The Use of Chemical Compounds to Identify the Regulatory Mechanisms of Vertebrate Circadian Clocks

2020 ◽  
Vol 21 (5) ◽  
pp. 425-432
Author(s):  
Yoshimi Okamoto-Uchida ◽  
Akari Nishimura ◽  
Junko Izawa ◽  
Atsuhiko Hattori ◽  
Nobuo Suzuki ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Chemical Compounds ◽  
Stability Control ◽  
Circadian Clocks ◽  
Light Signaling ◽  
Negative Feedback Loops ◽  
Exact Timing

Circadian clocks are intrinsic, time-tracking processes that confer a survival advantage on an organism. Under natural conditions, they follow approximately a 24-h day, modulated by environmental time cues, such as light, to maximize an organism’s physiological efficiency. The exact timing of this rhythm is established by cell-autonomous oscillators called cellular clocks, which are controlled by transcription–translation negative feedback loops. Studies of cell-based systems and wholeanimal models have utilized a pharmacological approach in which chemical compounds are used to identify molecular mechanisms capable of establishing and maintaining cellular clocks, such as posttranslational modifications of cellular clock regulators, chromatin remodeling of cellular clock target genes’ promoters, and stability control of cellular clock components. In addition, studies with chemical compounds have contributed to the characterization of light-signaling pathways and their impact on the cellular clock. Here, the use of chemical compounds to study the molecular, cellular, and behavioral aspects of the vertebrate circadian clock system is described.

scholarly journals Post-translational Modifications are Required for Circadian Clock Regulation in Vertebrates

2019 ◽  
Vol 20 (5) ◽  
pp. 332-339 ◽  
Author(s):  
Yoshimi Okamoto-Uchida ◽  
Junko Izawa ◽  
Akari Nishimura ◽  
Atsuhiko Hattori ◽  
Nobuo Suzuki ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Molecular Mechanisms ◽  
Feedback Loops ◽  
Circadian Clocks ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Negative Feedback Loops ◽  
Genetic Techniques ◽  
External Signals ◽  
Exact Timing

Circadian clocks are intrinsic, time-tracking systems that bestow upon organisms a survival advantage. Under natural conditions, organisms are trained to follow a 24-h cycle under environmental time cues such as light to maximize their physiological efficiency. The exact timing of this rhythm is established via cell-autonomous oscillators called cellular clocks, which are controlled by transcription/ translation-based negative feedback loops. Studies using cell-based systems and genetic techniques have identified the molecular mechanisms that establish and maintain cellular clocks. One such mechanism, known as post-translational modification, regulates several aspects of these cellular clock components, including their stability, subcellular localization, transcriptional activity, and interaction with other proteins and signaling pathways. In addition, these mechanisms contribute to the integration of external signals into the cellular clock machinery. Here, we describe the post-translational modifications of cellular clock regulators that regulate circadian clocks in vertebrates.

Abstract WMP41: Characterization of MicroRNAs and Their Target Proteins in Distal Axons of Cortical Neurons

Stroke ◽  
2016 ◽  
Vol 47 (suppl_1) ◽  
Author(s):  
Chao Li ◽  
Yi Zhang ◽  
Albert M Levin ◽  
Michael Chopp ◽  
Zheng Gang Zhang
Keyword(s):  
Cortical Neurons ◽  
Mirna Target ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Axonal Growth ◽  
Bioinformatic Analysis ◽  
Inhibitory Effect ◽  
Bioinformatic Tools ◽  
Molecular Information

