Transcription-Austin最新文献

{"title":"Archaeal transcription.","authors":"Breanna R Wenck, Thomas J Santangelo","doi":"10.1080/21541264.2020.1838865","DOIUrl":"10.1080/21541264.2020.1838865","url":null,"abstract":"<p><p>Increasingly sophisticated biochemical and genetic techniques are unraveling the regulatory factors and mechanisms that control gene expression in the Archaea. While some similarities in regulatory strategies are universal, archaeal-specific regulatory strategies are emerging to complement a complex patchwork of shared archaeal-bacterial and archaeal-eukaryotic regulatory mechanisms employed in the archaeal domain. The prokaryotic archaea encode core transcription components with homology to the eukaryotic transcription apparatus and also share a simplified eukaryotic-like initiation mechanism, but also deploy tactics common to bacterial systems to regulate promoter usage and influence elongation-termination decisions. We review the recently established complete archaeal transcription cycle, highlight recent findings of the archaeal transcription community and detail the expanding post-initiation regulation imposed on archaeal transcription.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"199-210"},"PeriodicalIF":3.6,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714419/pdf/KTRN_11_1838865.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38537161","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}

{"title":"Plant transcription links environmental cues and phenotypic plasticity.","authors":"M Crespi","doi":"10.1080/21541264.2020.1837498","DOIUrl":"https://doi.org/10.1080/21541264.2020.1837498","url":null,"abstract":"Photosynthetic organisms on land and in water produce the biomass and oxygen necessary for life on Earth. They are the first link in the food chain contributing to the life cycle. Plants, as sessile organisms, are forced to adapt to changing environmental constraints in order to ensure their growth and the faithful transmission of their genetic information. Plants are key elements for food, feed, human health, the environment and industry, and to improve plant production in a sustainable way is a major challenge for the future. In the current context of population growth and limitation of arable lands and fossil resources, global food security is intertwined with understanding how plants grow, differentiate and adapt to a changing environment. Indeed, plants have the ability to express different phenotypes from a given genotype, depending on multiple environmental stimuli as well as the capacity to regenerate their organs (e.g. leaves) in direct response to the environment (e.g. summer light conditions). This major phenotypic and developmental plasticity is a critical feature of plants and implies sophisticated molecular mechanisms regulating the expression of genes and the inheritance of expression patterns[1]. Indeed, environmental cues (e.g. light) have a strong impact on transcription in plant cells and changes in gene activity can also take place without altering the DNA sequence. These gene expression changes can pass on during cell divisions from one generation to the next (the foundation of “epigenetics”) or can be reversible once the environmental constraint fades. Plants partially achieve this growth and developmental plasticity by modulating the repertoire of transcribed genes. Advances in molecular biology and biotechnologies (e.g. high-throughput sequencing) have brought about a new dimension in the understanding of the mechanisms regulating the expression and transmission of genetic information in response to the environment. However, it also evidenced that post-transcriptional processes, such as alternative splicing, non-coding RNA mediated regulations or mRNA stability, also emerged as a key mechanism for gene regulation during plant adaptation to the environment[2]. Consequently, photosynthetic organisms, by their way of life, their phenotypic plasticity and their great ecological diversity constitute interesting experimental models to deciphering new ins and outs of transcriptional and epigenetic regulatory mechanisms in the regulation of developmental and phenotypic plasticity, adaptation to biotic and abiotic stresses and, in the longer term, the evolution of life in a changing environment. Due to these fascinating aspects of plant biology, in this issue of transcription, we decide to revise several emerging trends in plant transcriptional regulatory mechanisms and explore future research venues. We start with the review of de Leone et al [3]. which describes a thorough update on the transcriptional regulations involved in the","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 3-4","pages":"97-99"},"PeriodicalIF":3.6,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1837498","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38655206","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}

