Connected through the force: mechanical signals in plant development

2019 ◽  
Vol 70 (14) ◽  
pp. 3507-3519 ◽  
Author(s):  
Benoit Landrein ◽  
Gwyneth Ingram
Keyword(s):  
Gene Expression ◽  
Plant Development ◽  
Growth And Development ◽  
Biological Processes ◽  
Plant Morphogenesis ◽  
Mechanical Signals ◽  
Physical Forces ◽  
Multicellular Organisms ◽  
Biochemical Signals

Abstract As multicellular organisms, plants acquire characteristic shapes through a complex set of biological processes known as morphogenesis. Biochemical signalling underlies much of development, as it allows cells to acquire specific identities based on their position within tissues and organs. However, as growing physical structures, plants, and their constituent cells, also experience internal and external physical forces that can be perceived and can influence key processes such as growth, polarity, and gene expression. This process, which adds another layer of control to growth and development, has important implications for plant morphogenesis. This review provides an overview of recent research into the role of mechanical signals in plant development and aims to show how mechanical signalling can be used, in concert with biochemical signals, as a cue allowing cells and tissues to coordinate their behaviour and to add robustness to developmental processes.

scholarly journals Increased Expression of CCN2 in the Red Flashing Light-Induced Myopia in Guinea Pigs

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Hong Wang ◽  
Kang Zhuang ◽  
Lei Gao ◽  
Linna Zhang ◽  
Hongling Yang
Keyword(s):  
Gene Expression ◽  
Animal Model ◽  
Axial Length ◽  
Growth And Development ◽  
Visual Environment ◽  
Biological Processes ◽  
Cellular Functions ◽  
Ocular Growth ◽  
Flashing Light

Visual environment plays an important role in the occurrence of myopia. We previously showed that the different flashing lights could result in distinct effects on the ocular growth and development of myopia. CCN2 has been reported to regulate various cellular functions and biological processes. However, whether CCN2 signaling was involved in the red flashing light-induced myopia still remains unknown. In the present study, we investigated the effects of the red flashing lights exposure on the refraction and axial length of the eyesin vivoand then evaluated their effects on the expression of CCN2 and TGF-βin sclera tissues. Our data showed that the eyes exposed to the red flashing light became more myopic with a significant increase of the axial length and decrease of the refraction. Both CCN2 and TGF-β, as well as p38 MAPK and PI3K, were highly expressed in the sclera tissues exposed to the red flashing light. Both CCN2 and TGF-βwere found to have the same gene expression profilein vivo. In conclusion, our findings found that CCN2 signaling pathway plays an important role in the red flashing light-induced myopiain vivo. Moreover, our study establishes a useful animal model for experimental myopia research.

scholarly journals Mutational Signatures as Sensors of Environmental Exposures: Role of Smoking in COVID-19 Vulnerabilities

2021 ◽  
Author(s):  
Yoo-Ah Kim ◽  
Ermin Hodzic ◽  
Ariella Saslafsky ◽  
Damian Wojtowicz ◽  
Bayarbaatar Amgalan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Environmental Factors ◽  
Disease Progression ◽  
Environmental Exposures ◽  
Biological Processes ◽  
Mutational Signatures ◽  
Mutational Signature ◽  
The Impact ◽  
Pathway Level

