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RNA processing in skeletal muscle biology and disease. 骨骼肌生物学和疾病中的RNA加工。
IF 3.6
Transcription-Austin Pub Date : 2019-02-01 Epub Date: 2019-01-15 DOI: 10.1080/21541264.2018.1558677
Emma R Hinkle, Hannah J Wiedner, Adam J Black, Jimena Giudice
{"title":"RNA processing in skeletal muscle biology and disease.","authors":"Emma R Hinkle,&nbsp;Hannah J Wiedner,&nbsp;Adam J Black,&nbsp;Jimena Giudice","doi":"10.1080/21541264.2018.1558677","DOIUrl":"https://doi.org/10.1080/21541264.2018.1558677","url":null,"abstract":"<p><p>RNA processing encompasses the capping, cleavage, polyadenylation and alternative splicing of pre-mRNA. Proper muscle development relies on precise RNA processing, driven by the coordination between RNA-binding proteins. Recently, skeletal muscle biology has been intensely investigated in terms of RNA processing. High throughput studies paired with deletion of RNA-binding proteins have provided a high-level understanding of the molecular mechanisms controlling the regulation of RNA-processing in skeletal muscle. Furthermore, misregulation of RNA processing is implicated in muscle diseases. In this review, we comprehensively summarize recent studies in skeletal muscle that demonstrated: (i) the importance of RNA processing, (ii) the RNA-binding proteins that are involved, and (iii) diseases associated with defects in RNA processing.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"10 1","pages":"1-20"},"PeriodicalIF":3.6,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2018.1558677","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36790241","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: 28
Share and share alike: the role of Tra1 from the SAGA and NuA4 coactivator complexes. 分享和分享相似：来自SAGA和NuA4共激活子复合物的Tra1的作用。
IF 3.6
Transcription-Austin Pub Date : 2019-02-01 Epub Date: 2018-10-30 DOI: 10.1080/21541264.2018.1530936
Alan C M Cheung, Luis Miguel Díaz-Santín
{"title":"Share and share alike: the role of Tra1 from the SAGA and NuA4 coactivator complexes.","authors":"Alan C M Cheung,&nbsp;Luis Miguel Díaz-Santín","doi":"10.1080/21541264.2018.1530936","DOIUrl":"10.1080/21541264.2018.1530936","url":null,"abstract":"<p><p>SAGA and NuA4 are coactivator complexes required for transcription on chromatin. Although they contain different enzymatic and biochemical activities, both contain the large Tra1 subunit. Recent electron microscopy studies have resolved the complete structure of Tra1 and its integration in SAGA/NuA4, providing important insight into Tra1 function.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"10 1","pages":"37-43"},"PeriodicalIF":3.6,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2018.1530936","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36675030","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: 15
Global role for coactivator complexes in RNA polymerase II transcription. 助激活物复合物在RNA聚合酶II转录中的全局作用。
IF 3.6
Transcription-Austin Pub Date : 2019-02-01 Epub Date: 2018-10-09 DOI: 10.1080/21541264.2018.1521214
Veronique Fischer, Kenny Schumacher, Laszlo Tora, Didier Devys
{"title":"Global role for coactivator complexes in RNA polymerase II transcription.","authors":"Veronique Fischer,&nbsp;Kenny Schumacher,&nbsp;Laszlo Tora,&nbsp;Didier Devys","doi":"10.1080/21541264.2018.1521214","DOIUrl":"https://doi.org/10.1080/21541264.2018.1521214","url":null,"abstract":"<p><p>SAGA and TFIID are related transcription complexes, which were proposed to alternatively deliver TBP at different promoter classes. Recent genome-wide studies in yeast revealed that both complexes are required for the transcription of a vast majority of genes by RNA polymerase II raising new questions about the role of coactivators.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"10 1","pages":"29-36"},"PeriodicalIF":3.6,"publicationDate":"2019-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2018.1521214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36557907","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: 17
RNA polymerase I activation and hibernation: unique mechanisms for unique genes. RNA聚合酶I的激活和冬眠:独特基因的独特机制。
IF 3.6
Transcription-Austin Pub Date : 2018-01-01 Epub Date: 2018-01-26 DOI: 10.1080/21541264.2017.1416267
Carlos Fernández-Tornero
{"title":"RNA polymerase I activation and hibernation: unique mechanisms for unique genes.","authors":"Carlos Fernández-Tornero","doi":"10.1080/21541264.2017.1416267","DOIUrl":"https://doi.org/10.1080/21541264.2017.1416267","url":null,"abstract":"<p><p>In yeast, transcription of ribosomal DNA (rDNA) by RNA polymerase I (Pol I) is regulated by unique mechanisms acting at the level of the enzyme. Under stress situations such as starvation, Pol I hibernates through dimerization. When growth conditions are restored, dimer disassembly and Rrn3 binding drive enzyme activation and subsequent recruitment to rDNA.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"248-254"},"PeriodicalIF":3.6,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2017.1416267","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35769825","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: 26
