scholarly journals SBMOpenMM: A Builder of Structure-Based Models for OpenMM

2021 ◽  
Author(s):  
Martin Floor ◽  
Kengjie Li ◽  
Miquel Estévez-Gay ◽  
Luis Agulló ◽  
Pau Marc Muñoz ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Folding Process ◽  
Underlying Mechanisms ◽  
User Friendly

<p>Here we introduce SBMOpenMM, a python library to build Structure-Based Models (SBMs), that uses the OpenMM framework to create and run SBM simulations. The code is flexible, user-friendly, and profits from high customizability and GPU performance provided by the OpenMM platform. We demonstrate its use in the evaluation of the two-step folding process of FoxP1 transcription factor protein. Our results indicate that the newly developed SBM can be successfully applied to elucidating the underlying mechanisms of biomolecular processes.</p><div><br></div>

scholarly journals SBMOpenMM: A Builder of Structure-Based Models for OpenMM

2021 ◽  
Author(s):  
Martin Floor ◽  
Kengjie Li ◽  
Miquel Estévez-Gay ◽  
Luis Agulló ◽  
Pau Marc Muñoz ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Folding Process ◽  
Underlying Mechanisms ◽  
User Friendly

<p>Here we introduce SBMOpenMM, a python library to build Structure-Based Models (SBMs), that uses the OpenMM framework to create and run SBM simulations. The code is flexible, user-friendly, and profits from high customizability and GPU performance provided by the OpenMM platform. We demonstrate its use in the evaluation of the two-step folding process of FoxP1 transcription factor protein. Our results indicate that the newly developed SBM can be successfully applied to elucidating the underlying mechanisms of biomolecular processes.</p><div><br></div>

scholarly journals SBMOpenMM: A Builder of Structure-Based Models for OpenMM

2021 ◽  
Author(s):  
Martin Floor ◽  
Kengjie Li ◽  
Miquel Estévez-Gay ◽  
Luis Agulló ◽  
Pau Marc Muñoz ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Folding Process ◽  
Underlying Mechanisms ◽  
User Friendly

<p>Here we introduce SBMOpenMM, a python library to build Structure-Based Models (SBMs), that uses the OpenMM framework to create and run SBM simulations. The code is flexible, user-friendly, and profits from high customizability and GPU performance provided by the OpenMM platform. We demonstrate its use in the evaluation of the two-step folding process of FoxP1 transcription factor protein. Our results indicate that the newly developed SBM can be successfully applied to elucidating the underlying mechanisms of biomolecular processes.</p><div><br></div>

scholarly journals Brassinosteroids repress the seed maturation program during the seed-to-seedling transition

2021 ◽  
Author(s):  
Jiuxiao Ruan ◽  
Huhui Chen ◽  
Tao Zhu ◽  
Yaoguang Yu ◽  
Yawen Lei ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factor ◽  
Abscisic Acid ◽  
Plant Hormone ◽  
Flowering Plants ◽  
Seed Maturation ◽  
Domain Protein ◽  
Abscisic Acid Insensitive3 ◽  
Underlying Mechanisms ◽  
Embryonic Structure

Abstract In flowering plants, repression of the seed maturation program is essential for the transition from the seed to the vegetative phase, but the underlying mechanisms remain poorly understood. The B3-domain protein VIVIPAROUS1/ABSCISIC ACID-INSENSITIVE3-LIKE 1 (VAL1) is involved in repressing the seed maturation program. Here we uncovered a molecular network triggered by the plant hormone brassinosteroid (BR) that inhibits the seed maturation program during the seed-to-seedling transition in Arabidopsis (Arabidopsis thaliana). val1-2 mutant seedlings treated with a BR biosynthesis inhibitor form embryonic structures, whereas BR signaling gain-of-function mutations rescue the embryonic structure trait. Furthermore, the BR-activated transcription factors BRI1-EMS-SUPPRESSOR 1 and BRASSINAZOLE-RESISTANT 1 bind directly to the promoter of AGAMOUS-LIKE15 (AGL15), which encodes a transcription factor involved in activating the seed maturation program, and suppress its expression. Genetic analysis indicated that BR signaling is epistatic to AGL15 and represses the seed maturation program by downregulating AGL15. Finally, we showed that the BR-mediated pathway functions synergistically with the VAL1/2-mediated pathway to ensure the full repression of the seed maturation program. Together, our work uncovered a mechanism underlying the suppression of the seed maturation program, shedding light on how BR promotes seedling growth.