Background: Environmental exposures such as smoking are widely recognized risk factors in the emergence of lung diseases such as lung cancer and acute respiratory distress syndrome (ARDS). However, the strength of environmental exposures is difficult to measure, making it challenging to understand their impacts. On the other hand, some COVID-19 patients develop ARDS in an unfavorable disease progression and smoking has been suggested as a potential risk factor among others. Yet initial studies on COVID-19 cases reported contradictory results on the effects of smoking on the disease. Some suggest that smoking might have a protective effect against it while other studies report an increased risk. A better understanding of how the exposure to smoking and other environmental factors affect biological processes relevant to SARS-CoV-2 infection and unfavorable disease progression is needed. Approach: In this study, we utilize mutational signatures associated with environmental factors as sensors of their exposure level. Many environmental factors including smoking are mutagenic and leave characteristic patterns of mutations, called mutational signatures, in affected genomes. We postulated that analyzing mutational signatures, combined with gene expression, can shed light on the impact of the mutagenic environmental factors to the biological processes. In particular, we utilized mutational signatures from lung adenocarcinoma (LUAD) data set collected in TCGA to investigate the role of environmental factors in COVID-19 vulnerabilities. Integrating mutational signatures with gene expression in normal tissues and using a pathway level analysis, we examined how the exposure to smoking and other mutagenic environmental factors affects the infectivity of the virus and disease progression. Results: By delineating changes associated with smoking in pathway-level gene expression and cell type proportions, our study demonstrates that mutational signatures can be utilized to study the impact of exogenous mutagenic factors on them. Consistent with previous findings, our analysis showed that smoking mutational signature (SBS4) is associated with activation of cytokines mediated singling pathways, leading to inflammatory responses. Smoking related changes in cell composition were also observed, including the correlation of SBS4 with the expansion of goblet cells. On the other hand, increased basal cells and decreased ciliated cells in proportion were associated with the strength of a different mutational signature (SBS5), which is present abundantly but not exclusively in smokers. In addition, we found that smoking increases the expression levels of genes that are upregulated in severe COVID-19 cases. Jointly, these results suggest an unfavorable impact of smoking on the disease progression and also provide novel findings on how smoking impacts biological processes in lung.

scholarly journals Increased IGFBP7 Expression Correlates with Poor Prognosis and Immune Infiltration in Gastric Cancer: An Integrated Bioinformatics Analysis

2020 ◽  
Author(s):  
Qiaoyun Zhao ◽  
Rulin Zhao ◽  
Conghua Song ◽  
Huan Wang ◽  
Jianfang Rong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Poor Prognosis ◽  
Bioinformatics Analysis ◽  
Immune Cell ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Biological Processes ◽  
Coexpressed Genes

Abstract Background Insulin-like growth factor binding protein-7 (IGFBP7) contributes to multiple biological processes in various tumors. However, the role of IGFBP7 in gastric cancer (GC) is still undetermined. The study aims to explore the role of IGFBP7 in GC via an integrated bioinformatics analysis.Methods IGFBP7 expression levels in GC and its normal gastric tissues were analyzed using multiple databases, including the Tumor Immune Estimation Resource (TIMER), Oncomine, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The methylation analysis was conducted with MEXPRESS, UALCAN and Xena online tools. The survival analysis was conducted using the Kaplan-Meier Plotter and Gene Expression Profiling Interactive Analysis (GEPIA) databases. Coexpressed genes of IGFBP7 were selected with the cBioPortal tool and enrichment analysis was conducted with the clusterProfiler package in R software. Gene set enrichment analysis (GSEA) was performed to explore the IGFBP7-related biological processes involved in GC. Correlations between IGFBP7 and immune cell infiltrates were analyzed using the TIMER database.Results IGFBP7 expression was significantly upregulated in GC and correlated with stage, grade, tumor status and Helicobacter pylori infection. High IGFBP7 expression and low IGFBP7 methylation levels were significantly associated with short survival of patients with GC. Univariate and multivariate analyses revealed that IGFBP7 was an independent risk factor for GC. The coexpressed genes LHFPL6, SEPTIN4, HSPB2, LAYN and GGT5 predicted unfavorable outcomes of GC. Enrichment analysis showed that the coexpressed genes were involved in extracellular matrix (ECM)-related processes. GSEA indicated that IGFBP7 was positively related to ECM and inflammation-related pathways. TIMER analysis indicated that the IGFBP7 expression level was strongly correlated with genes related to various infiltrating immune cells in GC, especially with gene markers of tumor associated macrophages (TAMs).Conclusions We demonstrate that increased IGFBP7 expression correlates with poor prognosis and immune cell infiltration in GC. IGFBP7 might be a potential biomarker for the diagnosis and targeted therapy for GC.

