Biochimica et Biophysica Acta-Gene Regulatory Mechanisms最新文献_第4页

The nucleolus: Coordinating stress response and genomic stability 核仁：协调应激反应和基因组稳定性

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-04-19 DOI: 10.1016/j.bbagrm.2024.195029

Katiuska González-Arzola

{"title":"The nucleolus: Coordinating stress response and genomic stability","authors":"Katiuska González-Arzola","doi":"10.1016/j.bbagrm.2024.195029","DOIUrl":"https://doi.org/10.1016/j.bbagrm.2024.195029","url":null,"abstract":"<div><p>The perception that the nucleoli are merely the organelles where ribosome biogenesis occurs is challenged. Only around 30 % of nucleolar proteins are solely involved in producing ribosomes. Instead, the nucleolus plays a critical role in controlling protein trafficking during stress and, according to its dynamic nature, undergoes continuous protein exchange with nucleoplasm under various cellular stressors. Hence, the concept of nucleolar stress has evolved as cellular insults that disrupt the structure and function of the nucleolus. Considering the emerging role of this organelle in DNA repair and the fact that rDNAs are the most fragile genomic loci, therapies targeting the nucleoli are increasingly being developed. Besides, drugs that target ribosome synthesis and induce nucleolar stress can be used in cancer therapy. In contrast, agents that regulate nucleolar activity may be a potential treatment for neurodegeneration caused by abnormal protein accumulation in the nucleolus. Here, I explore the roles of nucleoli beyond their ribosomal functions, highlighting the factors triggering nucleolar stress and their impact on genomic stability.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1867 2","pages":"Article 195029"},"PeriodicalIF":4.7,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140650468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 role of nucleotide opening dynamics in facilitated target search by DNA-repair proteins 核苷酸开放动力学在 DNA 修复蛋白促进目标搜索中的作用

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-04-17 DOI: 10.1016/j.bbagrm.2024.195026

Sujeet Kumar Mishra , Sangeeta , Dieter W. Heermann , Arnab Bhattacherjee

引用次数: 0

The essential link: How STAT3 connects tumor metabolism to immunity 至关重要的联系STAT3 如何将肿瘤代谢与免疫联系起来

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-04-16 DOI: 10.1016/j.bbagrm.2024.195028

Shu Zhong, Jingjing Tong

引用次数: 0

Illuminating ligand-induced dynamics in nuclear receptors through MD simulations 通过 MD 模拟揭示核受体中配体诱导的动态变化

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-04-16 DOI: 10.1016/j.bbagrm.2024.195025

Tracy Yu , Nishanti Sudhakar , C. Denise Okafor

{"title":"Illuminating ligand-induced dynamics in nuclear receptors through MD simulations","authors":"Tracy Yu , Nishanti Sudhakar , C. Denise Okafor","doi":"10.1016/j.bbagrm.2024.195025","DOIUrl":"https://doi.org/10.1016/j.bbagrm.2024.195025","url":null,"abstract":"<div><p>Nuclear receptors (NRs) regulate gene expression in critical physiological processes, with their functionality finely tuned by ligand-induced conformational changes. While NRs may sometimes undergo significant conformational motions in response to ligand-binding, these effects are more commonly subtle and challenging to study by traditional structural or biophysical methods. Molecular dynamics (MD) simulations are a powerful tool to bridge the gap between static protein-ligand structures and dynamical changes that govern NR function. Here, we summarize a handful of recent studies that apply MD simulations to study NRs. We present diverse methodologies for analyzing simulation data with a detailed examination of the information each method can yield. By delving into the strengths, limitations and unique contributions of these tools, this review provides guidance for extracting meaningful data from MD simulations to advance the goal of understanding the intricate mechanisms by which ligands orchestrate a range of functional outcomes in NRs.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1867 2","pages":"Article 195025"},"PeriodicalIF":4.7,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S187493992400021X/pdfft?md5=7d5eb13de1394345e0d37b70621dfa76&pid=1-s2.0-S187493992400021X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140607084","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Global control of RNA polymerase II RNA 聚合酶 II 的全球控制。

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-03-27 DOI: 10.1016/j.bbagrm.2024.195024

Alexander Gillis, Scott Berry

引用次数: 0

Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases 长非编码 RNA（lncRNA）的转录格局及其在病毒性疾病中的影响。

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-03-19 DOI: 10.1016/j.bbagrm.2024.195023

