Exact distributions for stochastic gene expression models with arbitrary promoter architecture and translational bursting

2022 ◽  
Vol 105 (1) ◽  
Author(s):  
Meiling Chen ◽  
Songhao Luo ◽  
Mengfang Cao ◽  
Chengjun Guo ◽  
Tianshou Zhou ◽  
...  
BMC Biology ◽  
2013 ◽  
Vol 11 (1) ◽  
pp. 15 ◽  
Author(s):  
José Viñuelas ◽  
Gaël Kaneko ◽  
Antoine Coulon ◽  
Elodie Vallin ◽  
Valérie Morin ◽  
...  

2017 ◽  
Author(s):  
Lorena Espinar ◽  
Miquel Àngel Schikora Tamarit ◽  
Júlia Domingo ◽  
Lucas B. Carey

AbstractInformation that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of co-translational regulation on mRNA levels is determined by promoter architecture. Using a novel computational-genetic screen of 6402 RNA-seq experiments we identify the RNA helicase Dbp2 as the mechanism by which co-translational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus the ORF sequence is a major regulator of gene expression, and a non-linear interaction between promoters and ORFs determines mRNA levels.


2019 ◽  
Vol 63 (3) ◽  
pp. 485-500 ◽  
Author(s):  
Zihao Wang ◽  
Zhenquan Zhang ◽  
Tianshou Zhou

2020 ◽  
Vol 7 (7) ◽  
pp. 191243
Author(s):  
Ayoub Lasri ◽  
Viktorija Juric ◽  
Maité Verreault ◽  
Franck Bielle ◽  
Ahmed Idbaih ◽  
...  

Glioblastoma (GBM) is the most aggressive malignant primary brain tumour with a median overall survival of 15 months. To treat GBM, patients currently undergo a surgical resection followed by exposure to radiotherapy and concurrent and adjuvant temozolomide (TMZ) chemotherapy. However, this protocol often leads to treatment failure, with drug resistance being the main reason behind this. To date, many studies highlight the role of O-6-methylguanine-DNA methyltransferase (MGMT) in conferring drug resistance. The mechanism through which MGMT confers resistance is not well studied—particularly in terms of computational models. With only a few reasonable biological assumptions, we were able to show that even a minimal model of MGMT expression could robustly explain TMZ-mediated drug resistance. In particular, we showed that for a wide range of parameter values constrained by novel cell growth and viability assays, a model accounting for only stochastic gene expression of MGMT coupled with cell growth, division, partitioning and death was able to exhibit phenotypic selection of GBM cells expressing MGMT in response to TMZ. Furthermore, we found this selection allowed the cells to pass their acquired phenotypic resistance onto daughter cells in a stable manner (as long as TMZ is provided). This suggests that stochastic gene expression alone is enough to explain the development of chemotherapeutic resistance.


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