scholarly journals Metabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chun-Ying Wang ◽  
Martin Lempp ◽  
Niklas Farke ◽  
Stefano Donati ◽  
Timo Glatter ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Site ◽  
Metabolic Pathways ◽  
Glycerol Production ◽  
Inducible Promoters ◽  
E Coli ◽  
Inhibition Of Glycolysis ◽  
Underlying Mechanisms ◽  
Rate Limiting ◽  
Engineered Bacteria

AbstractSynthetic metabolic pathways are a burden for engineered bacteria, but the underlying mechanisms often remain elusive. Here we show that the misregulated activity of the transcription factor Cra is responsible for the growth burden of glycerol overproducing E. coli. Glycerol production decreases the concentration of fructose-1,6-bisphoshate (FBP), which then activates Cra resulting in the downregulation of glycolytic enzymes and upregulation of gluconeogenesis enzymes. Because cells grow on glucose, the improper activation of gluconeogenesis and the concomitant inhibition of glycolysis likely impairs growth at higher induction of the glycerol pathway. We solve this misregulation by engineering a Cra-binding site in the promoter controlling the expression of the rate limiting enzyme of the glycerol pathway to maintain FBP levels sufficiently high. We show the broad applicability of this approach by engineering Cra-dependent regulation into a set of constitutive and inducible promoters, and use one of them to overproduce carotenoids in E. coli.

CBIO-15. LOSS OF WILLIAMS SYNDROME TRANSCRIPTION FACTOR (WSTF) LEADS TO IMPROVED TEMOZOLOMIDE SENSITIVITY IN HUMAN GLIOBLASTOMA CELLS IRRESPECTIVE OF MGMT EXPRESSION

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi30-vi30
Author(s):  
Katharina Sarnow ◽  
Stephanie Schwab ◽  
Oline Rio ◽  
Joydeep Mukherjee ◽  
Rolf Bjerkvig ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Cell Lines ◽  
Williams Syndrome ◽  
Colony Formation ◽  
Dna Methyltransferase ◽  
Guide Rna ◽  
Methylguanine Dna Methyltransferase ◽  
Development Of Resistance ◽  
Dna Repair Protein ◽  
Underlying Mechanisms

Abstract BACKGROUND The prognosis for glioblastoma multiforme (GBM) patients is poor with a median survival of approximately 15 months. The DNA repair protein O 6-methylguanine-DNA methyltransferase (MGMT) counteracts the effects of temozolomide (TMZ) chemotherapy and is thus associated with poor outcome in GBM patients. Williams Syndrome Transcription Factor (WSTF) has been suggested to regulate the DNA damage response pathway (DDR) in both an indirect (through chromatin remodeling) and direct manner (by phosphorylating H2AX at Tyr142). However, whether WSTF has any role in the development of resistance against chemotherapy through its functions in the DDR in GBMs, is so far unknown. In this study, we investigated whether a loss of WSTF sensitizes different MGMT-proficient and -deficient GBM cell lines to TMZ treatment. METHODS We generated WSTF knockout clones from both MGMT-proficient (LN18, T98G) and -deficient GBM cell lines (U-251) using CRISPR/Cas9 gene-editing technology with lentiviral vectors. The PCR-based screening results combined with the T7 endonuclease mismatch assay for bi-allelic monoclonal knockouts were verified via sequencing and immunoblotting to identify candidate knockout clones. Colony formation assays were performed to determine the survival ability in response to TMZ treatment. Statistical analysis was performed using two-way ANOVA. RESULTS WSTF knockout clones showed a significant decrease in colony formation after TMZ-treatment compared to the corresponding control groups (non-target single guide RNA) (LN18: Clone 59 vs control: p= 0.0456, T98G: All three studied clones vs control: p&lt; 0.0001, U-251: Clone 7/35.1/70.2 vs control: p&lt; 0.0001/p= 0.0107/p= 0.0119). CONCLUSION WSTF is an important factor in both MGMT de- and proficient GBM cell lines for response against TMZ chemotherapy. The loss of WSTF leads to a significantly increased TMZ sensitivity in clinically relevant concentrations for all the studied cell lines. Ongoing studies are investigating the underlying mechanisms and potential alterations in the DDR pathway caused by WSTF loss.

