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141175210","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

Crossing boundaries of light microscopy resolution discerns novel assemblies in the nucleolus. 跨越光镜分辨率的界限，发现核仁中的新型组合。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-05-17 DOI: 10.1007/s00418-024-02297-7

Carl C Correll, Udo Rudloff, Jeremy D Schmit, David A Ball, Tatiana S Karpova, Eric Balzer, Miroslav Dundr

{"title":"Crossing boundaries of light microscopy resolution discerns novel assemblies in the nucleolus.","authors":"Carl C Correll, Udo Rudloff, Jeremy D Schmit, David A Ball, Tatiana S Karpova, Eric Balzer, Miroslav Dundr","doi":"10.1007/s00418-024-02297-7","DOIUrl":"10.1007/s00418-024-02297-7","url":null,"abstract":"The nucleolus is the largest membraneless organelle and nuclear body in mammalian cells. It is primarily involved in the biogenesis of ribosomes, essential macromolecular machines responsible for synthesizing all proteins required by the cell. The assembly of ribosomes is evolutionarily conserved and accounts for the most energy-consuming cellular process needed for cell growth, proliferation, and homeostasis. Despite the significance of this process, the substructural mechanistic principles of the nucleolar function in preribosome biogenesis have only recently begun to emerge. Here, we provide a new perspective using advanced super-resolution microscopy and single-molecule MINFLUX nanoscopy on the mechanistic principles governing ribosomal RNA-seeded nucleolar formation and the resulting tripartite suborganization of the nucleolus driven, in part, by liquid-liquid phase separation. With recent advances in the cryogenic electron microscopy (cryoEM) structural analysis of ribosome biogenesis intermediates, we highlight the current understanding of the step-wise assembly of preribosomal subunits in the nucleolus. Finally, we address how novel anticancer drug candidates target early steps in ribosome biogenesis to exploit these essential dependencies for growth arrest and tumor control.","PeriodicalId":13107,"journal":{"name":"Histochemistry and Cell Biology","volume":" ","pages":"161-183"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11330670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140957002","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

Allele-level visualization of transcription and chromatin by high-throughput imaging. 通过高通量成像技术实现转录和染色质的等位基因级可视化。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-05-09 DOI: 10.1007/s00418-024-02289-7

Faisal Almansour, Adib Keikhosravi, Gianluca Pegoraro, Tom Misteli

{"title":"Allele-level visualization of transcription and chromatin by high-throughput imaging.","authors":"Faisal Almansour, Adib Keikhosravi, Gianluca Pegoraro, Tom Misteli","doi":"10.1007/s00418-024-02289-7","DOIUrl":"10.1007/s00418-024-02289-7","url":null,"abstract":"The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are nonrandom, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection of DNA and nascent RNA. These optimized DNA and RNA FISH protocols were implemented in a 384-well plate format alongside automated image and data analysis and enable accurate detection of individual gene alleles and their gene expression status across a large cell population. We successfully visualized MYC and EGFR DNA and nascent RNA with allele-level resolution in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.","PeriodicalId":13107,"journal":{"name":"Histochemistry and Cell Biology","volume":" ","pages":"65-77"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227451/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140898123","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

Behaviors of nucleosomes with mutant histone H4s in euchromatic domains of living human cells. 活体人体细胞中带有突变组蛋白 H4 的核小体的行为。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-05-14 DOI: 10.1007/s00418-024-02293-x

Adilgazy Semeigazin, Shiori Iida, Katsuhiko Minami, Sachiko Tamura, Satoru Ide, Koichi Higashi, Atsushi Toyoda, Ken Kurokawa, Kazuhiro Maeshima