{"title":"It's a matter of time: the role of transcriptional regulation in the circadian clock-pathogen crosstalk in plants.","authors":"María José de Leone,&nbsp;C Esteban Hernando,&nbsp;Santiago Mora-García,&nbsp;Marcelo J Yanovsky","doi":"10.1080/21541264.2020.1820300","DOIUrl":"https://doi.org/10.1080/21541264.2020.1820300","url":null,"abstract":"<p><p>Most living organisms possess an internal timekeeping mechanism known as the circadian clock, which enhances fitness by synchronizing the internal timing of biological processes with diurnal and seasonal environmental changes. In plants, the pace of these biological rhythms relies on oscillations in the expression level of hundreds of genes tightly controlled by a group of core clock regulators and co-regulators that engage in transcriptional and translational feedback loops. In the last decade, the role of several core clock genes in the control of defense responses has been addressed, and a growing amount of evidence demonstrates that circadian regulation is relevant for plant immunity. A reciprocal connection between these pathways was also established following the observation that in <i>Arabidopsis thaliana</i>, as well as in crop species like tomato, plant-pathogen interactions trigger a reconfiguration of the circadian transcriptional network. In this review, we summarize the current knowledge regarding the interaction between the circadian clock and biotic stress responses at the transcriptional level, and discuss the relevance of this crosstalk in the plant-pathogen evolutionary arms race. A better understanding of these processes could aid in the development of genetic tools that improve traditional breeding practices, enhancing tolerance to plant diseases that threaten crop yield and food security all around the world.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 3-4","pages":"100-116"},"PeriodicalIF":3.6,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1820300","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38482919","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}

{"title":"Long noncoding RNAs shape transcription in plants.","authors":"Leandro Lucero,&nbsp;Camille Fonouni-Farde,&nbsp;Martin Crespi,&nbsp;Federico Ariel","doi":"10.1080/21541264.2020.1764312","DOIUrl":"https://doi.org/10.1080/21541264.2020.1764312","url":null,"abstract":"ABSTRACT The advent of novel high-throughput sequencing techniques has revealed that eukaryotic genomes are massively transcribed although only a small fraction of RNAs exhibits protein-coding capacity. In the last years, long noncoding RNAs (lncRNAs) have emerged as regulators of eukaryotic gene expression in a wide range of molecular mechanisms. Plant lncRNAs can be transcribed by alternative RNA polymerases, acting directly as long transcripts or can be processed into active small RNAs. Several lncRNAs have been recently shown to interact with chromatin, DNA or nuclear proteins to condition the epigenetic environment of target genes or modulate the activity of transcriptional complexes. In this review, we will summarize the recent discoveries about the actions of plant lncRNAs in the regulation of gene expression at the transcriptional level.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 3-4","pages":"160-171"},"PeriodicalIF":3.6,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1764312","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37935159","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}

{"title":"The contribution of transposable elements to transcriptional novelty in plants: the <i>FLC</i> affair.","authors":"Leandro Quadrana","doi":"10.1080/21541264.2020.1803031","DOIUrl":"https://doi.org/10.1080/21541264.2020.1803031","url":null,"abstract":"<p><p>Transposable elements (TEs) are repetitive DNA sequences with the ability to replicate across genomes and generate mutations with major transcriptional effects. Epigenetic silencing mechanisms that target TEs to limit their activity, including DNA methylation, add to the range of gene expression variants generated by TEs. Here, using the iconic gene flowering locus C (<i>FLC)</i> as a case study I discuss the multiple ways by which TEs can affect the expression of genes and contribute to the adaptation of plants to changing environments.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 3-4","pages":"192-198"},"PeriodicalIF":3.6,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1803031","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38256095","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}

{"title":"Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout <i>Arabidopsis thaliana's</i> life cycle.","authors":"Rocío S Tognacca,&nbsp;M Guillermina Kubaczka,&nbsp;Lucas Servi,&nbsp;Florencia S Rodríguez,&nbsp;Micaela A Godoy Herz,&nbsp;Ezequiel Petrillo","doi":"10.1080/21541264.2020.1796473","DOIUrl":"https://doi.org/10.1080/21541264.2020.1796473","url":null,"abstract":"<p><p>Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of <i>A. thaliana's</i> life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 3-4","pages":"117-133"},"PeriodicalIF":3.6,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1796473","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38233393","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}

