scholarly journals Transcription Factor Regulation of RNA polymerase’s Torsional Capacity

2018 ◽  
Author(s):  
Jie Ma ◽  
Chuang Tan ◽  
Xiang Gao ◽  
Robert M. Fulbright ◽  
Jeffrey W. Roberts ◽  
...  

ABSTRACTDuring transcription, RNA polymerase (RNAP) supercoils DNA as it forsward-translocates. Accumulation of this torsional stress in DNA can become a roadblock for an elongating RNAP and thus should be subject to regulation during transcription. Here, we investigate whether, and how, a transcription factor may regulate the torque generation capacity of RNAP and torque-induced RNAP stalling. Using a real-time assay based on an angular optical trap, we found that under a resisting torque, RNAP was highly prone to extensive backtracking. However, the presence of GreB, a transcription factor that facilitates the cleavage of the 3’ end of the extruded RNA transcript, greatly suppressed backtracking and remarkably increased the torque that RNAP was able to generate by 65%, from 11.2 to 18.5 pN·nm. Analysis of the real-time trajectories of RNAP position at a stall revealed the kinetic parameters of backtracking and GreB rescue. These results demonstrate that backtracking is the primary mechanism that limits transcription against DNA supercoiling and the transcription factor GreB effectively enhances the torsional capacity of RNAP. These findings broaden the potential impact of transcription factors on RNAP functionality.

2019 ◽  
Vol 116 (7) ◽  
pp. 2583-2588 ◽  
Author(s):  
Jie Ma ◽  
Chuang Tan ◽  
Xiang Gao ◽  
Robert M. Fulbright ◽  
Jeffrey W. Roberts ◽  
...  

During transcription, RNA polymerase (RNAP) supercoils DNA as it translocates. The resulting torsional stress in DNA can accumulate and, in the absence of regulatory mechanisms, becomes a barrier to RNAP elongation, causing RNAP stalling, backtracking, and transcriptional arrest. Here we investigate whether and how a transcription factor may regulate both torque-induced Escherichia coli RNAP stalling and the torque generation capacity of RNAP. Using a unique real-time angular optical trapping assay, we found that RNAP working against a resisting torque was highly prone to extensive backtracking. We then investigated transcription in the presence of GreB, a transcription factor known to rescue RNAP from the backtracked state. We found that GreB greatly suppressed RNAP backtracking and remarkably increased the torque that RNAP was able to generate by 65%, from 11.2 pN⋅nm to 18.5 pN·nm. Variance analysis of the real-time positional trajectories of RNAP after a stall revealed the kinetic parameters of backtracking and GreB rescue. These results demonstrate that backtracking is the primary mechanism by which torsional stress limits transcription and that the transcription factor GreB effectively enhances the torsional capacity of RNAP. These findings suggest a broader role for transcription factors in regulating RNAP functionality and elongation.


2019 ◽  
Vol 116 (3) ◽  
pp. 210a
Author(s):  
Jie Ma ◽  
Chuang Tan ◽  
Xiang Gao ◽  
Robert M. Fulbright ◽  
Jeffrey W. Roberts ◽  
...  

2019 ◽  
Vol 147 (8) ◽  
pp. 2961-2977 ◽  
Author(s):  
Kelly Ryan ◽  
Lisa Bucci ◽  
Javier Delgado ◽  
Robert Atlas ◽  
Shirley Murillo

