Transcription-Austin最新文献_第2页

An emerging paradigm in epigenetic marking: coordination of transcription and replication. 表观遗传标记的新范式：转录与复制的协调。

IF 3.6

Transcription-Austin Pub Date : 2024-02-01 Epub Date: 2024-02-20 DOI: 10.1080/21541264.2024.2316965

Tyler K Fenstermaker, Svetlana Petruk, Alexander Mazo

{"title":"An emerging paradigm in epigenetic marking: coordination of transcription and replication.","authors":"Tyler K Fenstermaker, Svetlana Petruk, Alexander Mazo","doi":"10.1080/21541264.2024.2316965","DOIUrl":"10.1080/21541264.2024.2316965","url":null,"abstract":"DNA replication and RNA transcription both utilize DNA as a template and therefore need to coordinate their activities. The predominant theory in the field is that in order for the replication fork to proceed, transcription machinery has to be evicted from DNA until replication is complete. If that does not occur, these machineries collide, and these collisions elicit various repair mechanisms which require displacement of one of the enzymes, often RNA polymerase, in order for replication to proceed. This model is also at the heart of the epigenetic bookmarking theory, which implies that displacement of RNA polymerase during replication requires gradual re-building of chromatin structure, which guides recruitment of transcriptional proteins and resumption of transcription. We discuss these theories but also bring to light newer data that suggest that these two processes may not be as detrimental to one another as previously thought. This includes findings suggesting that these processes can occur without fork collapse and that RNA polymerase may only be transiently displaced during DNA replication. We discuss potential mechanisms by which RNA polymerase may be retained at the replication fork and quickly rebind to DNA post-replication. These discoveries are important, not only as new evidence as to how these two processes are able to occur harmoniously but also because they have implications on how transcriptional programs are maintained through DNA replication. To this end, we also discuss the coordination of replication and transcription in light of revising the current epigenetic bookmarking theory of how the active gene status can be transmitted through S phase.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"22-37"},"PeriodicalIF":3.6,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11093037/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139913687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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. 更正。

IF 3.6

Transcription-Austin Pub Date : 2024-02-01 Epub Date: 2024-03-21 DOI: 10.1080/21541264.2024.2333606

引用次数: 0

Targeting bacterial transcription factors for infection control: opportunities and challenges. 针对细菌转录因子进行感染控制：机遇与挑战。

IF 3.6

Transcription-Austin Pub Date : 2023-12-21 DOI: 10.1080/21541264.2023.2293523

Ahmed Al-Tohamy, Anne Grove

{"title":"Targeting bacterial transcription factors for infection control: opportunities and challenges.","authors":"Ahmed Al-Tohamy, Anne Grove","doi":"10.1080/21541264.2023.2293523","DOIUrl":"10.1080/21541264.2023.2293523","url":null,"abstract":"The rising threat of antibiotic resistance in pathogenic bacteria emphasizes the need for new therapeutic strategies. This review focuses on bacterial transcription factors (TFs), which play crucial roles in bacterial pathogenesis. We discuss the regulatory roles of these factors through examples, and we outline potential therapeutic strategies targeting bacterial TFs. Specifically, we discuss the use of small molecules to interfere with TF function and the development of transcription factor decoys, oligonucleotides that compete with promoters for TF binding. We also cover peptides that target the interaction between the bacterial TF and other factors, such as RNA polymerase, and the targeting of sigma factors. These strategies, while promising, come with challenges, from identifying targets to designing interventions, managing side effects, and accounting for changing bacterial resistance patterns. We also delve into how Artificial Intelligence contributes to these efforts and how it may be exploited in the future, and we touch on the roles of multidisciplinary collaboration and policy to advance this research domain.Abbreviations: AI, artificial intelligence; CNN, convolutional neural networks; DTI: drug-target interaction; HTH, helix-turn-helix; IHF, integration host factor; LTTRs, LysR-type transcriptional regulators; MarR, multiple antibiotic resistance regulator; MRSA, methicillin resistant Staphylococcus aureus; MSA: multiple sequence alignment; NAP, nucleoid-associated protein; PROTACs, proteolysis targeting chimeras; RNAP, RNA polymerase; TF, transcription factor; TFD, transcription factor decoying; TFTRs, TetR-family transcriptional regulators; wHTH, winged helix-turn-helix.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"1-28"},"PeriodicalIF":3.6,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138832205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcription factors in the development and treatment of immune disorders. 转录因子在免疫疾病的发展和治疗中的作用。