{"title":"Behaviors of nucleosomes with mutant histone H4s in euchromatic domains of living human cells.","authors":"Adilgazy Semeigazin, Shiori Iida, Katsuhiko Minami, Sachiko Tamura, Satoru Ide, Koichi Higashi, Atsushi Toyoda, Ken Kurokawa, Kazuhiro Maeshima","doi":"10.1007/s00418-024-02293-x","DOIUrl":"10.1007/s00418-024-02293-x","url":null,"abstract":"Since Robert Feulgen first stained DNA in the cell, visualizing genome chromatin has been a central issue in cell biology to uncover how chromatin is organized and behaves in the cell. To approach this issue, we have developed single-molecule imaging of nucleosomes, a basic unit of chromatin, to unveil local nucleosome behavior in living cells. In this study, we investigated behaviors of nucleosomes with various histone H4 mutants in living HeLa cells to address the role of H4 tail acetylation, including H4K16Ac and others, which are generally associated with more transcriptionally active chromatin regions. We ectopically expressed wild-type (wt) or mutated H4s (H4K16 point; H4K5,8,12,16 quadruple; and H4 tail deletion) fused with HaloTag in HeLa cells. Cells that expressed wtH4-Halo, H4K16-Halo mutants, and multiple H4-Halo mutants had euchromatin-concentrated distribution. Consistently, the genomic regions of the wtH4-Halo nucleosomes corresponded to Hi-C contact domains (or topologically associating domains, TADs) with active chromatin marks (A-compartment). Utilizing single-nucleosome imaging, we found that none of the H4 deacetylation or acetylation mimicked H4 mutants altered the overall local nucleosome motion. This finding suggests that H4 mutant nucleosomes embedded in the condensed euchromatic domains with excess endogenous H4 nucleosomes cannot cause an observable change in the local motion. Interestingly, H4 with four lysine-to-arginine mutations displayed a substantial freely diffusing fraction in the nucleoplasm, whereas H4 with a truncated N-terminal tail was incorporated in heterochromatic regions as well as euchromatin. Our study indicates the power of single-nucleosome imaging to understand individual histone/nucleosome behavior reflecting chromatin environments in living cells.","PeriodicalId":13107,"journal":{"name":"Histochemistry and Cell Biology","volume":" ","pages":"23-40"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140921350","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

From feulgen to modern methods: marking a century of DNA imaging advances. 从费尔根到现代方法：DNA 成像发展的一个世纪。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-05-16 DOI: 10.1007/s00418-024-02291-z

Melike Lakadamyali

引用次数: 0

DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes. DNA 编排：从环到染色体，DNA 在不同分辨率下的移动性和组织相关性。

IF 2.1 4区生物学

Histochemistry and Cell Biology Pub Date : 2024-07-01 Epub Date: 2024-05-17 DOI: 10.1007/s00418-024-02285-x

Maruthi K Pabba, Janis Meyer, Kerem Celikay, Lothar Schermelleh, Karl Rohr, M Cristina Cardoso

{"title":"DNA choreography: correlating mobility and organization of DNA across different resolutions from loops to chromosomes.","authors":"Maruthi K Pabba, Janis Meyer, Kerem Celikay, Lothar Schermelleh, Karl Rohr, M Cristina Cardoso","doi":"10.1007/s00418-024-02285-x","DOIUrl":"10.1007/s00418-024-02285-x","url":null,"abstract":"The dynamics of DNA in the cell nucleus plays a role in cellular processes and fates but the interplay of DNA mobility with the hierarchical levels of DNA organization is still underexplored. Here, we made use of DNA replication to directly label genomic DNA in an unbiased genome-wide manner. This was followed by live-cell time-lapse microscopy of the labeled DNA combining imaging at different resolutions levels simultaneously and allowing one to trace DNA motion across organization levels within the same cells. Quantification of the labeled DNA segments at different microscopic resolution levels revealed sizes comparable to the ones reported for DNA loops using 3D super-resolution microscopy, topologically associated domains (TAD) using 3D widefield microscopy, and also entire chromosomes. By employing advanced chromatin tracking and image registration, we discovered that DNA exhibited higher mobility at the individual loop level compared to the TAD level and even less at the chromosome level. Additionally, our findings indicate that chromatin movement, regardless of the resolution, slowed down during the S phase of the cell cycle compared to the G1/G2 phases. Furthermore, we found that a fraction of DNA loops and TADs exhibited directed movement with the majority depicting constrained movement. Our data also indicated spatial mobility differences with DNA loops and TADs at the nuclear periphery and the nuclear interior exhibiting lower velocity and radius of gyration than the intermediate locations. On the basis of these insights, we propose that there is a link between DNA mobility and its organizational structure including spatial distribution, which impacts cellular processes.","PeriodicalId":13107,"journal":{"name":"Histochemistry and Cell Biology","volume":" ","pages":"109-131"},"PeriodicalIF":2.1,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140957006","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