scholarly journals Using computational modelling to reveal mechanisms of epigenetic Polycomb control

2021 ◽  
Vol 49 (1) ◽  
pp. 71-77
Author(s):  
Cecilia Lövkvist ◽  
Martin Howard
Keyword(s):  
Computational Modelling ◽  
Stable Gene ◽  
Epigenetic Memory ◽  
Cis Acting ◽  
Polycomb Repressive Complex 2 ◽  
Protein Levels ◽  
System A ◽  
Stable Memory ◽  
In Cis ◽  
Transcriptional Feedback

The Polycomb system is essential for stable gene silencing in many organisms. This regulation is achieved in part through addition of the histone modifications H3K27me2/me3 by Polycomb Repressive Complex 2 (PRC2). These modifications are believed to be the causative epigenetic memory elements of PRC2-mediated silencing. As these marks are stored locally in the chromatin, PRC2-based memory is a cis-acting system. A key feature of stable epigenetic memory in cis is PRC2-mediated, self-reinforcing feedback from K27-methylated histones onto nearby histones in a read-write paradigm. However, it was not clear under what conditions such feedback can lead to stable memory, able, for example, to survive the perturbation of histone dilution at DNA replication. In this context, computational modelling has allowed a rigorous exploration of possible underlying memory mechanisms and has also greatly accelerated our understanding of switching between active and silenced states. Specifically, modelling has predicted that switching and memory at Polycomb loci is digital, with a locus being either active or inactive, rather than possessing intermediate, smoothly varying levels of activation. Here, we review recent advances in models of Polycomb control, focusing on models of epigenetic switching through nucleation and spreading of H3K27me2/me3. We also examine models that incorporate transcriptional feedback antagonism and those including bivalent chromatin states. With more quantitative experimental data on histone modification kinetics, as well as single-cell resolution data on transcription and protein levels for PRC2 targets, we anticipate an expanded need for modelling to help dissect increasingly interconnected and complex memory mechanisms.

scholarly journals Gene Variations in Cis-Acting Elements between the Taiwan and Prototype Strains of Porcine Epidemic Diarrhea Virus Alter Viral Gene Expression

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 591
Author(s):  
Tsung-Lin Tsai ◽  
Chen-Chang Su ◽  
Ching-Chi Hsieh ◽  
Chao-Nan Lin ◽  
Hui-Wen Chang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Porcine Epidemic Diarrhea Virus ◽  
The Body ◽  
Economic Losses ◽  
Viral Gene ◽  
Sequence Motif ◽  
Cis Acting ◽  
Diarrhea Virus ◽  
Porcine Epidemic Diarrhea ◽  
In Cis

In 2013, the outbreak of porcine epidemic diarrhea (PED) in Taiwan caused serious economic losses. In this study, we examined whether the variations of the cis-acting elements between the porcine epidemic diarrhea virus (PEDV) Taiwan (TW) strain and the prototype strain CV777 alter gene expression. For this aim, we analyzed the variations of the cis-acting elements in the 5’ and 3’ untranslated regions (UTRs) between the PEDV TW, CV777, and other reference strains. We also determined the previously unidentified transcription regulatory sequence (TRS), a sequence motif required for coronavirus transcription, and found that a nucleotide deletion in the TW strain, in comparison with CV777 strain, immediately downstream of the leader core sequence alters the identity between the leader TRS and the body TRS. Functional analyses using coronavirus defective interfering (DI) RNA revealed that such variations in cis-acting elements for the TW strain compared with the CV777 strain have an influence on the efficiency of gene expression. The current data show for the first time the evolution of PEDV in terms of cis-acting elements and their effects on gene expression, and thus may contribute to our understanding of recent PED outbreaks worldwide.

The orexin system: a potential player in the pathophysiology of absence epilepsy?