scholarly journals Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2766
Author(s):  
Jiao Liu ◽  
Cheng Chang
Keyword(s):  
Gene Expression ◽  
Plant Development ◽  
Stress Responses ◽  
Epigenetic Mechanisms ◽  
Biological Processes ◽  
Post Translational Modifications ◽  
Plant Gene Expression ◽  
Plant Gene ◽  
Transcriptional Reprogramming ◽  
Development Processes

Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms are highly interconnected, thereby contributing to the complexity of transcriptional reprogramming in plant development processes and responses to environmental stresses. Here, we provide an overview of recent advances in understanding the epigenetic regulation of plant gene expression and highlight the crosstalk among different epigenetic mechanisms in making plant developmental and stress-responsive decisions. Structural, physical, transcriptional and metabolic bases for these epigenetic interplays are discussed.

scholarly journals The role of m6A, m5C and Ψ RNA modifications in cancer: Novel therapeutic opportunities

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Paz Nombela ◽  
Borja Miguel-López ◽  
Sandra Blanco
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Therapeutic Potential ◽  
Biological Processes ◽  
Rna Modifications ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
And Function ◽  
Made In

AbstractRNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programmes. Significant advances have been made in understanding the functional role of RNA modifications in regulating coding and non-coding RNA processing and function, which in turn thoroughly shape distinct gene expression programmes. They affect diverse biological processes, and the correct deposition of many of these modifications is required for normal development. Alterations of their deposition are implicated in several diseases, including cancer. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in coding and non-coding RNAs and describe their physiopathological role in cancer. We will highlight the latest insights into the mechanisms of how these posttranscriptional modifications influence tumour development, maintenance, and progression. Finally, we will summarize the latest advances on the development of small molecule inhibitors that target specific writers or erasers to rewind the epitranscriptome of a cancer cell and their therapeutic potential.

scholarly journals Metabolic hormones regulate insulin-like growth factor binding protein-1 mRNA levels in primary cultured salmon hepatocytes; lack of inhibition by insulin

2006 ◽  
Vol 191 (2) ◽  
pp. 379-386 ◽  
Author(s):  
A L Pierce ◽  
M Shimizu ◽  
L Felli ◽  
P Swanson ◽  
W W Dickhoff
Keyword(s):  
Gene Expression ◽  
Growth Factor ◽  
Hormonal Regulation ◽  
Growth And Development ◽  
Mrna Levels ◽  
Igf Binding Proteins ◽  
Metabolic Hormones ◽  
Igf I ◽  
Igf Binding

IGF-binding proteins (IGFBPs) modulate the effects of the IGFs, major stimulators of vertebrate growth and development. In mammals, IGFBP-1 inhibits the actions of IGF-I. Rapid increases in circulating IGFBP-1 occur during catabolic states. Insulin and glucocorticoids are the primary regulators of circulating IGFBP-1 in mammals. Insulin inhibits and glucocorticoids stimulate hepatocyte IGFBP-1 gene expression and production. A 22 kDa IGFBP in salmon blood also increases during catabolic states and has recently been identified as an IGFBP-1 homolog. We examined the hormonal regulation of salmon IGFBP-1 mRNA levels and protein secretion in primary cultured salmon hepatocytes. The glucocorticoid agonist dexamethasone progressively increased hepatocyte IGFBP-1 mRNA levels (eightfold) and medium IGFBP-1 immunoreactivity over concentrations comparable with stressed circulating cortisol levels (10−9–10−6 M). GH progressively reduced IGFBP-1 mRNA levels (0.3-fold) and medium IGFBP-1 immunoreactivity over physiological concentrations (5 × 10−11–5 × 10−9 M). Unexpectedly, insulin slightly increased hepatocyte IGFBP-1 mRNA (1.4-fold) and did not change medium IGFBP-1 immunoreactivity over physiological concentrations and above (10−9–10−6 M). Triiodothyronine had no effect on hepatocyte IGFBP-1 mRNA, whereas glucagon increased IGFBP-1 mRNA (2.2-fold) at supraphysiological concentrations (10−6 M). This study suggests that the major inhibitory role of insulin in the regulation of liver IGFBP-1 production in mammals is not found in salmon. However, regulation of salmon liver IGFBP-1 production by other metabolic hormones is similar to what is found in mammals.