Introduction: Axonal growth is essential for the establishment of a functional neuronal network. Molecular information of axon is limited. MicroRNAs (miRNAs) regulate post-transcriptional gene expression. We hypothesized that axonal miRNAs are locally relevant to their target genes. Methods: Proteins and RNAs were extracted from distal axons of cortical neurons cultured in a microfluidic device. A mass spectrometer and miRNA arrays were used to measure proteins and miRNAs, respectively. Ingenuity Pathway Analysis (IPA) and Database for Annotation, Visualization and Integrated Discovery (DAVID) bioinformatic tools were used to make in silico predictions of functionally relevant miRNA target genes. Results: Proteomic showed that distal axons contained 883 proteins. Bioinformatic analysis showed the presence of 94 proteins that regulate axonal growth. To identify relevant miRNAs to these 94 proteins, miRNAs with 8mer sites that exactly match target genes were considered, based on the fact that 8mer sites efficaciously affect miRNA-target interactions. Of the 94 genes, we found that there were 56 candidate genes that can be targeted by 62 miRNAs enriched in axons. Among them, we validated 13 proteins and 11 miRNAs, respectively, by means of Western blot and RT-PCR. To examine target genes, we treated axons with chondroitin sulfate proteoglycans (CSPGs) that inhibit axonal growth and examined alterations of these proteins and miRNAs in the distal axons. We found that elevation of miR-203a, -133b, -29abc and -92ab were associated with reduced AKT, MTOR, PI3Kp85, DPYSL2, MAP1B, PPP2CA and DCX proteins, whereas decreased miR-15b, -26b, -34b, -376b, -128, -381 and -195 were accompanied by increased proteins of EZR, KIF5A, RTN4, GSK3B, and ROCK2. Bioinformatic analysis revealed that these miRNAs and proteins are highly related to the axonal growth network. These data suggest that miRNAs altered by CSPGs functionally target these genes for mediating the inhibitory effect of CSPGs on axonal growth. Conclusions: Our bioinformatic analyses of miRNAs and proteins in the distal axon identifies an interconnected group of miRNAs and their target genes that regulate axonal growth, which provides new insight into the molecular mechanisms underlying axonal growth.

The metabolic coregulator RIP140: an update

2010 ◽  
Vol 299 (3) ◽  
pp. E335-E340 ◽  
Author(s):  
Asmaà Fritah ◽  
Mark Christian ◽  
Malcolm G. Parker
Keyword(s):  
Nuclear Receptors ◽  
Posttranslational Modifications ◽  
Energy Homeostasis ◽  
Target Genes ◽  
Peroxisome Proliferator ◽  
Transcriptional Coregulator ◽  
Peroxisome Proliferator Activated Receptors ◽  
Direct Regulation

RIP140 is a transcriptional coregulator highly expressed in metabolic tissues where it has important and diverse actions. RIP140-null mice show that it plays a crucial role in the control of lipid metabolism in adipose tissue, skeletal muscle, and the liver and is essential for female fertility. RIP140 has been shown to act as a ligand-dependent transcriptional corepressor for metabolic nuclear receptors such as estrogen-related receptors and peroxisome proliferator-activated receptors. The role of RIP140 as a corepressor has been strengthened by the characterization of RIP140-overexpressing mice, although it emerges through several studies that RIP140 can also behave as a coactivator. Nuclear localization of RIP140 is important for controlling transcription of target genes and is subject to regulation by posttranslational modifications. However, cytoplasmic RIP140 has been shown to play a role in the control of metabolism through direct regulation of glucose transport in adipocytes. In this review, we focus on recent advances highlighting the growing importance of RIP140 as a regulator of energy homeostasis.

Sequencing and characterization of lncRNAs in the breast muscle of Gushi and Arbor Acres chickens

Genome ◽  
2018 ◽  
Vol 61 (5) ◽  
pp. 337-347 ◽  
Author(s):  
Tuanhui Ren ◽  
Zhuanjian Li ◽  
Yu Zhou ◽  
Xuelian Liu ◽  
Ruili Han ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Muscle Development ◽  
Target Genes ◽  
Expression Profiles ◽  
Economic Value ◽  
Muscle Quality ◽  
Specific Expression ◽  
Chicken Muscle ◽  
Molecular Regulatory Mechanisms

Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens. We identified two muscle tissue specific expression lncRNAs. In addition, the target genes of these lncRNAs were significantly enriched in certain biological processes and molecular functions, as demonstrated by Gene Ontology (GO) analysis, and these target genes participate in five signaling pathway, as revealed by an analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Taken together, these data suggest that different lncRNAs might be involved in regulating chicken muscle development and growth and provide new insight into the molecular mechanisms of lncRNAs.

scholarly journals Chemical screening pipeline for identification of specific plant autophagy modulators