2021 ◽  
Vol 19 ◽  
Author(s):  
Roberta Celli ◽  
Gilles Van Luijtelaar
Keyword(s):  
Somatosensory Cortex ◽  
Molecular Mechanisms ◽  
Recent Literature ◽  
Absence Epilepsy ◽  
Experimental Animals ◽  
Future Studies ◽  
Protein Levels ◽  
System A ◽  
Cortical Circuit

Background : Absence epilepsy is characterized by the presence of spike-and-wave discharges (SWDs) at the EEG generated within the cortico-thalamo-cortical circuit. The molecular mechanisms involved in the pathophysiology of absence epilepsy are only partially known. WAG/Rij rats older than 2-3 months develop spontaneous SWDs, and they are sensitive to anti-absence medications. Hence, WAG/Rij rats are extensively used as a model for absence epilepsy with predictive validity. Objective : To examine the possibility that the orexin system, which supports the wake status in experimental animals and humans, plays a role in the pathophysiology of absence seizures. Methods : The perspective grounds its method on recent literature along with measurements of orexin receptor type-1 (OX1) protein levels in the thalamus and somatosensory cortex of WAG/Rij rats and non-epileptic Wistar control rats at two ages (25 days and 6-7 months). OX1 protein levels were measured by immunoblotting. Results : The analysis of the current literature suggests that the orexin system might be involved in the pathophysiology of absence epilepsy and might be targeted by therapeutic intervention. Experimental data are in line with this hypothesis showing that OX1 protein levels were reduced in the thalamus and somatosensory cortex of symptomatic WAG/Rij rats (6-7 months of age) with respect to non-epileptic controls, whereas these differences were not seen in pre-symptomatic, 25 days-old WAG/Rij rats. Conclusions : This might pave the way to future studies on the involvement of the orexinergic system in the pathophysiology of SWDs associated with absence epilepsy and its comorbidities.

scholarly journals Proteomic analysis of Drosophila CLOCK complexes identifies rhythmic interactions with SAGA and Tip60 complex component NIPPED-A

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Guruswamy Mahesh ◽  
Gustavo B. S. Rivas ◽  
Courtney Caster ◽  
Evan B. Ost ◽  
Ravi Amunugama ◽  
...  
Keyword(s):  
Feedback Loop ◽  
Clock Cycle ◽  
Protein A ◽  
Interacting Proteins ◽  
Saga Complex ◽  
Protein Levels ◽  
Genes Encoding ◽  
Circadian Behavior ◽  
Transcriptional Output ◽  
Transcriptional Feedback

Abstract Circadian clocks keep time via ~ 24 h transcriptional feedback loops. In Drosophila, CLOCK-CYCLE (CLK-CYC) activators and PERIOD-TIMELESS (PER-TIM) repressors are feedback loop components whose transcriptional status varies over a circadian cycle. Although changes in the state of activators and repressors has been characterized, how their status is translated to transcriptional activity is not understood. We used mass spectrometry to identify proteins that interact with GFP-tagged CLK (GFP-CLK) in fly heads at different times of day. Many expected and novel interacting proteins were detected, of which several interacted rhythmically and were potential regulators of protein levels, activity or transcriptional output. Genes encoding these proteins were tested to determine if they altered circadian behavior via RNAi knockdown in clock cells. The NIPPED-A protein, a scaffold for the SAGA and Tip60 histone modifying complexes, interacts with GFP-CLK as transcription is activated, and reducing Nipped-A expression lengthens circadian period. RNAi analysis of other SAGA complex components shows that the SAGA histone deubiquitination (DUB) module lengthened period similarly to Nipped-A RNAi knockdown and weakened rhythmicity, whereas reducing Tip60 HAT expression drastically weakened rhythmicity. These results suggest that CLK-CYC binds NIPPED-A early in the day to promote transcription through SAGA DUB and Tip60 HAT activity.

scholarly journals Computational modelling and digital materialization of Alberti’s column system: a reflection on results obtained

2014 ◽  
Author(s):  
Eduardo Castro e Costa ◽  
José P. Duarte ◽  
Mário Kruger
Keyword(s):  
Complex Geometry ◽  
Formal Model ◽  
Computational Modelling ◽  
De Re ◽  
Column System ◽  
System A ◽  
De Re Aedificatoria ◽  
Research Initiative ◽  
Depth Analysis ◽  
Architectural Tradition

