Transcription-Austin最新文献_第3页

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

RNA visualization and single-cell transcriptomics: methods and applications. RNA可视化和单细胞转录组学:方法和应用。

IF 3.6

Transcription-Austin Pub Date : 2023-06-01 Epub Date: 2024-01-23 DOI: 10.1080/21541264.2023.2286761

Zdenek Andrysik, Micah G Donovan

引用次数: 0

Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies. 利用单分子 RNA 成像技术了解基因表达的时空耦合。

IF 3.6

Transcription-Austin Pub Date : 2023-06-01 Epub Date: 2023-04-12 DOI: 10.1080/21541264.2023.2199669

Alan Gerber, Sander van Otterdijk, Frank J Bruggeman, Evelina Tutucci

{"title":"Understanding spatiotemporal coupling of gene expression using single molecule RNA imaging technologies.","authors":"Alan Gerber, Sander van Otterdijk, Frank J Bruggeman, Evelina Tutucci","doi":"10.1080/21541264.2023.2199669","DOIUrl":"10.1080/21541264.2023.2199669","url":null,"abstract":"Across all kingdoms of life, gene regulatory mechanisms underlie cellular adaptation to ever-changing environments. Regulation of gene expression adjusts protein synthesis and, in turn, cellular growth. Messenger RNAs are key molecules in the process of gene expression. Our ability to quantitatively measure mRNA expression in single cells has improved tremendously over the past decades. This revealed an unexpected coordination between the steps that control the life of an mRNA, from transcription to degradation. Here, we provide an overview of the state-of-the-art imaging approaches for measurement and quantitative understanding of gene expression, starting from the early visualizations of single genes by electron microscopy to current fluorescence-based approaches in single cells, including live-cell RNA-imaging approaches to FISH-based spatial transcriptomics across model organisms. We also highlight how these methods have shaped our current understanding of the spatiotemporal coupling between transcriptional and post-transcriptional events in prokaryotes. We conclude by discussing future challenges of this multidisciplinary field.Abbreviations: mRNA: messenger RNA; rRNA: ribosomal rDNA; tRNA: transfer RNA; sRNA: small RNA; FISH: fluorescence in situ hybridization; RNP: ribonucleoprotein; smFISH: single RNA molecule FISH; smiFISH: single molecule inexpensive FISH; HCR-FISH: Hybridization Chain-Reaction-FISH; RCA: Rolling Circle Amplification; seqFISH: Sequential FISH; MERFISH: Multiplexed error robust FISH; UTR: Untranslated region; RBP: RNA binding protein; FP: fluorescent protein; eGFP: enhanced GFP, MCP: MS2 coat protein; PCP: PP7 coat protein; MB: Molecular beacons; sgRNA: single guide RNA.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"105-126"},"PeriodicalIF":3.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10807504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9778673","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

Neural cell diversity in the light of single-cell transcriptomics. 从单细胞转录组学看神经细胞的多样性

IF 3.6

Transcription-Austin Pub Date : 2023-06-01 Epub Date: 2024-01-23 DOI: 10.1080/21541264.2023.2295044

Sandra María Fernández-Moya, Akshay Jaya Ganesh, Mireya Plass

{"title":"Neural cell diversity in the light of single-cell transcriptomics.","authors":"Sandra María Fernández-Moya, Akshay Jaya Ganesh, Mireya Plass","doi":"10.1080/21541264.2023.2295044","DOIUrl":"10.1080/21541264.2023.2295044","url":null,"abstract":"The development of highly parallel and affordable high-throughput single-cell transcriptomics technologies has revolutionized our understanding of brain complexity. These methods have been used to build cellular maps of the brain, its different regions, and catalog the diversity of cells in each of them during development, aging and even in disease. Now we know that cellular diversity is way beyond what was previously thought. Single-cell transcriptomics analyses have revealed that cell types previously considered homogeneous based on imaging techniques differ depending on several factors including sex, age and location within the brain. The expression profiles of these cells have also been exploited to understand which are the regulatory programs behind cellular diversity and decipher the transcriptional pathways driving them. In this review, we summarize how single-cell transcriptomics have changed our view on the cellular diversity in the human brain, and how it could impact the way we study neurodegenerative diseases. Moreover, we describe the new computational approaches that can be used to study cellular differentiation and gain insight into the functions of individual cell populations under different conditions and their alterations in disease.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"158-176"},"PeriodicalIF":3.6,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10807474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139479182","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

Approaches for single-cell RNA sequencing across tissues and cell types. 跨组织和细胞类型的单细胞 RNA 测序方法。

IF 3.6

Transcription-Austin Pub Date : 2023-06-01 Epub Date: 2023-04-16 DOI: 10.1080/21541264.2023.2200721

Pooja Sant, Karsten Rippe, Jan-Philipp Mallm

引用次数: 0