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Epigenetic plasticity of enhancers in cancer. 癌症增强子的表观遗传可塑性。
IF 3.6
Transcription-Austin Pub Date : 2020-02-01 Epub Date: 2020-01-16 DOI: 10.1080/21541264.2020.1713682
Jie Yao, Ji Chen, Lian-Yun Li, Min Wu
{"title":"Epigenetic plasticity of enhancers in cancer.","authors":"Jie Yao,&nbsp;Ji Chen,&nbsp;Lian-Yun Li,&nbsp;Min Wu","doi":"10.1080/21541264.2020.1713682","DOIUrl":"https://doi.org/10.1080/21541264.2020.1713682","url":null,"abstract":"<p><p>Enhancers are cis-acting elements with many sites bound by transcription factors and activate transcription over long distance. Histone modifications are critical for enhancer activity and utilized as hallmarks for the identification of putative enhancers. Monomethylation of histone H3 lysine 4 (H3K4me1) is the mark for enhancer priming; acetylation of histone H3 lysine 27 (H3K27ac) for active enhancers and trimethylation of histone H3 lysine 27 (H3K27me3) for silent enhancers. Recent studies from multiple groups have provided evidence that enhancer reprogramming, especially gain of enhancer activity, is closely related to tumorigenesis and cancer development. In this review, we will summarize the recent discoveries about enhancer regulation and the mechanisms of enhancer reprogramming in tumorigenesis, and discuss the potential application of enhancer manipulation in precision medicine.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"11 1","pages":"26-36"},"PeriodicalIF":3.6,"publicationDate":"2020-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2020.1713682","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37547505","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: 20
Change in inorganic phosphate physical state can regulate transcription 无机磷酸盐物理状态的改变可以调控转录
IF 3.6
Transcription-Austin Pub Date : 2019-10-20 DOI: 10.1080/21541264.2019.1682454
M. Gottesman, A. Mustaev
{"title":"Change in inorganic phosphate physical state can regulate transcription","authors":"M. Gottesman, A. Mustaev","doi":"10.1080/21541264.2019.1682454","DOIUrl":"https://doi.org/10.1080/21541264.2019.1682454","url":null,"abstract":"ABSTRACT Inorganic phosphate (Pi), a ubiquitous metabolite, is involved in all major biochemical pathways. We demonstrate that, in vitro, MgHPO4 (the intracellular Pi form) at physiological concentrations can exist in a metastable supersaturated dissolved state or as a precipitate. We have shown that in solution, MgHPO4 strongly stimulates exonuclease nascent transcript cleavage by RNA polymerase. We report here that MgHPO4 precipitate selectively and efficiently inhibits transcription initiation in vitro. In view of the MgHPO4 solubility and in vitro sensitivity of RNA synthesis to MgHPO4 precipitate, at physiological concentrations, MgHPO4 should cause a 50–98% inhibition of cellular RNA synthesis, thus exerting a strong regulatory action. The effects of Pi on transcription in vivo will, therefore, reflect the physical state of intracellular Pi.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"104 1","pages":"187 - 194"},"PeriodicalIF":3.6,"publicationDate":"2019-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80672770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evidence that dissociation of Spt16 from transcribed genes is partially dependent on RNA Polymerase II termination 证据表明Spt16与转录基因的分离部分依赖于RNA聚合酶II的终止
IF 3.6
Transcription-Austin Pub Date : 2019-10-20 DOI: 10.1080/21541264.2019.1685837
Jessica B Campbell, M. Edwards, Sydney A Ozersky, Andrea A Duina
{"title":"Evidence that dissociation of Spt16 from transcribed genes is partially dependent on RNA Polymerase II termination","authors":"Jessica B Campbell, M. Edwards, Sydney A Ozersky, Andrea A Duina","doi":"10.1080/21541264.2019.1685837","DOIUrl":"https://doi.org/10.1080/21541264.2019.1685837","url":null,"abstract":"ABSTRACT FACT (FAcilitates Chromatin Transactions) is a highly conserved histone chaperone complex in eukaryotic cells that can interact and manipulate nucleosomes in order to promote a variety of DNA-based processes and to maintain the integrity of chromatin throughout the genome. Whereas key features of the physical interactions that occur between FACT and nucleosomes in vitro have been elucidated in recent years, less is known regarding FACT functional dynamics in vivo. Using the Saccharomyces cerevisiae system, we now provide evidence that at least at some genes dissociation of the FACT subunit Spt16 from their 3′ ends is partially dependent on RNA Polymerase II (Pol II) termination. Combined with other studies, our results are consistent with a two-phase mechanism for FACT dissociation from genes, one that occurs upstream from Pol II dissociation and is Pol II termination-independent and the other that occurs further downstream and is dependent on Pol II termination.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"21 1","pages":"195 - 206"},"PeriodicalIF":3.6,"publicationDate":"2019-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85065934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Clock-controlled rhythmic transcription: is the clock enough and how does it work? 时钟控制节奏转录:时钟足够了吗?它是如何工作的?
