Transcription-Austin最新文献

{"title":"Incomplete removal of ribosomal RNA can affect chromatin RNA-seq data analysis.","authors":"Michael Tellier, Shona Murphy","doi":"10.1080/21541264.2020.1794491","DOIUrl":"https://doi.org/10.1080/21541264.2020.1794491","url":null,"abstract":"Next-generation sequencing has become one of the major approaches to investigate transcription regulation. RNA-seq, which sequences the RNA complement, can provide a snapshot of the steady-state le...","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 5","pages":"230-235"},"PeriodicalIF":3.6,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1794491","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10749510","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":"Chromatin accessibility and transcription factor binding through the perspective of mitosis.","authors":"Rémi-Xavier Coux,&nbsp;Nick D L Owens,&nbsp;Pablo Navarro","doi":"10.1080/21541264.2020.1825907","DOIUrl":"https://doi.org/10.1080/21541264.2020.1825907","url":null,"abstract":"<p><p>Chromatin accessibility is generally perceived as a common property of active regulatory elements where transcription factors are recruited via DNA-specific interactions and other physico-chemical properties to regulate gene transcription. Recent work in the context of mitosis provides less trivial and potentially more interesting relationships than previously anticipated.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"236-240"},"PeriodicalIF":3.6,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1825907","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38583255","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-range chromatin interactions in pathogenic gene expression control.","authors":"Nahyun Kong,&nbsp;Inkyung Jung","doi":"10.1080/21541264.2020.1843958","DOIUrl":"https://doi.org/10.1080/21541264.2020.1843958","url":null,"abstract":"<p><p>A large number of distal <i>cis</i>-regulatory elements (<i>c</i>REs) have been annotated in the human genome, which plays a central role in orchestrating spatiotemporal gene expression. Since many <i>c</i>REs regulate non-adjacent genes, long-range <i>c</i>RE-promoter interactions are an important factor in the functional characterization of the engaged <i>c</i>REs. In this regard, recent studies have demonstrated that identification of long-range target genes can decipher the effect of genetic mutations residing within <i>c</i>REs on abnormal gene expression. In addition, investigation of altered long-range <i>c</i>REs-promoter interactions induced by chromosomal rearrangements has revealed their critical roles in pathogenic gene expression. In this review, we briefly discuss how the analysis of 3D chromatin structure can help us understand the functional impact of <i>c</i>REs harboring disease-associated genetic variants and how chromosomal rearrangements disrupting topologically associating domains can lead to pathogenic gene expression.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"211-216"},"PeriodicalIF":3.6,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1843958","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38570375","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":"RNA polymerase II-binding aptamers in human ACRO1 satellites disrupt transcription <i>in cis</i>.","authors":"Jennifer L Boots,&nbsp;Frederike von Pelchrzim,&nbsp;Adam Weiss,&nbsp;Bob Zimmermann,&nbsp;Theres Friesacher,&nbsp;Maximilian Radtke,&nbsp;Marek Żywicki,&nbsp;Doris Chen,&nbsp;Katarzyna Matylla-Kulińska,&nbsp;Bojan Zagrovic,&nbsp;Renée Schroeder","doi":"10.1080/21541264.2020.1790990","DOIUrl":"https://doi.org/10.1080/21541264.2020.1790990","url":null,"abstract":"<p><p>Transcription elongation is a highly regulated process affected by many proteins, RNAs and the underlying DNA. Here we show that the nascent RNA can interfere with transcription in human cells, extending our previous findings from bacteria and yeast. We identified a variety of Pol II-binding aptamers (RAPs), prominent in repeat elements such as ACRO1 satellites, LINE1 retrotransposons and CA simple repeats, and also in several protein-coding genes. ACRO1 repeat, when translated <i>in silico</i>, exhibits ~50% identity with the Pol II CTD sequence. Taken together with a recent proposal that proteins in general tend to interact with RNAs similar to their cognate mRNAs, this suggests a mechanism for RAP binding. Using a reporter construct, we show that ACRO1 potently inhibits Pol II elongation <i>in cis</i>. We propose a novel mode of transcriptional regulation in humans, in which the nascent RNA binds Pol II to silence its own expression.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 5","pages":"217-229"},"PeriodicalIF":3.6,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1790990","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10592515","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":"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}