We hereby focus the study of the Albertian column system, as part of the Digital Alberti project, a research initiative that aims to shed some light on the influence of Alberti on Portuguese architecture. Starting from Alberti’s treatise on architecture, De Re Aedificatoria, and its translation into Portuguese, Da Arte Edificatória, a generative computational model was developed that encodes Alberti’s prescriptions about the elements of the column system, as well as their proportions and shapes.  This research complements the elaboration of the corresponding shape grammar on Alberti’s column system. This project is a paradigmatic example of the use of digital technology for understanding architectural tradition. The development of the referred models implied deepening the understanding of Alberti’s rules about the column elements. This in-depth analysis revealed a very coherent hierarchical structure ruling the relationships among the several elements. It also revealed that information was insufficient to inform a formal model of all them, especially the ones showing more complex geometry, such as the corinthian and composite capitals. Therefore, it can be considered that the application of digital technologies allowed to more accurately understand and reproduce Alberti’s guidelines for the art of building.Foca-se o estudo do sistema de coluna Albertiano, no âmbito do projecto Alberti Digital, cuja investigação pretende elucidar sobre a influência de Alberti na arquitetura portuguesa. Partindo do tratado de Alberti sobre arquitetura, De re aedificatoria, e da sua tradução para português, Da Arte Edificatória, foi desenvolvido um modelo computacional generativo que codifica as instruções de Alberti respeitantes aos elementos do sistema de coluna, bem como as suas proporções e formas. A investigação complementa a elaboração da gramática da forma correspondente ao sistema de coluna Albertiano. O projecto é um exemplo paradigmático do uso de tecnologias digitais na compreensão da tradição arquitetónica. O desenvolvimento dos modelos referidos implicou um entendimento aprofundado das regras de Alberti sobre os elementos da coluna. Esta análise revelou uma estrutura hierárquica consistente que rege as relações entre os diversos elementos. Revelou também que, para uma modelação exacta de todos esses elementos, a informação fornecida por Alberti não é suficiente, nomeadamente nos casos mais complexos dos capitéis coríntio e compósito. Considera-se assim que a aplicação de tecnologias digitais permitiram compreender e reproduzir mais exactamente as orientações de Alberti para a arte da construção.

scholarly journals The histone variant H2A.Z is required to establish normal patterns of H3K27 methylation in Neurospora crassa

2020 ◽  
Author(s):  
Abigail J. Courtney ◽  
Masayuki Kamei ◽  
Aileen R. Ferraro ◽  
Kexin Gai ◽  
Qun He ◽  
...  
Keyword(s):  
Neurospora Crassa ◽  
Molecular Mechanisms ◽  
Histone Variant ◽  
Polycomb Group ◽  
Stable Gene ◽  
Polycomb Group Proteins ◽  
Polycomb Repressive Complex ◽  
Facultative Heterochromatin ◽  
Polycomb Repressive Complex 2 ◽  
H3k27 Methylation