PRDM16 Is a Compact Myocardium-Enriched Transcription Factor Required to Maintain Compact Myocardial Cardiomyocyte Identity in Left Ventricle

Circulation ◽  
2021 ◽  
Author(s):  
Tongbin Wu ◽  
Zhengyu Liang ◽  
Zengming Zhang ◽  
Canzhao Liu ◽  
Lunfeng Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
Rna Sequencing ◽  
Mouse Models ◽  
Molecular Mechanisms ◽  
Left Ventricular ◽  
Ventricular Noncompaction ◽  
Chip Sequencing ◽  
Transcriptional Signature ◽  
Underlying Mechanisms

Background: Left ventricular noncompaction cardiomyopathy (LVNC) was discovered half a century ago as a cardiomyopathy with excessive trabeculation and a thin ventricular wall. In the decades since, numerous studies have demonstrated that LVNC primarily impacts left ventricles (LVs), and is often associated with LV dilation and dysfunction. However, owing in part to the lack of suitable mouse models that faithfully mirror the selective LV vulnerability in patients, mechanisms underlying susceptibility of LV to dilation and dysfunction in LVNC remain unknown. Genetic studies have revealed that deletions and mutations in PRDM16 cause LVNC, but previous conditional Prdm16 knockout mouse models do not mirror the LVNC phenotype in patients, and importantly, the underlying molecular mechanisms by which PRDM16 deficiency causes LVNC are still unclear. Methods: Prdm16 cardiomyocyte (CM)-specific knockout ( Prdm16 cKO ) mice were generated and analyzed for cardiac phenotypes. RNA sequencing and ChIP sequencing were performed to identify direct transcriptional targets of PRDM16 in CMs. Single cell RNA sequencing in combination with Spatial Transcriptomics were employed to determine CM identity at single cell level. Results: CM-specific ablation of Prdm16 in mice caused LV-specific dilation and dysfunction, as well as biventricular noncompaction, which fully recapitulated LVNC in patients. Mechanistically, PRDM16 functioned as a compact myocardium-enriched transcription factor, which activated compact myocardial genes while repressing trabecular myocardial genes in LV compact myocardium. Consequently, Prdm16 cKO LV compact myocardial CMs shifted from their normal transcriptomic identity to a transcriptional signature resembling trabecular myocardial CMs and/or neurons. Chamber-specific transcriptional regulation by PRDM16 was in part due to its cooperation with LV-enriched transcription factors Tbx5 and Hand1. Conclusions: These results demonstrate that disruption of proper specification of compact CM may play a key role in the pathogenesis of LVNC. They also shed light on underlying mechanisms of LV-restricted transcriptional program governing LV chamber growth and maturation, providing a tangible explanation for the susceptibility of LV in a subset of LVNC cardiomyopathies.

scholarly journals Novel Zinc Finger Transcription Factor ZFP580 Facilitates All-Trans Retinoic Acid -Induced Vascular Smooth Muscle Cells Differentiation by Rarα-Mediated PI3K/Akt and ERK Signaling

2018 ◽  
Vol 50 (6) ◽  
pp. 2390-2405 ◽  
Author(s):  
Shuping Wei ◽  
Jingjing Zhang ◽  
Biao Han ◽  
Jianxun Liu ◽  
Xiaohui Xiang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Zinc Finger ◽  
Erk Signaling ◽  
The Novel ◽  
Differentiation Markers ◽  
Zinc Finger Transcription Factor ◽  
Trans Retinoic Acid ◽  
All Trans Retinoic Acid ◽  
Injury Model ◽  
Underlying Mechanisms