IF 3.6

Transcription-Austin Pub Date : 2023-12-15 DOI: 10.1080/21541264.2023.2294623

Samantha D Patalano, Paula Fuxman Bass, Juan I Fuxman Bass

{"title":"Transcription factors in the development and treatment of immune disorders.","authors":"Samantha D Patalano, Paula Fuxman Bass, Juan I Fuxman Bass","doi":"10.1080/21541264.2023.2294623","DOIUrl":"10.1080/21541264.2023.2294623","url":null,"abstract":"Immune function is highly controlled at the transcriptional level by the binding of transcription factors (TFs) to promoter and enhancer elements. Several TF families play major roles in immune gene expression, including NF-κB, STAT, IRF, AP-1, NRs, and NFAT, which trigger anti-pathogen responses, promote cell differentiation, and maintain immune system homeostasis. Aberrant expression, activation, or sequence of isoforms and variants of these TFs can result in autoimmune and inflammatory diseases as well as hematological and solid tumor cancers. For this reason, TFs have become attractive drug targets, even though most were previously deemed \"undruggable\" due to their lack of small molecule binding pockets and the presence of intrinsically disordered regions. However, several aspects of TF structure and function can be targeted for therapeutic intervention, such as ligand-binding domains, protein-protein interactions between TFs and with cofactors, TF-DNA binding, TF stability, upstream signaling pathways, and TF expression. In this review, we provide an overview of each of the important TF families, how they function in immunity, and some related diseases they are involved in. Additionally, we discuss the ways of targeting TFs with drugs along with recent research developments in these areas and their clinical applications, followed by the advantages and disadvantages of targeting TFs for the treatment of immune disorders.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"1-23"},"PeriodicalIF":3.6,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138802192","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcriptional and spatiotemporal regulation of the dauer program. 脑电程序的转录和时空调控。

IF 3.6

Transcription-Austin Pub Date : 2023-11-01 Epub Date: 2023-03-23 DOI: 10.1080/21541264.2023.2190295

Luciana F Godoy, Daniel Hochbaum

{"title":"Transcriptional and spatiotemporal regulation of the dauer program.","authors":"Luciana F Godoy, Daniel Hochbaum","doi":"10.1080/21541264.2023.2190295","DOIUrl":"10.1080/21541264.2023.2190295","url":null,"abstract":"Caenorhabditis elegans can enter a diapause stage called \"dauer\" when it senses that the environment is not suitable for development. This implies a detour from the typical developmental trajectory and requires a tight control of the developmental clock and a massive tissue remodeling. In the last decades, core components of the signaling pathways that govern the dauer development decision have been identified, but the tissues where they function for the acquisition of dauer-specific traits are still under intense study. Growing evidence demonstrates that these pathways engage in complex cross-talk and feedback loops. In this review, we summarize the current knowledge regarding the transcriptional regulation of the dauer program and the relevant tissues for its achievement. A better understanding of this process will provide insight on how developmental plasticity is achieved and how development decisions are under a robust regulation to ensure an all-or-nothing response. Furthermore, this developmental decision can also serve as a simplified model for relevant developmental disorders.Abbreviations: AID Auxin Induced Degron DA dafachronic acid Daf-c dauer formation constitutive Daf-d dauer formation defective DTC Distal Tip Cells ECM modified extracellular matrix GPCRs G protein-coupled receptors IIS insulin/IGF-1 signaling ILPs insulin-like peptides LBD Ligand Binding Domain PDL4 Post Dauer L4 TGF-β transforming growth factor beta WT wild-type.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"14 1-2","pages":"27-48"},"PeriodicalIF":3.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10353326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9833792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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 circular logic of mRNA homeostasis. mRNA稳态的循环逻辑。

IF 3.6

Transcription-Austin Pub Date : 2023-11-01 Epub Date: 2023-02-26 DOI: 10.1080/21541264.2023.2183684

Alysia R Bryll, Craig L Peterson

引用次数: 0

Never a dull enzyme, RNA polymerase II. 决不是一种迟钝的酶，RNA聚合酶II。

IF 3.6

Transcription-Austin Pub Date : 2023-11-01 Epub Date: 2023-05-02 DOI: 10.1080/21541264.2023.2208023