IF 3.6
Transcription-Austin Pub Date : 2019-10-09 DOI: 10.1080/21541264.2019.1673636
Joshua R Beytebiere, Ben J Greenwell, A. Sahasrabudhe, J. Menet
{"title":"Clock-controlled rhythmic transcription: is the clock enough and how does it work?","authors":"Joshua R Beytebiere, Ben J Greenwell, A. Sahasrabudhe, J. Menet","doi":"10.1080/21541264.2019.1673636","DOIUrl":"https://doi.org/10.1080/21541264.2019.1673636","url":null,"abstract":"ABSTRACT Circadian clocks regulate the rhythmic expression of thousands of genes underlying the daily oscillations of biological functions. Here, we discuss recent findings showing that circadian clock rhythmic transcriptional outputs rely on additional mechanisms than just clock gene DNA binding, which may ultimately contribute to the plasticity of circadian transcriptional programs.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"20 1","pages":"212 - 221"},"PeriodicalIF":3.6,"publicationDate":"2019-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81989959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
New means to an end: mRNA export activity impacts alternative polyadenylation 新手段的目的:mRNA出口活动影响替代聚腺苷化
IF 3.6
Transcription-Austin Pub Date : 2019-09-02 DOI: 10.1080/21541264.2019.1658557
Jihae Shin, Hong Cheng, B. Tian
{"title":"New means to an end: mRNA export activity impacts alternative polyadenylation","authors":"Jihae Shin, Hong Cheng, B. Tian","doi":"10.1080/21541264.2019.1658557","DOIUrl":"https://doi.org/10.1080/21541264.2019.1658557","url":null,"abstract":"ABSTRACT Gene expression involves multiple co- and post-transcriptional processes that have been increasingly found intertwined. A recent work by our groups (Chen et al. Mol Cell, 2019) indicates that expression of alternative polyadenylation isoforms in mammalian cells can be controlled by nuclear export activities. This regulation has distinct impacts on genes having different sizes and nucleotide contents, and involves RNA polymerase II distribution toward the 3ʹ end of genes. This work raises a number of intriguing questions concerning how 3ʹ end processing and nuclear export are integrated and how their regulation feeds back to transcription.","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"300 1","pages":"207 - 211"},"PeriodicalIF":3.6,"publicationDate":"2019-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73590160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Exploiting phage strategies to modulate bacterial transcription. 利用噬菌体策略调节细菌转录。
IF 3.6
Transcription-Austin Pub Date : 2019-08-01 Epub Date: 2019-10-30 DOI: 10.1080/21541264.2019.1684137
Markus C Wahl, Ranjan Sen
{"title":"Exploiting phage strategies to modulate bacterial transcription.","authors":"Markus C Wahl,&nbsp;Ranjan Sen","doi":"10.1080/21541264.2019.1684137","DOIUrl":"https://doi.org/10.1080/21541264.2019.1684137","url":null,"abstract":"<p><p>Bacteriophages employ small proteins to usurp host molecular machinery, thereby interfering with central metabolic processes in infected bacteria. Generally, phages inhibit or redirect host transcription to favor transcription of their own genomes. Mechanistic and structural studies of phage-modulated host transcription may provide inspirations for the development of novel antibacterial substances.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":" ","pages":"222-230"},"PeriodicalIF":3.6,"publicationDate":"2019-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2019.1684137","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40552370","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: 5
Identify gene expression pattern change at transcriptional and post-transcriptional levels. 确定基因表达模式在转录和转录后水平的变化。
IF 3.6
Transcription-Austin Pub Date : 2019-06-01 Epub Date: 2019-02-05 DOI: 10.1080/21541264.2019.1575159
Ji-Gang Zhang, Chao Xu, Lan Zhang, Wei Zhu, Hui Shen, Hong-Wen Deng
{"title":"Identify gene expression pattern change at transcriptional and post-transcriptional levels.","authors":"Ji-Gang Zhang,&nbsp;Chao Xu,&nbsp;Lan Zhang,&nbsp;Wei Zhu,&nbsp;Hui Shen,&nbsp;Hong-Wen Deng","doi":"10.1080/21541264.2019.1575159","DOIUrl":"https://doi.org/10.1080/21541264.2019.1575159","url":null,"abstract":"<p><p>Gene transcription is regulated with distinct sets of regulatory factors at multiple levels. Transcriptional and post-transcriptional regulation constitute two major regulation modes of gene expression to either activate or repress the initiation of transcription and thereby control the number of proteins synthesized during translation. Disruptions of the proper regulation patterns at transcriptional and post-transcriptional levels are increasingly recognized as causes of human diseases. Consequently, identifying the differential gene expression at transcriptional and post-transcriptional levels respectively is vital to identify potential disease-associated and/or causal genes and understand their roles in the disease development. Here, we proposed a novel method with a linear mixed model that can identify a set of differentially expressed genes at transcriptional and post-transcriptional levels. The simulation and real data analysis showed our method could provide an accurate way to identify genes subject to aberrant transcriptional and post-transcriptional regulation and reveal the potential causal genes that contributed to the diseases.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"10 3","pages":"137-146"},"PeriodicalIF":3.6,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2019.1575159","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36910378","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: 9