Ankita Rai, Tannu Bhagchandani, Ravi Tandon

引用次数: 0

MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques MicroRNA 介导的无意义 mRNA 衰减因子调控：对 microRNA 预测工具和剖析技术的见解。

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-03-02 DOI: 10.1016/j.bbagrm.2024.195022

Priyanka Yadav, Raja Tamilselvan, Harita Mani, Kusum Kumari Singh

{"title":"MicroRNA-mediated regulation of nonsense-mediated mRNA decay factors: Insights into microRNA prediction tools and profiling techniques","authors":"Priyanka Yadav, Raja Tamilselvan, Harita Mani, Kusum Kumari Singh","doi":"10.1016/j.bbagrm.2024.195022","DOIUrl":"10.1016/j.bbagrm.2024.195022","url":null,"abstract":"<div><p>Nonsense-mediated mRNA decay (NMD) stands out as a prominent RNA surveillance mechanism within eukaryotes, meticulously overseeing both RNA abundance and integrity by eliminating aberrant transcripts. These defective transcripts are discerned through the concerted efforts of translating ribosomes, eukaryotic release factors (eRFs), and trans-acting NMD factors, with Up-Frameshift 3 (UPF3) serving as a noteworthy component. Remarkably, in humans, UPF3 exists in two paralogous forms, UPF3A (UPF3) and UPF3B (UPF3X). Beyond its role in quality control, UPF3 wields significant influence over critical cellular processes, including neural development, synaptic plasticity, and axon guidance. However, the precise regulatory mechanisms governing UPF3 remain elusive.</p><p>MicroRNAs (miRNAs) emerge as pivotal post-transcriptional gene regulators, exerting substantial impact on diverse pathological and physiological pathways. This comprehensive review encapsulates our current understanding of the intricate regulatory nexus between NMD and miRNAs, with particular emphasis on the essential role played by UPF3B in neurodevelopment. Additionally, we bring out the significance of the 3’-untranslated region (3’-UTR) as the molecular bridge connecting NMD and miRNA-mediated gene regulation. Furthermore, we provide an in-depth exploration of diverse computational tools tailored for the prediction of potential miRNA targets. To complement these computational approaches, we delineate experimental techniques designed to validate predicted miRNA-mRNA interactions, empowering readers with the knowledge necessary to select the most appropriate methodology for their specific research objectives.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1867 2","pages":"Article 195022"},"PeriodicalIF":4.7,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140029634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Histone H3K4ac, as a marker of active transcription start sites and enhancers, plays roles in histone eviction and RNA transcription 组蛋白 H3K4ac 是活跃转录起始位点和增强子的标记，在组蛋白驱逐和 RNA 转录中发挥作用。

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-02-27 DOI: 10.1016/j.bbagrm.2024.195021

Jin Kang , Yujin Kang , AeRi Kim

{"title":"Histone H3K4ac, as a marker of active transcription start sites and enhancers, plays roles in histone eviction and RNA transcription","authors":"Jin Kang , Yujin Kang , AeRi Kim","doi":"10.1016/j.bbagrm.2024.195021","DOIUrl":"10.1016/j.bbagrm.2024.195021","url":null,"abstract":"<div><p>The lysine 4 of histone H3 (H3K4) can be methylated or acetylated into four states: H3K4me1, H3K4me2, H3K4me3, or H3K4ac. Unlike H3K4 methylation, the genome-wide distribution and functional roles of H3K4ac remain unclear. To understand the relationship of acetylation with methylation at H3K4 and to explore the roles of H3K4ac in the context of chromatin, we analyzed H3K4ac across the human genome and compared it with H3K4 methylation in K562 cells. H3K4ac was positively correlated with H3K4me1/2/3 in reciprocal analysis. A decrease in H3K4ac through the mutation of the histone acetyltransferase p300 reduced H3K4me1 and H3K4me3 at the H3K4ac peaks. H3K4ac was also impaired by H3K4me depletion in the histone methyltransferase MLL3/4-mutated cells. H3K4ac peaks were enriched at enhancers in addition to the transcription start sites (TSSs) of genes. H3K4ac of TSSs and enhancers was positively correlated with mRNA and eRNA transcription. A decrease in H3K4ac reduced H3K4me3 and H3K4me1 in TSSs and enhancers, respectively, and inhibited the eviction of histone H3 from them. The mRNA transcription of highly transcribed genes was affected by the reduced H3K4ac. Interestingly, H3K4ac played a redundant role with regard to H3K27ac in eRNA transcription. These results indicate that H3K4ac serves as a marker of both active TSSs and enhancers and plays a role in histone eviction and RNA transcription by leading to H3K4me1/3.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1867 2","pages":"Article 195021"},"PeriodicalIF":4.7,"publicationDate":"2024-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139991980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