Jie Huang, Xiong Ji

引用次数: 0

Transcription machinery of the minimalist: comparative genomic analysis provides insights into the (de)regulated transcription mechanism of microsporidia - fungal-relative parasites. 极简转录机制:比较基因组分析提供了对微孢子虫-真菌相关寄生虫(非)调节转录机制的见解。

IF 3.6

Transcription-Austin Pub Date : 2023-11-01 Epub Date: 2023-02-09 DOI: 10.1080/21541264.2023.2174765

Sittinan Chanarat

{"title":"Transcription machinery of the minimalist: comparative genomic analysis provides insights into the (de)regulated transcription mechanism of microsporidia - fungal-relative parasites.","authors":"Sittinan Chanarat","doi":"10.1080/21541264.2023.2174765","DOIUrl":"10.1080/21541264.2023.2174765","url":null,"abstract":"Microsporidia are eukaryotic obligate intracellular parasites closely related to fungi. Co-evolving with infected hosts, microsporidia have highly reduced their genomes and lacked several biological components. As it is beneficial for intracellular parasites like microsporidia to reduce their genome size, it is therefore reasonable to assume that genes encoding multifactorial complex machinery of transcription could be a potential target to be excluded from microsporidian genomes during the reductive evolution. In such a case, an evolutionary dilemma occurs because microsporidia cannot remove all transcription-machinery-encoding genes, products of which are essential for initialthe initial steps of gene expression. Here, I propose that while genes encoding core machinery are conserved, several genes known to function in fine-tune regulation of transcription are absent. This genome compaction strategy may come at the cost of loosely regulated or less controllable transcription. Alternatively, analogous to microsporidian polar tube, the parasites may have specialized factors to regulate their RNA synthesis.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"14 1-2","pages":"1-17"},"PeriodicalIF":3.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10353337/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10210024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Emerging insights into enhancer biology and function. 增强子生物学和功能的新见解。

IF 3.6

Transcription-Austin Pub Date : 2023-11-01 Epub Date: 2023-06-13 DOI: 10.1080/21541264.2023.2222032

Mirjam Arnold, Kristy R Stengel

{"title":"Emerging insights into enhancer biology and function.","authors":"Mirjam Arnold, Kristy R Stengel","doi":"10.1080/21541264.2023.2222032","DOIUrl":"10.1080/21541264.2023.2222032","url":null,"abstract":"Cell type-specific gene expression is coordinated by DNA-encoded enhancers and the transcription factors (TFs) that bind to them in a sequence-specific manner. As such, these enhancers and TFs are critical mediators of normal development and altered enhancer or TF function is associated with the development of diseases such as cancer. While initially defined by their ability to activate gene transcription in reporter assays, putative enhancer elements are now frequently defined by their unique chromatin features including DNase hypersensitivity and transposase accessibility, bidirectional enhancer RNA (eRNA) transcription, CpG hypomethylation, high H3K27ac and H3K4me1, sequence-specific transcription factor binding, and co-factor recruitment. Identification of these chromatin features through sequencing-based assays has revolutionized our ability to identify enhancer elements on a genome-wide scale, and genome-wide functional assays are now capitalizing on this information to greatly expand our understanding of how enhancers function to provide spatiotemporal coordination of gene expression programs. Here, we highlight recent technological advances that are providing new insights into the molecular mechanisms by which these critical cis-regulatory elements function in gene control. We pay particular attention to advances in our understanding of enhancer transcription, enhancer-promoter syntax, 3D organization and biomolecular condensates, transcription factor and co-factor dependencies, and the development of genome-wide functional enhancer screens.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"14 1-2","pages":"68-87"},"PeriodicalIF":3.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10353330/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9890048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

From words to complete phrases: insight into single-cell isoforms using short and long reads. 从单词到完整短语：利用长短读数深入了解单细胞同工酶。

IF 3.6

Transcription-Austin Pub Date : 2023-06-01 Epub Date: 2023-06-14 DOI: 10.1080/21541264.2023.2213514

Anoushka Joglekar, Careen Foord, Julien Jarroux, Shaun Pollard, Hagen U Tilgner

引用次数: 0