Balanced between order and disorder: a new phase in transcription elongation control and beyond. 平衡之间的秩序和无序:在转录延伸控制和超越的新阶段。
IF 3.6
Transcription-Austin Pub Date : 2019-06-01 Epub Date: 2019-01-31 DOI: 10.1080/21541264.2019.1570812
Huasong Lu, Rongdiao Liu, Qiang Zhou
{"title":"Balanced between order and disorder: a new phase in transcription elongation control and beyond.","authors":"Huasong Lu,&nbsp;Rongdiao Liu,&nbsp;Qiang Zhou","doi":"10.1080/21541264.2019.1570812","DOIUrl":"https://doi.org/10.1080/21541264.2019.1570812","url":null,"abstract":"<p><p>We recently reported that the cyclin T1 histidine-rich domain creates a phase-separated environment to promote hyperphosphorylation of RNA polymerase II C-terminal domain and robust transcriptional elongation by P-TEFb. Here, we discuss this and several other recent discoveries to demonstrate that phase separation is important for controlling various aspects of transcription.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"10 3","pages":"157-163"},"PeriodicalIF":3.6,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2019.1570812","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36870818","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: 5
Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription. 这样转录Rap1 通过抑制不同的转录来赋予启动子方向性。
IF 3.6
Transcription-Austin Pub Date : 2019-06-01 Epub Date: 2019-05-05 DOI: 10.1080/21541264.2019.1608716
Andrew C K Wu, Folkert J Van Werven
{"title":"Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription.","authors":"Andrew C K Wu, Folkert J Van Werven","doi":"10.1080/21541264.2019.1608716","DOIUrl":"10.1080/21541264.2019.1608716","url":null,"abstract":"<p><p>In eukaryotes, divergent transcription is a major source of noncoding RNAs. Recent studies have uncovered that in yeast, the transcription factor Rap1 restricts transcription in the divergent direction and thereby controls promoter directionality. Here, we summarize these findings, propose regulatory principles, and discuss the implications for eukaryotic gene regulation.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"10 3","pages":"164-170"},"PeriodicalIF":3.6,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602560/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37376592","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
PML-RARα induces all-trans retinoic acid-dependent transcriptional activation through interaction with MED1. PML-RARα通过与MED1相互作用诱导全反式维甲酸依赖性转录激活。
IF 3.6
Transcription-Austin Pub Date : 2019-06-01 Epub Date: 2019-06-05 DOI: 10.1080/21541264.2019.1624467
Tomoya Fukuoka, Asami Kawai, Taku Takahara, Mahiro Mori, Robert G Roeder, Natsumi Hasegawa, Mitsuhiro Ito
{"title":"PML-RARα induces all-trans retinoic acid-dependent transcriptional activation through interaction with MED1.","authors":"Tomoya Fukuoka,&nbsp;Asami Kawai,&nbsp;Taku Takahara,&nbsp;Mahiro Mori,&nbsp;Robert G Roeder,&nbsp;Natsumi Hasegawa,&nbsp;Mitsuhiro Ito","doi":"10.1080/21541264.2019.1624467","DOIUrl":"https://doi.org/10.1080/21541264.2019.1624467","url":null,"abstract":"<p><p>Transcriptional activation by PML-RARα, an acute promyelocytic leukemia-related oncofusion protein, requires pharmacological concentrations of all-trans retinoic acid (ATRA). However, the mechanism by which the liganded PML-RARα complex leads to the formation of the preinitiation complex has been unidentified. Here we demonstrate that the Mediator subunit MED1 plays an important role in the ATRA-dependent activation of the PML-RARα-bound promoter. Luciferase reporter assays showed that PML-RARα induced significant transcription at pharmacological doses (1 μM) of ATRA; however, this was submaximal and equivalent to the level of transcription driven by intact RARα at physiological doses (1 nM) of ATRA. Transcription depended upon the interaction of PML-RARα with the two LxxLL nuclear receptor recognition motifs of MED1, and LxxLL→LxxAA mutations led to minimal transcription. Mechanistically, MED1 interacted ATRA-dependently with the RARα portion of PML-RARα through the two LxxLL motifs of MED1. These results suggest that PML-RARα initiates ATRA-induced transcription through its interaction with MED1.</p>","PeriodicalId":47009,"journal":{"name":"Transcription-Austin","volume":"10 3","pages":"147-156"},"PeriodicalIF":3.6,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21541264.2019.1624467","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37278822","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
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