scholarly journals Nucleotide Metabolism Behind Epigenetics

2021 ◽  
Vol 12 ◽  
Author(s):  
Tamaki Suganuma ◽  
Jerry L. Workman
Keyword(s):  
Gene Expression ◽  
Chromatin Remodeling ◽  
Rna Processing ◽  
Noncoding Rna ◽  
Nucleotide Metabolism ◽  
Biological Processes ◽  
Cellular Processes ◽  
Epigenetic Gene Regulation ◽  
Translation Gene

The mechanisms of epigenetic gene regulation—histone modifications, chromatin remodeling, DNA methylation, and noncoding RNA—use metabolites as enzymatic cofactors and substrates in reactions that allow chromatin formation, nucleotide biogenesis, transcription, RNA processing, and translation. Gene expression responds to demands from cellular processes that use specific metabolites and alters or maintains cellular metabolic status. However, the roles of metabolites—particularly nucleotides—as regulatory molecules in epigenetic regulation and biological processes remain largely unknown. Here we review the crosstalk between gene expression, nucleotide metabolism, and cellular processes, and explore the role of metabolism in epigenetics as a critical regulator of biological events.

scholarly journals Integrated mRNA-miRNA transcriptome analysis of bladder biopsies from patients with bladder pain syndrome identifies signaling alterations contributing to the disease pathogenesis

BMC Urology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ali Hashemi Gheinani ◽  
Akshay Akshay ◽  
Mustafa Besic ◽  
Annette Kuhn ◽  
Irene Keller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Interstitial Cystitis ◽  
Transcriptome Analysis ◽  
System Organization ◽  
Pain Syndrome ◽  
Bladder Pain Syndrome ◽  
Biological Processes ◽  
Bladder Pain

Abstract Background Interstitial cystitis, or bladder pain syndrome (IC/BPS), is a chronic bladder disorder characterized by lower abdominal pain associated with the urinary bladder and accompanied by urinary frequency and urgency in the absence of identifiable causes. IC/PBS can be separated into the classic Hunner’s ulcerative type and the more prevalent non-ulcerative disease. Our aim was to unravel the biological processes and dysregulated cell signaling pathways leading to the bladder remodeling in non-ulcerative bladder pain syndrome (BPS) by studying the gene expression changes in the patients’ biopsies. Methods We performed paired microRNA (miRNA) and mRNA expression profiling in the bladder biopsies of BPS patients with non-Hunner interstitial cystitis phenotype, using comprehensive Next-generation sequencing (NGS) and studied the activated pathways and altered biological processes based on the global gene expression changes. Paired mRNA-miRNA transcriptome analysis delineated the regulatory role of the dysregulated miRNAs by identifying their targets in the disease-induced pathways. Results EIF2 Signaling and Regulation of eIF4 and p70S6K Signaling, activated in response to cellular stress, were among the most significantly regulated processes during BPS. Leukotriene Biosynthesis nociceptive pathway, important in inflammatory diseases and neuropathic pain, was also significantly activated. The biological processes identified using Gene Ontology over-representation analysis were clustered into six main functional groups: cell cycle regulation, chemotaxis of immune cells, muscle development, muscle contraction, remodeling of extracellular matrix and peripheral nervous system organization and development. Compared to the Hunner’s ulcerative type IC, activation of the immune pathways was modest in non-ulcerative BPS, limited to neutrophil chemotaxis and IFN-γ-mediated signaling. We identified 62 miRNAs, regulated and abundant in BPS and show that they target the mRNAs implicated in eIF2 signalling pathway. Conclusions The bladders of non-ulcerative BPS patients recruited in this study had alterations consistent with a strong cell proliferative response and an up-regulation of smooth muscle contractility, while the contribution of inflammatory processes was modest. Pathway analysis of the integrated mRNA-miRNA NGS dataset pinpointed important regulatory miRNAs whose dysregulation might contribute to the pathogenesis. Observed molecular changes in the peripheral nervous system organization and development indicate the potential role of local bladder innervation in the pain perceived in this type of BPS.

