Transcription-Austin最新文献

{"title":"Bacterial RNA synthesis: back to the limelight.","authors":"Irina Artsimovitch","doi":"10.1080/21541264.2021.2001236","DOIUrl":"https://doi.org/10.1080/21541264.2021.2001236","url":null,"abstract":"Bacterial RNA synthesis: back to the limelight Bacteria have been a mainstay of molecular biology, shaping our understanding of the fundamental principles of gene expression control for over half a century. The elegant simplicity of bacterial systems led to many textbook models. Early studies of transcription in bacteria and phages provided a foundation for analysis of more complex eukaryotic systems, and bacterial research started falling out of fashion, with its subjects increasingly seen as over-studied and far removed from modern public-health concerns. While bacterial systems are indeed simpler – from smaller, more information-packed genomes to fewer subunits in RNA polymerase (RNAP) – part of the simplicity in our explanatory models is due to experimental choices made by those who developed them. Limited by the tools and methods of earlier decades, researchers relied on elementary and direct approaches that nevertheless provided an evergreen source of insights that were generalized across the bacterial kingdom and beyond. However, bacteria live in complex environments and exchange not only metabolites but also genetic information. Studies of bacteria in exotic niches and extensive communities, from soils to shales to the human gut, prompted the development of new experimental and computational approaches, revealing that bacteria are very diverse, and many “bacterial” stereotypes do not apply to them all. In this Special Focus issue, we present a collection of reviews that reflect the rapidly changing field of bacterial transcription, highlighting the dawning realization that every aspect – the players, their parts, and their purpose in life and evolution – is more complex than we ever imagined. Key enzymes of the Central Dogma, RNAP and ribosome, are viewed as highly conserved machines. Yet, Miller et al. show that even the best-studied model bacteria, such as Bacillus subtilis and Escherichia coli, have notably diverse RNAPs [1]. Although biochemical and genetic data suggested that they used distinct strategies to regulate RNA synthesis, it took high-resolution cryo-EM structures to make it clear that even their enzymes are different, with two additional auxiliary subunits in B. subtilis “core” RNAP, ε and δ, thought to contribute to the transcription complex stability and disassembly, respectively [1]. Each RNAP has to adapt to the unique needs of its cell, and acquiring additional modules, either as large domain insertions in E. coli or as dissociable subunits, appears to be a common strategy; e.g., bacterial-type chloroplast RNAP apparently needs ten essential subunits to transcribe a ~150-kb genome. New approaches, such as cryo-electron tomography, can capture transcription complexes in their native environments and will no doubt show that bacteria use astonishingly diverse RNAPs and accessory factors. Coupling of transcription and translation is an accepted paradigm in prokaryotes that lack physical barriers between the two machinerie","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 4","pages":"89-91"},"PeriodicalIF":3.6,"publicationDate":"2021-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8632100/pdf/KTRN_12_2001236.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39737001","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":"CREB-mediated transcriptional activation of NRMT1 drives muscle differentiation.","authors":"John G Tooley, James P Catlin, Christine E Schaner Tooley","doi":"10.1080/21541264.2021.1963627","DOIUrl":"10.1080/21541264.2021.1963627","url":null,"abstract":"<p><p>The N-terminal methyltransferase NRMT1 is an important regulator of protein/DNA interactions and plays a role in many cellular processes, including mitosis, cell cycle progression, chromatin organization, DNA damage repair, and transcriptional regulation. Accordingly, loss of NRMT1 results in both developmental pathologies and oncogenic phenotypes. Though NRMT1 plays such important and diverse roles in the cell, little is known about its own regulation. To better understand the mechanisms governing NRMT1 expression, we first identified its predominant transcriptional start site and minimal promoter region with predicted transcription factor motifs. We then used a combination of luciferase and binding assays to confirm CREB1 as the major regulator of NRMT1 transcription. We tested which conditions known to activate CREB1 also activated NRMT1 transcription, and found CREB1-mediated NRMT1 expression was increased during recovery from serum starvation and muscle cell differentiation. To determine how NRMT1 expression affects myoblast differentiation, we used CRISPR/Cas9 technology to knock out NRMT1 expression in immortalized C2C12 mouse myoblasts. C2C12 cells depleted of NRMT1 lacked <i>Pax7</i> expression and were unable to proceed down the muscle differentiation pathway. Instead, they took on characteristics of C2C12 cells that have transdifferentiated into osteoblasts, including increased alkaline phosphatase and type I collagen expression and decreased proliferation. These data implicate NRMT1 as an important downstream target of CREB1 during muscle cell differentiation.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 2-3","pages":"72-88"},"PeriodicalIF":3.6,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8555533/pdf/KTRN_12_1963627.