Background/Aims: Phenotypic switching of vascular smooth muscle cells (VSMC) plays a vital role in the development of vascular diseases. All-trans retinoic acid (ATRA) is known to regulate VSMC phenotypes. However, the underlying mechanisms remain completely unknown. Here, we have investigated the probable roles and underlying mechanisms of the novel C2H2 zinc finger transcription factor ZFP580 on ATRA-induced VSMC differentiation. Methods: VSMCs were isolated, cultured, and identified. VSMCs were infected with an adenovirus encoding ZFP580 or Ad-siRNA to silence ZFP580. The expression levels of ZFP580, SMα-actin, SM22α, SMemb, RARα, RARβ, and RARγ were assayed by Q-PCR and western blot. A rat carotid artery injury model and morphometric analysis of intimal thickening were also used in this study. Results: ATRA caused a significant reduction of VSMC proliferation and migration in a doseand time-dependent manner. Moreover, it promoted VSMC differentiation by enhancing expression of differentiation markers and reducing expression of dedifferentiation markers. This ATRA activity was accompanied by up-regulation of ZFP580, with concomitant increases in RARα expression. In contrast, silencing of the RARα gene or inhibiting RARα with its antagonist Ro41-5253 abrogated the ATRA-induced ZFP580 expression. Furthermore, ATRA binding to RARα induced ZFP580 expression via the PI3K/Akt and ERK pathways. Adenovirusmediated overexpression of ZFP580 promoted VSMC differentiation by enhancing expression of SM22α and SMα-actin and reducing expression of SMemb. In contrast, silencing ZFP580 dramatically reduced the expression of differentiation markers and increased expression of dedifferentiation markers. The classic rat carotid artery balloon injury model demonstrated that ZFP580 inhibited proliferation and intimal hyperplasia in vivo. Conclusion: The novel zinc finger transcription factor ZFP580 facilitates ATRA-induced VSMC differentiation by the RARα-mediated PI3K/Akt and ERK signaling pathways. This might represent a novel mechanism of regulation of ZFP580 by ATRA and RARα, which is critical for understanding the biological functions of retinoids during VSMC phenotypic modulation.

scholarly journals IPEV: a web server for inferring pathogenic enhancers with variants

2019 ◽  
Author(s):  
Guanxiong Zhang ◽  
Aimin Xie ◽  
Jing Bai ◽  
Tao Luo ◽  
Huating Yuan ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Genetic Variants ◽  
Target Genes ◽  
Genetic Alterations ◽  
Enhancer Activity ◽  
Web Environment ◽  
One Stop ◽  
User Friendly ◽  
Coding Variants ◽  
Interactive User

Abstract Background Enhancer has been recognized as an important driver whose genetic alterations contribute to disease progression. However, there is still no easy-to-use tools to identify pathogenic enhancers, allowing for deciphering functional influence of genetic variants on enhancer. Results We developed a user-friendly one-stop shop platform, named inferring pathogenic enhancer with variant (IPEV), only requiring variants as input, to quickly infer the pathogenic enhancers that harbor variants affecting their activities. Results of IPEV are explored in an interactive, user-friendly web environment, which is designed to highlight the most probable pathogenic enhancers and their target genes. Furthermore, IPEV provides intuitive visualizations of how a variant affects the corresponding enhancer activity by mediating TF binding changes. Conclusions IPEV is specially designed to prioritize the potentially pathogenic enhancers with genetic variants, and provides intuitive visualizations how a variant affects the corresponding enhancer activity by mediating which transcription factor binding changes. The use of IPEV does not require any specialized computer skills. We believe that IPEV will be useful in interpreting non-coding variants by the inferring pathogenic enhancers. It is freely available at http://biocc.hrbmu.edu.cn/IPEV/ or http://210.46.80.168/IPEV and supports recent versions of all major browsers.

Abstract 103: Mechanistic Interplay Between Cardioprotection And Heart Regeneration Mediated By The ER-bound Transcription Factor Nrf1

2021 ◽  
Vol 129 (Suppl_1) ◽  
Author(s):  
Miao Cui ◽  
Atmanli Ayhan ◽  
Ning Liu ◽  
Rhonda S Bassel-duby ◽  
Eric N Olson
Keyword(s):  
Transcription Factor ◽  
Ischemia Reperfusion Injury ◽  
Heart Diseases ◽  
Ischemia Reperfusion ◽  
Induced Pluripotent Stem Cell ◽  
Redox Balance ◽  
Mouse Heart ◽  
Heart Regeneration ◽  
Neonatal Cardiomyocytes ◽  
Underlying Mechanisms