Architecture of the RNA polymerase II elongation complex: new insights into Spt4/5 and Elf1. RNA聚合酶II延伸复合物的结构:Spt4/5和Elf1的新见解。
IF 3.6
Transcription-Austin Pub Date : 2018-01-01 Epub Date: 2018-05-07 DOI: 10.1080/21541264.2018.1454817
Haruhiko Ehara, Shun-Ichi Sekine
{"title":"Architecture of the RNA polymerase II elongation complex: new insights into Spt4/5 and Elf1.","authors":"Haruhiko Ehara,&nbsp;Shun-Ichi Sekine","doi":"10.1080/21541264.2018.1454817","DOIUrl":"https://doi.org/10.1080/21541264.2018.1454817","url":null,"abstract":"<p><p>Transcription by RNA polymerase II (Pol II) is accomplished with the aid of numerous accessory factors specific to each transcriptional stage. The structure of the Pol II elongation complex (EC) bound with Spt4/5, Elf1, and TFIIS unveiled the sophisticated basal EC architecture essential for transcription elongation and other transcription-related events.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"9 5","pages":"286-291"},"PeriodicalIF":3.6,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2018.1454817","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35982700","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: 10
Hinge action versus grip in translocation by RNA polymerase. RNA聚合酶在易位中的铰链作用与紧握作用。
IF 3.6
Transcription-Austin Pub Date : 2018-01-01 Epub Date: 2017-08-30 DOI: 10.1080/21541264.2017.1330179
Yuri A Nedialkov, Kristopher Opron, Hailey L Caudill, Fadi Assaf, Amanda J Anderson, Robert I Cukier, Guowei Wei, Zachary F Burton
{"title":"Hinge action versus grip in translocation by RNA polymerase.","authors":"Yuri A Nedialkov,&nbsp;Kristopher Opron,&nbsp;Hailey L Caudill,&nbsp;Fadi Assaf,&nbsp;Amanda J Anderson,&nbsp;Robert I Cukier,&nbsp;Guowei Wei,&nbsp;Zachary F Burton","doi":"10.1080/21541264.2017.1330179","DOIUrl":"https://doi.org/10.1080/21541264.2017.1330179","url":null,"abstract":"<p><p>Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA-DNA hybrid resulting in opening of the furthest upstream i-8 RNA-DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β' Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel. Because the β flap tip connects to the RNAP active site through the β subunit double-Ψ-β-barrel and the associated sandwich barrel hybrid motif (also called the flap domain), the RNAP active site is coupled to the RNA exit channel and to the translocation of RNA-DNA. Using an exonuclease III assay to monitor translocation of RNAP elongation complexes, we show that K<sup>+</sup> and Mg<sup>2+</sup> and also an RNA 3'-OH or a 3'-H<sub>2</sub> affect RNAP sliding. Because RNAP grip to template suggests a sticky translocation mechanism, and because grip is enhanced by increasing K<sup>+</sup> and Mg<sup>2+</sup>concentration, biochemical assays are consistent with a conformational change that drives forward translocation as observed in simulations. Mutational analysis of the bridge helix indicates that 778-GARKGL-783 (Escherichia coli numbering) is a homeostatic hinge that undergoes multiple bends to compensate for complex conformational dynamics during phosphodiester bond formation and translocation.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"9 1","pages":"1-16"},"PeriodicalIF":3.6,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2017.1330179","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35357945","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: 8
Measuring dynamics of eukaryotic transcription initiation: Challenges, insights and opportunities. 测量真核生物转录起始的动力学:挑战，见解和机遇。
IF 3.6
Transcription-Austin Pub Date : 2018-01-01 Epub Date: 2017-10-09 DOI: 10.1080/21541264.2017.1363017
Zhengjian Zhang, Robert Tjian
{"title":"Measuring dynamics of eukaryotic transcription initiation: Challenges, insights and opportunities.","authors":"Zhengjian Zhang,&nbsp;Robert Tjian","doi":"10.1080/21541264.2017.1363017","DOIUrl":"https://doi.org/10.1080/21541264.2017.1363017","url":null,"abstract":"<p><p>Transcription of protein-encoding genes in eukaryotic cells is a dynamically coordinated process. Many of the key transcription regulators contain functionally essential intrinsically disordered regions (IDRs), the dynamic nature of which creates extra challenges to traditional biochemical analyses. Recent advances in single-molecule fluorescence imaging technology have enabled direct visualization of these rapid, complex and dynamic molecular interactions in real time.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"9 3","pages":"159-165"},"PeriodicalIF":3.6,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2017.1363017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35417131","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: 13
The mixed lineage leukemia 4 (MLL4) methyltransferase complex is involved in transforming growth factor beta (TGF-β)-activated gene transcription. 混合谱系白血病4 (MLL4)甲基转移酶复合物参与转化生长因子β (TGF-β)激活基因的转录。
IF 3.6
Transcription-Austin Pub Date : 2018-01-01 Epub Date: 2017-11-03 DOI: 10.1080/21541264.2017.1373890