ABSTRACTNeurospora crassa contains a minimal Polycomb repression system, which provides rich opportunities to explore Polycomb-mediated repression across eukaryotes and enables genetic studies that can be difficult in plant and animal systems. Polycomb Repressive Complex 2 is a multi-subunit complex that deposits mono-, di-, and tri-methyl groups on lysine 27 of histone H3, and tri-methyl H3K27 is a molecular marker of transcriptionally repressed facultative heterochromatin. In mouse embryonic stem cells and multiple plant species, H2A.Z has been found to be co-localized with H3K27 methylation. H2A.Z is required for normal H3K27 methylation in these experimental systems, though the regulatory mechanisms are not well understood. We report here that Neurospora crassa mutants lacking H2A.Z or SWR-1, the ATP-dependent histone variant exchanger, exhibit a striking reduction in levels of H3K27 methylation. RNA-sequencing revealed downregulation of eed, encoding a subunit of PRC2, in an hH2Az mutant compared to wild type and overexpression of EED in a ΔhH2Az;Δeed background restored most H3K27 methylation. Reduced eed expression leads to region-specific losses of H3K27 methylation suggesting that EED-dependent mechanisms are critical for normal H3K27 methylation at certain regions in the genome.AUTHOR SUMMARYEukaryotic DNA is packaged with histone proteins to form a DNA-protein complex called chromatin. Inside the nucleus, chromatin can be assembled into a variety of higher-order structures that profoundly impact gene expression. Polycomb Group proteins are important chromatin regulators that control assembly of a highly condensed form of chromatin. The functions of Polycomb Group proteins are critical for maintaining stable gene repression during development of multicellular organisms, and defects in Polycomb proteins are linked to disease. There is significant interest in elucidating the molecular mechanisms that regulate the activities of Polycomb Group proteins and the assembly of transcriptionally repressed chromatin domains. In this study, we used a model fungus to investigate the regulatory relationship between a histone variant, H2A.Z, and a conserved histone modifying enzyme complex, Polycomb Repressive Complex 2 (PRC2). We found that H2A.Z is required for normal expression of a PRC2 component. Mutants that lack H2A.Z have defects in chromatin structure at some parts of the genome, but not others. Identification of PRC2-target domains that are differentially dependent on EED provides insights into the diverse mechanisms that regulate assembly and maintenance of facultative heterochromatin in a simple model system.Data Reference NumbersGSE146611

A cis-acting element in the promoter region of the murine c-myc gene is necessary for transcriptional block

1989 ◽  
Vol 9 (12) ◽  
pp. 5340-5349
Author(s):  
H Miller ◽  
C Asselin ◽  
D Dufort ◽  
J Q Yang ◽  
K Gupta ◽  
...  
Keyword(s):  
Physiological State ◽  
S1 Nuclease ◽  
Cis Acting ◽  
Transcription Start Sites ◽  
Mapping Analysis ◽  
Exon 1 ◽  
Myc Gene ◽  
S1 Nuclease Mapping ◽  
Nuclease Mapping ◽  
In Cis

A block to elongation of transcription has been shown to occur within the first exon of the human and murine c-myc genes. The extent of this block was found to vary with the physiological state of cells, indicating that modulation of the transcriptional block can serve to control the expression of this gene. To determine which sequences are required in cis for the transcriptional block, we generated a series of constructs containing various portions of murine c-myc 5'-flanking and exon 1 sequences. We established populations of HeLa and CV-1 cells stably transfected with these constructs. The transcription start sites were determined by S1 nuclease mapping analysis, and the extent of transcriptional block was measured by nuclear run-on transcription assays. Our results demonstrate that at least two cis-acting elements are necessary for the transcriptional block. A 3' element was found to be located in the region where transcription stopped and showed features reminiscent of some termination sites found in procaryotes. A 5' element was positioned between the P1 and P2 (C. Asselin, A. Nepveu, and K. B. Marcu, Oncogene 4:549-558, 1989). Removal of the more 3' binding site abolished the transcriptional block.

scholarly journals Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Luis H. Orellana ◽  
Janet K. Hatt ◽  
Ramsunder Iyer ◽  
Karuna Chourey ◽  
Robert L. Hettich ◽  
...  
Keyword(s):  
Fold Increase ◽  
Strong Relationship ◽  
Qualitative Assessment ◽  
Stable Gene ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Protein Levels ◽  
Nitrification Activity ◽  
Measured Activity ◽  
Agricultural Site

AbstractTo what extent multi-omic techniques could reflect in situ microbial process rates remains unclear, especially for highly diverse habitats like soils. Here, we performed microcosm incubations using sandy soil from an agricultural site in Midwest USA. Microcosms amended with isotopically labeled ammonium and urea to simulate a fertilization event showed nitrification (up to 4.1 ± 0.87 µg N-NO3− g−1 dry soil d−1) and accumulation of N2O after 192 hours of incubation. Nitrification activity (NH4+ → NH2OH → NO → NO2- → NO3−) was accompanied by a 6-fold increase in relative expression of the 16S rRNA gene (RNA/DNA) between 10 and 192 hours of incubation for ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira, unlike archaea and comammox bacteria, which showed stable gene expression. A strong relationship between nitrification activity and betaproteobacterial ammonia monooxygenase and nitrite oxidoreductase transcript abundances revealed that mRNA quantitatively reflected measured activity and was generally more sensitive than DNA under these conditions. Although peptides related to housekeeping proteins from nitrite-oxidizing microorganisms were detected, their abundance was not significantly correlated with activity, revealing that meta-proteomics provided only a qualitative assessment of activity. Altogether, these findings underscore the strengths and limitations of multi-omic approaches for assessing diverse microbial communities in soils and provide new insights into nitrification.