2019 ◽  
Author(s):  
Adrian N. Dauphinee ◽  
Catarina Cardoso ◽  
Kerstin Dalman ◽  
Jonas A. Ohlsson ◽  
Stina Berglund Fick ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Molecular Mechanisms ◽  
Chemical Compounds ◽  
In Planta ◽  
Chemical Screening ◽  
Screening Protocol ◽  
Vegetative Biomass ◽  
As Stress ◽  
Catabolic Process

AbstractAutophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death and aging. In plants, autophagy is also known to regulate agriculturally important traits such as stress resistance, longevity, vegetative biomass and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (i) high-throughput screening of chemical compounds in cell cultures of Nicotiana tabacum; (ii) confirmation of the identified hits in planta using Arabidopsis thaliana; (iii) further characterization of the effect using conventional molecular biology methods; (iv) verification of chemical specificity on autophagy in planta. The methods detailed here streamline identification of specific plant autophagy modulators and aid in unravelling the molecular mechanisms of plant autophagy.

scholarly journals Genome-wide strategies reveal target genes of Npas4l associated with cardiovascular development in zebrafish

2018 ◽  
Author(s):  
Michele Marass ◽  
Arica Beisaw ◽  
Claudia Gerri ◽  
Francesca Luzzani ◽  
Nana Fukuda ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Chromatin Immunoprecipitation ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Building Blocks ◽  
Phenotypic Characterization ◽  
Cardiovascular Development ◽  
Genome Wide ◽  
Transcription Factor Genes

ABSTRACTThe development of a vascular network is essential to nourish tissues and sustain organ function throughout life. Endothelial cells (ECs) are the building blocks of blood vessels, yet our understanding of EC specification remains incomplete. zebrafish cloche/npas4l mutants have been used broadly as an avascular model, but little is known about the molecular mechanisms of action of the Npas4l transcription factor. Here, to identify its direct and indirect target genes, we combined complementary genome-wide approaches including transcriptome analyses and chromatin immunoprecipitation (ChIP). The cross-analysis of these datasets indicates that Npas4l functions as a master regulator by directly inducing a group of transcription factor genes crucial for hematoendothelial specification such as etv2, tal1 and lmo2. We also identified new targets of Npas4l and investigated the function of a subset of them using the CRISPR/Cas9 technology. Phenotypic characterization of tspan18b mutants reveals a novel player in developmental angiogenesis, confirming the reliability of the datasets generated. Collectively, these data represent a useful resource for future studies aimed to better understand EC fate determination and vascular development.

scholarly journals Gli Proteins: Regulation in Development and Cancer

Cells ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 147 ◽  
Author(s):  
Paweł Niewiadomski ◽  
Sylwia M. Niedziółka ◽  
Łukasz Markiewicz ◽  
Tomasz Uśpieński ◽  
Brygida Baran ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Birth Defects ◽  
Tissue Regeneration ◽  
Posttranslational Modifications ◽  
Hedgehog Signaling ◽  
Intracellular Transport ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Gli Proteins ◽  
Fine Tune

Gli proteins are transcriptional effectors of the Hedgehog signaling pathway. They play key roles in the development of many organs and tissues, and are deregulated in birth defects and cancer. We review the molecular mechanisms of Gli protein regulation in mammals, with special emphasis on posttranslational modifications and intracellular transport. We also discuss how Gli proteins interact with co-activators and co-repressors to fine-tune the expression of Hedgehog target genes. Finally, we provide an overview of the regulation of developmental processes and tissue regeneration by Gli proteins and discuss how these proteins are involved in cancer progression, both through canonical regulation via the Hedgehog pathway and through cross-talk with other signaling pathways.

scholarly journals Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Zilong Zhao ◽  
Dan Liu ◽  
Yanjiao Cui ◽  
Suying Li ◽  
Dan Liang ◽  
...  
Keyword(s):  
Grain Yield ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Foxtail Millet ◽  
Differentially Expressed ◽  
High Yield ◽  
Yield Formation ◽  
Identification And Characterization