Cardiomyocyte loss is the underlying basis for a majority of heart diseases. Preventing cardiomyocytes from death (cardioprotection) and replenishing the lost myocardium (regeneration) are the central goals for heart repair. Although cardioprotection and heart regeneration have been traditionally thought to involve separate mechanisms, protection of cardiomyocytes from injury or disease stimuli is a prerequisite to any meaningful regenerative response. In our study, we sought to understand how neonatal cardiomyocytes cope with injury-induced stress to regenerate damaged myocardium and whether the underlying mechanisms could be leveraged to promote heart regeneration and repair in adults. Using spatial transcriptomic profiling, we visualized regenerative cardiomyocytes reconstituting damaged myocardium after ischemia, and found that they are marked by expression of Nrf1, an ER-bound stress responsive transcription factor. Single-nucleus RNA sequencing revealed that genetic deletion of Nrf1 prevented neonatal cardiomyocytes from activating a transcriptional program required for heart regeneration. Conversely, overexpression of Nrf1 protected the adult mouse heart from ischemia/reperfusion injury. Nrf1 also protected human induced pluripotent stem cell-derived cardiomyocytes from cardiotoxicity induced by the chemotherapeutic drug doxorubicin. The cardioprotective function of Nrf1 is mediated by a dual stress response mechanism involving activation of the proteasome and maintenance of redox balance. Taken together, our study uncovers a unique adaptive mechanism activated in response to injury that maintains the tissue homeostatic balance required for heart regeneration. Reactivating these mechanisms in the adult heart represents a potential therapeutic approach for cardiac repair.

P15.02 Loss of Williams Syndrome Transcription Factor (WSTF) leads to improved temozolomide sensitivity in human glioblastoma cells irrespective of MGMT expression

2021 ◽  
Vol 23 (Supplement_2) ◽  
pp. ii56-ii56
Author(s):  
K Sarnow ◽  
S G Schwab ◽  
O Rio ◽  
J Mukherjee ◽  
R Bjerkvig ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Cell Lines ◽  
Williams Syndrome ◽  
Colony Formation ◽  
Dna Methyltransferase ◽  
Guide Rna ◽  
Methylguanine Dna Methyltransferase ◽  
Development Of Resistance ◽  
Dna Repair Protein ◽  
Underlying Mechanisms

Abstract BACKGROUND The prognosis for newly diagnosed adult glioblastoma multiforme (GBM) patients is poor even after standard therapy with a median survival of approximately 14–15 months. The DNA repair protein O 6 -methylguanine-DNA methyltransferase (MGMT) efficiently counteracts formation of the most lethal DNA adducts by temozolomide (TMZ) chemotherapy, and is thus associated with poor outcome in GBM patients. Williams Syndrome Transcription Factor (WSTF) has previously been suggested to regulate the DNA damage response pathway (DDR) in both an indirect (through chromatin remodeling together with SMARCA5 in the WICH complex) and direct manner (by phosphorylating H2AX at Tyr142). However, whether WSTF has any role in the development of resistance against chemotherapy through its ability to regulate the DDR in GBMs, is so far not known. In this study, we investigated whether loss of WSTF sensitizes different MGMT-proficient and -deficient GBM cell lines to TMZ treatment. MATERIAL AND METHODS We generated WSTF knockout clones from both MGMT-proficient (LN18, T98G) and -deficient GBM cell lines (U-251) using CRISPR/Cas9 gene-editing technology with lentiviral vectors. The PCR-based screening results combined with the T7 endonuclease mismatch assay for bi-allelic monoclonal knockouts were verified via sequencing and immunoblotting to identify candidate knockout clones. For each cell line, three knockout clones were chosen for further investigation. Colony formation assays were performed to determine the survival ability in response to TMZ treatment. Statistical analysis was performed using two-way ANOVA. RESULTS WSTF knockout clones showed a significant decrease in colony formation after TMZ-treatment compared to the corresponding WSTF-expressing control groups (non-target single guide RNA) (LN18: Clone 59 vs control: p= 0.0456, T98G: All three studied clones vs control: p &lt;0.0001, U-251: Clone 7/35.1/70.2 vs control: p &lt;0.0001/p= 0.0107/p= 0.0119). Furthermore, two out of three clones of T98G and U-251 (T98G Clone 13 and 128 vs control, p &lt;0.0001, U-251 Clone 7 vs control, p= 0.0062; clone 70.2, p= 0.0052) showed significantly reduced plating efficiency compared to control cells. CONCLUSION WSTF is an important factor in both MGMT de- and proficient GBM cell lines for response against TMZ chemotherapy. The loss of WSTF leads to a significantly increased TMZ sensitivity in clinically relevant concentrations for all the studied cell lines. Ongoing studies are investigating the underlying mechanisms and potential alterations in the DDR pathway caused by WSTF loss.

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