{"title":"Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants.","authors":"Bart Rymen,&nbsp;Laura Ferrafiat,&nbsp;Todd Blevins","doi":"10.1080/21541264.2020.1825906","DOIUrl":"https://doi.org/10.1080/21541264.2020.1825906","url":null,"abstract":"<p><p>Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant-pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and <i>Brassica</i><i>rapa</i> suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 3-4","pages":"172-191"},"PeriodicalIF":3.6,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1825906","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38593613","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}

{"title":"Unique and contrasting effects of light and temperature cues on plant transcriptional programs.","authors":"Mai Jarad, Rea Antoniou-Kourounioti, Jo Hepworth, Julia I Qüesta","doi":"10.1080/21541264.2020.1820299","DOIUrl":"10.1080/21541264.2020.1820299","url":null,"abstract":"<p><p>Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression in response to stress or to drive developmental transitions. Among the many signals that plants perceive, light and temperature are of particular interest due to their intensely fluctuating nature which is combined with a long-term seasonal trend. Whereas specific receptors are key in the light-sensing mechanism, the identity of plant thermosensors for high and low temperatures remains far from fully addressed. This review aims at discussing common as well as divergent characteristics of gene expression regulation in plants, controlled by light and temperature. Light and temperature signaling control the abundance of specific transcription factors, as well as the dynamics of co-transcriptional processes such as RNA polymerase elongation rate and alternative splicing patterns. Additionally, sensing both types of cues modulates gene expression by altering the chromatin landscape and through the induction of long non-coding RNAs (lncRNAs). However, while light sensing is channeled through dedicated receptors, temperature can broadly affect chemical reactions inside plant cells. Thus, direct thermal modifications of the transcriptional machinery add another level of complexity to plant transcriptional regulation. Besides the rapid transcriptome changes that follow perception of environmental signals, plant developmental transitions and acquisition of stress tolerance depend on long-term maintenance of transcriptional states (active or silenced genes). Thus, the rapid transcriptional response to the signal (Phase I) can be distinguished from the long-term memory of the acquired transcriptional state (Phase II - remembering the signal). In this review we discuss recent advances in light and temperature signal perception, integration and memory in <i>Arabidopsis thaliana</i>, focusing on transcriptional regulation and highlighting the contrasting and unique features of each type of cue in the process.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 3-4","pages":"134-159"},"PeriodicalIF":3.6,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1820299","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38550193","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}

{"title":"A combinatorial view of old and new RNA polymerase II modifications.","authors":"Danielle E Lyons,&nbsp;Sarah McMahon,&nbsp;Melanie Ott","doi":"10.1080/21541264.2020.1762468","DOIUrl":"https://doi.org/10.1080/21541264.2020.1762468","url":null,"abstract":"<p><p>The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 2","pages":"66-82"},"PeriodicalIF":3.6,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1762468","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37930563","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}

{"title":"Transcription initiation in mycobacteria: a biophysical perspective.","authors":"Hande Boyaci,&nbsp;Ruth M Saecker,&nbsp;Elizabeth A Campbell","doi":"10.1080/21541264.2019.1707612","DOIUrl":"https://doi.org/10.1080/21541264.2019.1707612","url":null,"abstract":"<p><p>Recent biophysical studies of mycobacterial transcription have shed new light on this fundamental process in a group of bacteria that includes deadly pathogens such as <i>Mycobacterium tuberculosis</i> (<i>Mtb), Mycobacterium abscessus</i> (<i>Mab), Mycobacterium leprae</i> (<i>Mlp</i>), as well as the nonpathogenic <i>Mycobacterium smegmatis</i> (<i>Msm</i>). Most of the research has focused on <i>Mtb</i>, the causative agent of tuberculosis (TB), which remains one of the top ten causes of death globally. The enzyme RNA polymerase (RNAP) is responsible for all bacterial transcription and is a target for one of the crucial antibiotics used for TB treatment, rifampicin (Rif). Here, we summarize recent biophysical studies of mycobacterial RNAP that have advanced our understanding of the basic process of transcription, have revealed novel paradigms for regulation, and thus have provided critical information required for developing new antibiotics against this deadly disease.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 2","pages":"53-65"},"PeriodicalIF":3.6,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2019.1707612","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37493204","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}