Abstract Background Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail millet is nearly blank. Results In this study, we performed high-throughput sequencing of young spikelets from four foxtail millet varieties in different yield levels at booting stage. As a result, a total of 12,378 novel lncRNAs were identified, and 70 were commonly significantly differentially expressed in comparisons between high-yield varieties and conventional varieties, suggesting that they involved in yield formation and regulation in foxtail millet. Functional analysis revealed that among the 70 significantly differentially expressed lncRNAs, 67 could transcriptionally modulate target genes in cis and in trans. Moreover, 18 lncRNAs related to grain yield in foxtail millet were predicted to function as miRNA target mimics and regulate gene expression by competing for the interaction between miRNAs and their target mRNAs. Conclusion Our results will provide materials for elucidation of the molecular mechanisms of lncRNAs participate in yield regulation, and will contribute to high yield foxtail millet breeding.

Characterization of Healthy and Tumor Oral Cell Lines of Human Origin. The preliminary stage in the assessment of relevant chemical compounds with impact on dentistry

2018 ◽  
Vol 69 (10) ◽  
pp. 2889-2894
Author(s):  
Ion Virgil Corlan ◽  
Adelina Cheveresan ◽  
Delia Berceanu Vaduva ◽  
Cristian Nica ◽  
Alin Faur ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Cell Lines ◽  
Squamous Cell ◽  
Chemical Compounds ◽  
Tongue Squamous Cell Carcinoma ◽  
Gingival Fibroblasts ◽  
Human Origin ◽  
Preliminary Stage

The present study was aimed to evaluate the confluence percentage of three oral cell lines, namely primary gingival keratinocytes (PGK), primary gingival fibroblasts (HGF) and tongue squamous cell carcinoma (SCC-4). All cells have been monitored at different passages for 21 days. Evaluation of confluence percentage reveals the fact that primary gingival keratinocytes and tongue squamous cell carcinoma at small passages requires a period of about two weeks to reach a confluence of approximately 80% while for the gingival fibroblasts a period of about three times smaller is satisfactory.

scholarly journals The Integrated RNA Landscape of Renal Preconditioning against Ischemia-Reperfusion Injury

2020 ◽  
Vol 31 (4) ◽  
pp. 716-730 ◽  
Author(s):  
Marc Johnsen ◽  
Torsten Kubacki ◽  
Assa Yeroslaviz ◽  
Martin Richard Späth ◽  
Jannis Mörsdorf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reperfusion Injury ◽  
Caloric Restriction ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Ischemia Reperfusion Injury ◽  
Ischemia Reperfusion ◽  
Hypoxic Preconditioning ◽  
Preventive Strategies ◽  
Gene Expression Signatures

BackgroundAlthough AKI lacks effective therapeutic approaches, preventive strategies using preconditioning protocols, including caloric restriction and hypoxic preconditioning, have been shown to prevent injury in animal models. A better understanding of the molecular mechanisms that underlie the enhanced resistance to AKI conferred by such approaches is needed to facilitate clinical use. We hypothesized that these preconditioning strategies use similar pathways to augment cellular stress resistance.MethodsTo identify genes and pathways shared by caloric restriction and hypoxic preconditioning, we used RNA-sequencing transcriptome profiling to compare the transcriptional response with both modes of preconditioning in mice before and after renal ischemia-reperfusion injury.ResultsThe gene expression signatures induced by both preconditioning strategies involve distinct common genes and pathways that overlap significantly with the transcriptional changes observed after ischemia-reperfusion injury. These changes primarily affect oxidation-reduction processes and have a major effect on mitochondrial processes. We found that 16 of the genes differentially regulated by both modes of preconditioning were strongly correlated with clinical outcome; most of these genes had not previously been directly linked to AKI.ConclusionsThis comparative analysis of the gene expression signatures in preconditioning strategies shows overlapping patterns in caloric restriction and hypoxic preconditioning, pointing toward common molecular mechanisms. Our analysis identified a limited set of target genes not previously known to be associated with AKI; further study of their potential to provide the basis for novel preventive strategies is warranted. To allow for optimal interactive usability of the data by the kidney research community, we provide an online interface for user-defined interrogation of the gene expression datasets (http://shiny.cecad.uni-koeln.de:3838/IRaP/).

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