Abstract Aircraft reconnaissance missions remain the primary means of collecting direct measurements of marine atmospheric conditions affecting tropical cyclone formation and evolution. The National Hurricane Center tasks the NOAA G-IV aircraft to sample environmental conditions that may impact the development of a tropical cyclone threatening to make landfall in the United States or its territories. These aircraft data are assimilated into deterministic models and used to produce real-time analyses and forecasts for a given tropical cyclone. Existing targeting techniques aim to optimize the use of reconnaissance observations and partially rely on regions of highest uncertainty in the Global Ensemble Forecast System. Evaluating the potential impact of various trade-offs in the targeting process is valuable for determining the ideal aircraft flight track for a prospective mission. AOML’s Hurricane Research Division has developed a system for performing regional observing system simulation experiments (OSSEs) to assess the potential impact of proposed observing systems on hurricane track and intensity forecasting. This study focuses on improving existing targeting methods by investigating the impact of proposed aircraft observing system designs through various sensitivity studies. G-IV dropsonde retrievals were simulated from a regional nature run, covering the life cycle of a rapidly intensifying Atlantic hurricane. Results from sensitivity studies provide insight into improvements for real-time operational synoptic surveillance targeting for hurricanes and tropical storms, where dropsondes released closer to the vortex–environment interface provide the largest impact on the track forecast. All dropsonde configurations provide a positive 2-day impact on intensity forecasts by improving the environmental conditions known to impact tropical cyclone intensity.


2019 ◽  
Vol 29 (Supplement_4) ◽  
Author(s):  

Abstract Digital health has revolutionised healthcare, with implications for understanding public reaction to health emergencies and interventions. Social media provides a space where like-minded people can share interests and concerns in real-time, regardless of their location. This can be a force for good, as platforms like Twitter can spread correct information about outbreaks, for example in the 2009 swine flu pandemic. However, social media can also disseminate incorrect information or deliberately spread misinformation leading to adverse public health sentiment and outcomes. The current issues around trust in vaccines is the best-known example. Vaccine hesitancy, traditionally linked to issues of trust, misinformation and prior beliefs, has been increasingly fueled by influential groups on social media and the Internet. Ultimately, anti-vaccination movements have the potential to lead to outbreaks of vaccine-preventable diseases, especially if refusal is concentrated locally, creating vulnerable populations. For example, 2018-19 saw a large increase in incidence of measles in the US and Europe (where cases tripled from 2017), two regions where the disease was already or almost eliminated. In 2019, the World Health Organisation listed anti-vaccination movements as one of the top 10 threats to global public health. HPV vaccination is another example of the impact of anti-vaccination movements. As viral videos originating on YouTube spread across social networks, uptake has tumbled in a number of countries, with Japan, Denmark, Colombia and Ireland being badly hit. In Japan, the government came under sufficient pressure that they de-recommended HPV vaccine, seeing an 80% uptake rate fall below 1% in 2014. There have been reports of successful interventions by national governments. A recent campaign run by the HPV Alliance (a coalition of some 35 private companies, charities and public institutions) in Ireland has seen rates below 40% back up to a national average of 75%. A combination of hard-hitting personal testimonials, social media and traditional media promoted the HPV vaccine. Despite this, systematic engagement and supranational strategies are still in the early stages of being formulated. As misleading information spread through social media and digital networks has undesirable impact on attitudes to vaccination (and uptake rates), urgent actions are required. Analysis and visualisation techniques mining data streams from social media platforms, such as Twitter, Youtube enable real-time understanding of vaccine sentiments and information flows. Through identification of key influencers and flashpoints in articles about vaccination going viral, targeted public health responses could be developed. This roundtable discussion will showcase different ways in which media and social networks, accessible in real-time provide an opportunity for detecting a change in public confidence in vaccines, for identifying users and rumors and for assessing potential impact in order to know how to best respond. Key messages Social media has significantly enhanced our understanding of anti-vaccination movements and potential impact on public health attitudes and behaviors regarding vaccination. Innovative methods of analysing social media data, from digital health, data science and computer science, have an important role in developing health promotions to counter anti-vaccination movements.


Brachytherapy ◽  
2019 ◽  
Vol 18 (3) ◽  
pp. S95-S96
Author(s):  
Ryan Thibodeau ◽  
Sean Tanny ◽  
Gary Eastwick ◽  
Seung Shin Hahn ◽  
Jeffrey Bogart ◽  
...  

1991 ◽  
Vol 10 (3) ◽  
pp. 223-232
Author(s):  
JOANN M. SEKIGUCHI ◽  
ERIC B. KMIEC

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