LncRNA-mediated orchestrations of alternative splicing in the landscape of breast cancer LncRNA 介导的乳腺癌景观中替代剪接的协调。

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-02-08 DOI: 10.1016/j.bbagrm.2024.195017

Samarth Kansara , Prajwali Sawant , Taranjeet Kaur , Manoj Garg , Amit Kumar Pandey

{"title":"LncRNA-mediated orchestrations of alternative splicing in the landscape of breast cancer","authors":"Samarth Kansara , Prajwali Sawant , Taranjeet Kaur , Manoj Garg , Amit Kumar Pandey","doi":"10.1016/j.bbagrm.2024.195017","DOIUrl":"10.1016/j.bbagrm.2024.195017","url":null,"abstract":"<div><p>Alternative splicing (AS) is a fundamental post-transcriptional process in eukaryotes, enabling a single gene to generate diverse mRNA transcripts, thereby enhancing protein variability. This process involves the excision of introns and the joining of exons in pre-mRNA(s) to form mature mRNA. The resulting mature mRNAs exhibit various combinations of exons, contributing to functional diversity. Dysregulation of AS can substantially modulate protein functions, impacting the onset and progression of numerous diseases, including cancer. Non-coding RNAs (ncRNAs) are distinct from protein-coding RNAs and consist of short and long types. Long non-coding RNAs (lncRNAs) play an important role in regulating several cellular processes, particularly alternative splicing, according to new research. This review provides insight into the latest discoveries concerning how lncRNAs influence alternative splicing within the realm of breast cancer. Additionally, it explores potential therapeutic strategies focused on targeting lncRNAs.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1867 2","pages":"Article 195017"},"PeriodicalIF":4.7,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

An epitope-tagged Swd2 reveals the different requirements of Swd2 concentration in H3K4 methylation and viability 表位标记的 Swd2 揭示了 H3K4 甲基化和活力对 Swd2 浓度的不同要求。

IF 4.7 3区生物学

Biochimica et Biophysica Acta-Gene Regulatory Mechanisms Pub Date : 2024-02-06 DOI: 10.1016/j.bbagrm.2024.195009

Junsoo Oh , Seho Kim , SangMyung Kim , Jueun Kim , Soojin Yeom , Jung-Shin Lee

{"title":"An epitope-tagged Swd2 reveals the different requirements of Swd2 concentration in H3K4 methylation and viability","authors":"Junsoo Oh , Seho Kim , SangMyung Kim , Jueun Kim , Soojin Yeom , Jung-Shin Lee","doi":"10.1016/j.bbagrm.2024.195009","DOIUrl":"10.1016/j.bbagrm.2024.195009","url":null,"abstract":"<div><p>Swd2/Cps35 is a common component of the COMPASS H3K4 methyltransferase and CPF transcription termination complex in <em>Saccharomyces cerevisiae</em>. The deletion of <em>SWD2</em> is lethal, which results from transcription termination defects in snoRNA genes. This study isolated a yeast strain that showed significantly reduced protein level of Swd2 following epitope tagging at its N-terminus (<em>9MYC-SWD2</em>). The reduced level of Swd2 in the <em>9MYC-SWD2</em> strain was insufficient for the stability of the Set1 H3K4 methyltransferase, H3K4me3 and snoRNA termination, but the level was enough for viability and growth similar to the wildtype strain. In addition, we presented the genes differentially regulated by the essential protein Swd2 under optimal culture conditions for the first time. The expression of genes known to be decreased in the absence of Set1 and H3K4me3, including NAD biosynthetic process genes and histone genes, was decreased in the <em>9MYC-SWD2</em> strain, as expected. However, the effects of Swd2 on the ribosome biogenesis (RiBi) genes were opposite to those of Set1, suggesting that the expression of RiBi genes is regulated by more complex relationship between COMPASS and other Swd2-containing complexes. These data suggest that different concentrations of Swd2 are required for its roles in H3K4me3 and viability and that it may be either contributory or contrary to the transcriptional regulation of Set1/H3K4me3, depending on the gene group.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1867 2","pages":"Article 195009"},"PeriodicalIF":4.7,"publicationDate":"2024-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139708562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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