Renal gene expression profiling using kinin B1 and B2 receptor knockout mice reveals comparable modulation of functionally related genes

2006 ◽  
Vol 387 (1) ◽  
pp. 15-22 ◽  
Author(s):  
Dimcho Bachvarov ◽  
Magdalena Bachvarova ◽  
Rainelli Koumangaye ◽  
Julie Klein ◽  
João Bosco Pesquero ◽  
...  
Keyword(s):  
Gene Expression ◽  
Biological Effects ◽  
Renal Physiology ◽  
Null Mouse ◽  
Biological Processes ◽  
Wild Type ◽  
Microarray Experiments ◽  
B1 Receptor ◽  
Pathological Conditions

Abstract The kinin B2 receptor, which is constitutively expressed in a large number of tissues, mediates most of the known effects of bradykinin (BK). Normally undetectable in healthy tissues, the B1 receptor is strongly over-expressed under pathological conditions. BK is an important mediator in renal homeostasis and is mainly known for its natriuretic and vasodilatory effects. Recent data evidenced a role for BK in many other biological processes, such as apoptosis, development, extracellular matrix regulation and angiogenesis. In a first step to better understand how BK and its receptors could be involved in such a large variety of biological effects, we used microarray analysis to identify, under physiological conditions, the global renal gene expression profile in mice lacking either the kinin B1 or B2 receptor. Microarray experiments were performed using Agilent Mouse Oligonucleotide Microarrays (21 000 genes/microarray). Interestingly, there was a considerable number of mostly downregulated genes in both BK null mouse models compared with wild-type mice. Furthermore, a number of genes that are known to be implicated in renal physiology and/or pathology were differentially expressed in the BK null mice, which is indicative of the important role of both BK receptors in renal function.

scholarly journals Mechanoregulation of h2-Calponin Gene Expression and the Role of Notch Signaling

2013 ◽  
Vol 289 (3) ◽  
pp. 1617-1628 ◽  
Author(s):  
Wen-rui Jiang ◽  
Geoffrey Cady ◽  
M. Moazzem Hossain ◽  
Qi-Quan Huang ◽  
Xin Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Activity ◽  
C2c12 Cells ◽  
Host Cells ◽  
Gene Encoding ◽  
Signaling Mechanism ◽  
Mechanical Signals ◽  
Promoter Construct ◽  
In Cells

The essential role of mechanical signals in regulating the function of living cells is universally observed. However, how mechanical signals are transduced in cells to regulate gene expression is largely unknown. We previously demonstrated that the gene encoding h2-calponin (Cnn2) is sensitively regulated by mechanical tension. In the present study, mouse genomic DNA containing the Cnn2 promoter was cloned, and a nested set of 5′ truncations was studied. Transcriptional activity of the Cnn2 promoter-reporter constructs was examined in transfected NIH/3T3, HEK293, and C2C12 cells for their responses to the stiffness of culture substrate. The results showed significant transcriptional activities of the −1.00- and −1.24-kb promoter constructs, whereas the −0.61-kb construct was inactive. The −1.38-, −1.57-, and −2.12-kb constructs showed higher transcriptional activity, whereas only the −1.57- and −2.12-kb constructs exhibited repression of expression when the host cells were cultured on low stiffness substrate. Internal deletion of the segment between −1.57 and −1.38 kb in the −2.12-kb promoter construct abolished the low substrate stiffness-induced repression. Site-specific deletion or mutation of an HES-1 transcription factor binding site in this region also abolished this repression effect. The level of HES-1 increased in cells cultured under a low tension condition, corresponding to the down-regulation of h2-calponin. h2-Calponin gene expression is further affected by the treatment of cells with Notch inhibitor and activator, suggesting an upstream signaling mechanism.

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