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39319379","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":"Interplay between splicing and transcriptional pausing exerts genome-wide control over alternative polyadenylation.","authors":"Carmen Mora Gallardo,&nbsp;Ainhoa Sánchez de Diego,&nbsp;Carlos Martínez-A,&nbsp;Karel H M van Wely","doi":"10.1080/21541264.2021.1959244","DOIUrl":"https://doi.org/10.1080/21541264.2021.1959244","url":null,"abstract":"<p><p>Recent studies have identified multiple polyadenylation sites in nearly all mammalian genes. Although these are interpreted as evidence for alternative polyadenylation, our knowledge of the underlying mechanisms is still limited. Most studies only consider the immediate surroundings of gene ends, even though <i>in vitro</i> experiments have uncovered the involvement of external factors such as splicing. Whereas <i>in vivo</i> splicing manipulation was impracticable until recently, we now used mutants in the <i>Death Inducer Obliterator</i> (<i>DIDO</i>) gene to study their impact on 3' end processing. We observe multiple rounds of readthrough and gene fusions, suggesting that no arbitration between polyadenylation sites occurs. Instead, a window of opportunity seems to control end processing. Through the identification of T-rich sequence motifs, our data indicate that splicing and transcriptional pausing interact to regulate alternative polyadenylation. We propose that 3' splice site activation comprises a variable timer, which determines how long transcription proceeds before polyadenylation signals are recognized. Thus, the role of core polyadenylation signals could be more passive than commonly believed. Our results provide new insights into the mechanisms of alternative polyadenylation and expand the catalog of related aberrations.<b>Abbreviations</b> APA: alternative polyadenylation; bp: basepair; MEF: mouse embryonic fibroblasts; PA: polyadenylation; PAS: polyadenylation site; Pol II: (RNA) polymerase II ; RT-PCR:reverse-transcriptase PCR; SF:splicing factor; SFPQ:splicing factor rich in proline and glutamine; SS:splice site; TRSM:Thymidine rich sequence motif; UTR:untranslated terminal region.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 2-3","pages":"55-71"},"PeriodicalIF":3.6,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8555548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39299005","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: role and contribution in pancreatic cancer.","authors":"K T Ramya Devi,&nbsp;Dharshene Karthik,&nbsp;TharunSelvam Mahendran,&nbsp;M K Jaganathan,&nbsp;Sanjana Prakash Hemdev","doi":"10.1080/21541264.2021.1922071","DOIUrl":"https://doi.org/10.1080/21541264.2021.1922071","url":null,"abstract":"<p><p>Noncoding RNAs are proclaimed to be expressed in various cancer types and one such type is found to be pancreatic ductal adenocarcinoma (PDAC). The long noncoding RNAs (LncRNAs) affect the migration, invasion, and growth of tumor cells by playing important roles in the process of epigenesis, post-transcription, and transcriptional regulation along with the maintenance of apoptosis and cell cycle. It is quite subtle whether the alterations in lncRNAs would impact PDAC progression and development. This review throws a spotlight on the lncRNAs associated with tumor functions: MALAT-1, HOTAIR, HOXA13, H19, LINC01559, LINC00460, SNHG14, SNHG16, DLX6-AS1, MSC-AS1, ABHD11-AS1, DUXAP8, DANCR, XIST, DLEU2, etc. are upregulated lncRNAs whereas GAS5, HMlincRNA717, MIAT, LINC01111, lncRNA KCNK15-AS1, etc. are downregulated lncRNAs inhibiting the invasion and progression of PDAC. These data provided helps in the assessment of lncRNAs in the development, metastasis, and occurrence of PDAC and also play a vital role in the evolution of biomarkers and therapeutic agents for the treatment of PDAC.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 1","pages":"12-27"},"PeriodicalIF":3.6,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2021.1922071","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39033187","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":"Evolution of the genetic code.","authors":"Lei Lei, Zachary Frome Burton","doi":"10.1080/21541264.2021.1927652","DOIUrl":"10.1080/21541264.2021.1927652","url":null,"abstract":"<p><p>Diverse models have been advanced for the evolution of the genetic code. Here, models for tRNA, aminoacyl-tRNA synthetase (aaRS) and genetic code evolution were combined with an understanding of EF-Tu suppression of tRNA 3^rd anticodon position wobbling. The result is a highly detailed scheme that describes the placements of all amino acids in the standard genetic code. The model describes evolution of 6-, 4-, 3-, 2- and 1-codon sectors. Innovation in column 3 of the code is explained. Wobbling and code degeneracy are explained. Separate distribution of serine sectors between columns 2 and 4 of the code is described. We conclude that very little chaos contributed to evolution of the genetic code and that the pattern of evolution of aaRS enzymes describes a history of the evolution of the code. A model is proposed to describe the biological selection for the earliest evolution of the code and for protocell evolution.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 1","pages":"28-53"},"PeriodicalIF":3.6,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/cf/79/KTRN_12_1927652.PMC8172153.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38992935","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 III and antiviral innate immune response.","authors":"Nayef Jarrous,&nbsp;Alexander Rouvinski","doi":"10.1080/21541264.2021.1890915","DOIUrl":"https://doi.org/10.1080/21541264.2021.1890915","url":null,"abstract":"<p><p>The innate immune system has numerous signal transduction pathways that lead to the production of type I interferons in response to exposure of cells to external stimuli. One of these pathways comprises RNA polymerase (Pol) III that senses common DNA viruses, such as cytomegalovirus, vaccinia, herpes simplex virus-1 and varicella zoster virus. This polymerase detects and transcribes viral genomic regions to generate AU-rich transcripts that bring to the induction of type I interferons. Remarkably, Pol III is also stimulated by foreign non-viral DNAs and expression of one of its subunits is induced by an RNA virus, the Sindbis virus. Moreover, a protein subunit of RNase P, which is known to associate with Pol III in initiation complexes, is induced by viral infection. Accordingly, alliance of the two tRNA enzymes in innate immunity merits a consideration.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"12 1","pages":"1-11"},"PeriodicalIF":3.6,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2021.1890915","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25397710","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":"Incomplete removal of ribosomal RNA can affect chromatin RNA-seq data analysis.","authors":"Michael Tellier,&nbsp;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}