Roy Baas, Hetty A A M van Teeffelen, Sjoerd J D Tjalsma, H Th Marc Timmers
{"title":"The mixed lineage leukemia 4 (MLL4) methyltransferase complex is involved in transforming growth factor beta (TGF-β)-activated gene transcription.","authors":"Roy Baas,&nbsp;Hetty A A M van Teeffelen,&nbsp;Sjoerd J D Tjalsma,&nbsp;H Th Marc Timmers","doi":"10.1080/21541264.2017.1373890","DOIUrl":"https://doi.org/10.1080/21541264.2017.1373890","url":null,"abstract":"<p><p>Sma and Mad related (SMAD)-mediated Transforming Growth Factor β (TGF-β) and Bone Morphogenetic Protein (BMP) signaling is required for various cellular processes. The activated heterotrimeric SMAD protein complexes associate with nuclear proteins such as the histone acetyltransferases p300, PCAF and the Mixed Lineage Leukemia 4 (MLL4) subunit Pax Transactivation domain-Interacting Protein (PTIP) to regulate gene transcription. We investigated the functional role of PTIP and PTIP Interacting protein 1 (PA1) in relation to TGF-β-activated SMAD signaling. We immunoprecipitated PTIP and PA1 with all SMAD family members to identify the TGF-β and not BMP-specific SMADs as interacting proteins. Gene silencing experiments of MLL4 and the subunits PA1 and PTIP confirm TGF-β-specific genes to be regulated by the MLL4 complex, which links TGF-β signaling to transcription regulation by the MLL4 methyltransferase complex.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"9 2","pages":"67-74"},"PeriodicalIF":3.6,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2017.1373890","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35467747","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: 6
linc00673 (ERRLR01) is a prognostic indicator of overall survival in breast cancer. linc00673 (ERRLR01)是乳腺癌总生存期的预后指标。
IF 3.6
Transcription-Austin Pub Date : 2018-01-01 Epub Date: 2017-10-04 DOI: 10.1080/21541264.2017.1329684
Ubaidat Abdul-Rahman, Balázs Győrffy, Brian D Adams
{"title":"linc00673 (ERRLR01) is a prognostic indicator of overall survival in breast cancer.","authors":"Ubaidat Abdul-Rahman,&nbsp;Balázs Győrffy,&nbsp;Brian D Adams","doi":"10.1080/21541264.2017.1329684","DOIUrl":"https://doi.org/10.1080/21541264.2017.1329684","url":null,"abstract":"<p><p>LncRNAs are novel noncoding RNAs involved in the epigenetic regulation of gene expression by recruiting ribonucleoprotein complexes to specific genomic loci to initiate histone methylation and/or other chromatin modifications. LncRNAs themselves function as tumor suppressors or oncogenes, depending on the gene regulatory networks they govern. We identified lnc00673 (ERRLR01) as a marker of overall survival (OS) in breast cancer patients. Specifically, ERRLR01 levels were elevated in triple-negative breast cancer (TNBC) as compared with Luminal-A, Luminal-B, and HER2 breast cancer subtypes. ERRLR01 levels were also inversely correlated with breast cancer survival across all breast cancer patients. Upon stratification, OS in ERα<sup>-</sup> tumors correlated with negative overall survival, while in ERα<sup>+</sup> tumors, ERRLR01 correlated with positive outcomes. This suggests ERRLR01 is modulated by hormone signaling in breast cancer. Gene-network analysis revealed ERRLR01 correlated with distinct pathways including \"epithelial development\" and \"cellular differentiation.\" These data suggest ERRLR01 operates as an oncogene in TNBC, as well as a biomarker in breast cancer patients.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"9 1","pages":"17-29"},"PeriodicalIF":3.6,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2017.1329684","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35308502","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: 25
Helicases as transcription termination factors: Different solutions for a common problem. 解旋酶作为转录终止因子:一个共同问题的不同解决方案。
IF 3.6
Transcription-Austin Pub Date : 2018-01-01 Epub Date: 2017-10-04 DOI: 10.1080/21541264.2017.1361503
Zhong Han, Odil Porrua
{"title":"Helicases as transcription termination factors: Different solutions for a common problem.","authors":"Zhong Han,&nbsp;Odil Porrua","doi":"10.1080/21541264.2017.1361503","DOIUrl":"https://doi.org/10.1080/21541264.2017.1361503","url":null,"abstract":"<p><p>Helicases are enzymes that remodel nucleic acids or protein-nucleic acid complexes in an ATP-dependent manner. They are ubiquitous and can play many diverse functions related to the metabolism of nucleic acids. A few helicases from both the prokaryotic and the eukaryotic worlds have the ability to induce transcription termination. Here we discuss how the same biological function is achieved by different helicases with quite divergent structures and mechanisms of action.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"9 3","pages":"152-158"},"PeriodicalIF":3.6,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2017.1361503","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35337080","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: 2
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