Transcriptional regulation mechanism mediated by miRNA–DNA•DNA triplex structure stabilized by Argonaute

Enhancers are short genomic regions exerting tissue-specific regulatory roles, usually for remote coding regions. Enhancers are observed in both prokaryotic and eukaryotic genomes, and their detections facilitate a better understanding of the transcriptional regulation mechanism. The accurate detection and transcriptional regulation strength evaluation of the enhancers remain a major bioinformatics challenge. Most of the current studies utilized the statistical features of short fixed-length nucleotide sequences. This study introduces the location information of each k-mer (SeqPose) into the encoding strategy of a DNA sequence and employs the attention mechanism in the two-layer bi-directional long-short term memory (BD-LSTM) model (spEnhancer) for the enhancer detection problem. The first layer of the delivered classifier discriminates between enhancers and non-enhancers, and the second layer evaluates the transcriptional regulation strength of the detected enhancer. The SeqPose-encoded features are selected by the Chi-squared test, and 45 positions are removed from further analysis. The existing studies may focus on selecting the statistical DNA sequence descriptors with large contributions to the prediction models. This study does not utilize these statistical DNA sequence descriptors. Then the word vector of the SeqPose-encoded features is obtained by using the word embedding layer. This study hypothesizes that different word vector features may contribute differently to the enhancer detection model, and assigns different weights to these word vectors through the attention mechanism in the BD-LSTM model. The previous study generously provided the training and independent test datasets, and the proposed spEnhancer is compared with the three existing state-of-the-art studies using the same experimental procedure. The leave-one-out validation data on the training dataset shows that the proposed spEnhancer achieves similar detection performances as the three existing studies. While spEnhancer achieves the best overall performance metric MCC for both of the two binary classification problems on the independent test dataset. The experimental data shows that the strategy of removing redundant positions (SeqPose) may help improve the DNA sequence-based prediction models. spEnhancer may serve well as a complementary model to the existing studies, especially for the novel query enhancers that are not included in the training dataset.

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Termination within Oligo(dT) Tracts in Template DNA by DNA Polymerase γ Occurs with Formation of a DNA Triplex Structure and Is Relieved by Mitochondrial Single-stranded DNA-binding Protein

Journal of Biological Chemistry ◽

10.1074/jbc.271.48.30774 ◽

1996 ◽

Vol 271 (48) ◽

pp. 30774-30780 ◽

Cited By ~ 17

Author(s):

Victor S. Mikhailov ◽

Daniel F. Bogenhagen

Keyword(s):

Dna Binding ◽

Dna Polymerase ◽

Binding Protein ◽

Dna Binding Protein ◽

Single Stranded Dna ◽

Dna Triplex ◽

Triplex Structure ◽

Template Dna ◽

Dna Polymerase Γ

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Arabinose-Induced Catabolite Repression as a Mechanism for Pentose Hierarchy Control inClostridium acetobutylicumATCC 824

mSystems ◽

10.1128/msystems.00064-18 ◽

2018 ◽

Vol 3 (5) ◽

Cited By ~ 2

Author(s):

Matthew D. Servinsky ◽

Rebecca L. Renberg ◽

Matthew A. Perisin ◽

Elliot S. Gerlach ◽

Sanchao Liu ◽

...

Keyword(s):

Transcriptional Regulation ◽

Genetic Engineering ◽

Catabolite Repression ◽

Clostridium Acetobutylicum ◽

Regulation Mechanism ◽

Mrna Levels ◽

Chemical Production ◽

Content Type ◽

Commodity Chemicals ◽

Pentose Utilization

ABSTRACTBacterial fermentation of carbohydrates from sustainable lignocellulosic biomass into commodity chemicals by the anaerobic bacteriumClostridium acetobutylicumis a promising alternative source to fossil fuel-derived chemicals. Recently, it was demonstrated that xylose is not appreciably fermented in the presence of arabinose, revealing a hierarchy of pentose utilization in this organism (L. Aristilde, I. A. Lewis, J. O. Park, and J. D. Rabinowitz, Appl Environ Microbiol 81:1452–1462, 2015,https://doi.org/10.1128/AEM.03199-14). The goal of the current study is to characterize the transcriptional regulation that occurs and perhaps drives this pentose hierarchy. Carbohydrate consumption rates showed that arabinose, like glucose, actively represses xylose utilization in cultures fermenting xylose. Further, arabinose addition to xylose cultures led to increased acetate-to-butyrate ratios, which indicated a transition of pentose catabolism from the pentose phosphate pathway to the phosphoketolase pathway. Transcriptome sequencing (RNA-Seq) confirmed that arabinose addition to cells actively growing on xylose resulted in increased phosphoketolase (CA_C1343) mRNA levels, providing additional evidence that arabinose induces this metabolic switch. A significant overlap in differentially regulated genes after addition of arabinose or glucose suggested a common regulation mechanism. A putative open reading frame (ORF) encoding a potential catabolite repression phosphocarrier histidine protein (Crh) was identified that likely participates in the observed transcriptional regulation. These results substantiate the claim that arabinose is utilized preferentially over xylose inC. acetobutylicumand suggest that arabinose can activate carbon catabolite repression via Crh. Furthermore, they provide valuable insights into potential mechanisms for altering pentose utilization to modulate fermentation products for chemical production.IMPORTANCEClostridium acetobutylicumcan ferment a wide variety of carbohydrates to the commodity chemicals acetone, butanol, and ethanol. Recent advances in genetic engineering have expanded the chemical production repertoire ofC. acetobutylicumusing synthetic biology. Due to its natural properties and genetic engineering potential, this organism is a promising candidate for converting biomass-derived feedstocks containing carbohydrate mixtures to commodity chemicals via natural or engineered pathways. Understanding how this organism regulates its metabolism during growth on carbohydrate mixtures is imperative to enable control of synthetic gene circuits in order to optimize chemical production. The work presented here unveils a novel mechanism via transcriptional regulation by a predicted Crh that controls the hierarchy of carbohydrate utilization and is essential for guiding robust genetic engineering strategies for chemical production.

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DNA triplex structure, thermodynamics, and destabilisation: insight from molecular simulations

Physical Chemistry Chemical Physics ◽

10.1039/c8cp02385a ◽

2018 ◽

Vol 20 (20) ◽

pp. 14013-14023 ◽

Cited By ~ 6

Author(s):

Belinda J. Boehm ◽

Charles Whidborne ◽

Alexander L. Button ◽

Tara L. Pukala ◽

David M. Huang

Keyword(s):

Molecular Dynamics ◽

Neurodegenerative Disease ◽

Molecular Dynamics Simulations ◽

Small Molecule ◽

Molecular Simulations ◽

Friedreich’S Ataxia ◽

Dna Triplexes ◽

Dna Triplex ◽

Triplex Structure ◽

Dynamics Simulations

Molecular dynamics simulations are used to elucidate the structure and thermodynamics of DNA triplexes associated with the neurodegenerative disease Friedreich's ataxia (FRDA), as well as complexes of these triplexes with the small molecule netropsin, which is known to destabilise triplexes.

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