scholarly journals MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Andigoni Malousi ◽  
Sofia Kouidou ◽  
Maria Tsagiopoulou ◽  
Nikos Papakonstantinou ◽  
Emmanouil Bouras ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Structural Characteristics ◽  
Regulatory Element ◽  
Unmet Need ◽  
Regulatory Elements ◽  
Driver Genes ◽  
Computational Framework ◽  
Cis Acting ◽  
Element Enrichment ◽  
In Cis

AbstractDNA methylation studies have been reformed with the advent of single-base resolution arrays and bisulfite sequencing methods, enabling deeper investigation of methylation-mediated mechanisms. In addition to these advancements, numerous bioinformatics tools address important computational challenges, covering DNA methylation calling up to multi-modal interpretative analyses. However, contrary to the analytical frameworks that detect driver mutational signatures, the identification of putatively actionable epigenetic events remains an unmet need. The present work describes a novel computational framework, called MeinteR, that prioritizes critical DNA methylation events based on the following hypothesis: critical aberrations of DNA methylation more likely occur on a genomic substrate that is enriched in cis-acting regulatory elements with distinct structural characteristics, rather than in genomic “deserts”. In this context, the framework incorporates functional cis-elements, e.g. transcription factor binding sites, tentative splice sites, as well as conformational features, such as G-quadruplexes and palindromes, to identify critical epigenetic aberrations with potential implications on transcriptional regulation. The evaluation on multiple, public cancer datasets revealed significant associations between the highest-ranking loci with gene expression and known driver genes, enabling for the first time the computational identification of high impact epigenetic changes based on high-throughput DNA methylation data.

Cortisol stimulates system A amino acid transport and SNAT2 expression in a human placental cell line (BeWo)

2006 ◽  
Vol 291 (3) ◽  
pp. E596-E603 ◽  
Author(s):  
Helen N. Jones ◽  
Cheryl J. Ashworth ◽  
Ken R. Page ◽  
Harry J. McArdle
Keyword(s):  
Amino Acid ◽  
Cell Line ◽  
Expression System ◽  
Isobutyric Acid ◽  
Fetal Plasma ◽  
Functional Studies ◽  
Protein Levels ◽  
System A ◽  
Cortisol Levels ◽  
Amino Isobutyric Acid

Both placental system A activity and fetal plasma cortisol concentrations are associated with intrauterine growth retardation, but it is not known if these factors are mechanistically related. Previous functional studies using hepatoma cells and fibroblasts produced conflicting results regarding the regulation of system A by cortisol. Using the b30 BeWo choriocarcinoma cell line, we investigated the regulation of system A by cortisol. System A function was analyzed using methyl amino isobutyric acid (MeAIB) transcellular transport studies. Transporter expression [system A transporter (SNAT)1/2] was studied at the mRNA and protein levels using Northern and Western blotting, respectively. Localization was carried out using immunocytochemistry. The [14C]MeAIB transfer rate across BeWo monolayers after preincubation with cortisol for 24 h was significantly increased compared with control. This was associated with a relocalization of the SNAT2 transporter at lower cortisol levels and significant upregulation of mRNA and protein expression levels at cortisol levels >1 μM. This is the first study to show functional and molecular regulation of system A by cortisol in BeWo cells. It is also the first study to identify which system A isoform is regulated. These results suggest that cortisol may be involved in upregulation of system A in the placenta to ensure sufficient amino acid supply to the developing fetus.

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