scholarly journals Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor

2021 ◽  
Author(s):  
Erica D'Incà ◽  
Chiara Foresti ◽  
Luis Orduña ◽  
Alessandra Amato ◽  
Elodie Vandelle ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Fruit Maturation ◽  
Fruit Crops ◽  
Promoter Activation ◽  
High Confidence ◽  
Developmental Transitions ◽  
Perennial Plant ◽  
Mature Phase ◽  
Regulatory Complex ◽  
Nac Family

Grapevine is a woody temperate perennial plant and one of the most important fruit crops with global relevance in both the fresh fruit and winemaking industries. Unfortunately, global warming is affecting viticulture by altering developmental transitions and fruit maturation processes. In this context, uncovering the molecular mechanisms controlling the onset and progression of ripening could prove essential to maintain high-quality grapes and wines. Through a deep inspection of previously published transcriptomic data we identified the NAC family member VviCARPO (Controlled Adjustment of Ripening and maturation of Plant Organs) as a key regulator of grapevine maturation whose induction precedes the expression of well-known ripening associated genes. We explored VviCARPO binding landscapes through DAP-seq and overlapped its bound genes with transcriptomics datasets from stable and transient VviCARPO overexpressing grapevine plants to define a set of high-confidence targets. Among these, we identified key molecular ripening markers. Physiological, metabolic and promoter activation analyses showed that VviCARPO induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of VviSGR1 and VviMYBA1, respectively, with the latter being up-regulated through a VviCARPO-VviNAC03 regulatory complex. Despite showing a closer phylogenetic relationship to senescent-related AtNAP homologues, VviCARPO complemented the nor mutant phenotype in tomato, suggesting it may have acquired a dual role as an orchestrator of both ripening- and senescence-related processes. Our data supports CARPO as a master regulator of the grapevine vegetative-to-mature phase organ transition and therefore an essential target for insuring fruit quality and environmental resilience.

scholarly journals Beneficial Actions of Orostachys japonica and Its Compounds against Tumors via MAPK Signaling Pathways

Nutrients ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 555
Author(s):  
Soyoung Hur ◽  
Eungyeong Jang ◽  
Jang-Hoon Lee
Keyword(s):  
Molecular Mechanisms ◽  
Epithelial To Mesenchymal Transition ◽  
Malignant Tumors ◽  
Treatment Options ◽  
Underlying Mechanism ◽  
Mapk Signaling ◽  
Mitogen Activated Protein Kinase ◽  
Antitumor Effects ◽  
Mesenchymal Transition ◽  
Perennial Plant

Tumors are one of the most life-threatening diseases, and a variety of cancer treatment options have been continuously introduced in order to overcome cancer and improve conventional therapy. Orostachys japonica (O. japonica), which is a perennial plant belonging to the genus Orostachys of the Crassulaceae family, has been revealed to exhibit pharmacological properties against various tumors in numerous studies. The present review aimed to discuss the biological actions and underlying molecular mechanisms of O. japonica and its representative compounds—kaempferol and quercetin—against tumors. O. japonica reportedly has antiproliferative, anti-angiogenic, and antimetastatic activities against various types of malignant tumors through the induction of apoptosis and cell cycle arrest, a blockade of downstream vascular endothelial growth factor (VEGF)-VEGFR2 pathways, and the regulation of epithelial-to-mesenchymal transition. In addition, emerging studies have highlighted the antitumor efficacy of kaempferol and quercetin. Interestingly, it was found that alterations of the mitogen-activated protein kinase (MAPK) signaling cascades are involved in the pivotal mechanisms of the antitumor effects of O. japonica and its two compounds against cancer cell overgrowth, angiogenesis, and metastasis. In summary, O. japonica could be considered a preventive and therapeutic medicinal plant which exhibits antitumor actions by reversing altered patterns of MAPK cascades, and kaempferol and quercetin might be potential components that can contribute to the efficacy and underlying mechanism of O. japonica.

scholarly journals Hierarchical assembly and disassembly of a transcriptionally active RAG locus in CD4+CD8+ thymocytes

2018 ◽  
Vol 216 (1) ◽  
pp. 231-243 ◽  
Author(s):  
Abani Kanta Naik ◽  
Aaron T. Byrd ◽  
Aaron C.K. Lucander ◽  
Michael S. Krangel
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Molecular Mechanisms ◽  
Promoter Activation ◽  
Active Chromatin ◽  
Gene Assembly ◽  
Down Regulation ◽  
Hierarchical Assembly ◽  
Rag2 Gene

Expression of Rag1 and Rag2 is tightly regulated in developing T cells to mediate TCR gene assembly. Here we have investigated the molecular mechanisms governing the assembly and disassembly of a transcriptionally active RAG locus chromatin hub in CD4+CD8+ thymocytes. Rag1 and Rag2 gene expression in CD4+CD8+ thymocytes depends on Rag1 and Rag2 promoter activation by a distant antisilencer element (ASE). We identify GATA3 and E2A as critical regulators of the ASE, and Runx1 and E2A as critical regulators of the Rag1 promoter. We reveal hierarchical assembly of a transcriptionally active chromatin hub containing the ASE and RAG promoters, with Rag2 recruitment and expression dependent on assembly of a functional ASE–Rag1 framework. Finally, we show that signal-dependent down-regulation of RAG gene expression in CD4+CD8+ thymocytes depends on Ikaros and occurs with disassembly of the RAG locus chromatin hub. Our results provide important new insights into the molecular mechanisms that orchestrate RAG gene expression in developing T cells.

scholarly journals Date Palm Biotechnology: Recent Research an Overview

2018 ◽  
pp. 1-5
Author(s):  
Wessam M. Rslan
Keyword(s):  
Middle East ◽  
North Africa ◽  
Date Palm ◽  
Phoenix Dactylifera ◽  
Fruit Maturation ◽  
Fruit Crops ◽  
Distinctive Features ◽  
Phoenix Dactylifera L ◽  
Genomic Studies ◽  
Plant Characteristics

Date palm (Phoenix dactylifera L.) is among the earliest fruit crops cultivated in the arid Arab Peninsula, North Africa, and Middle East territories. Dates are a significant source of food and revenue for Middle East and North Africa's local communities. It has distinctive features of biology and development that require special methods of reproduction, culture and governance. In varying date-growing regions, there are thousands of date plant cultivars and varieties. The lengthy life cycle, long juvenile lifespan, and date palm dioecism produce cultivation difficult. Every year, the percentage of crop genomes sequenced has continued to increase. The incredible rate at which DNA samples become accessible is mainly due to the enhancement in cost-and speed-related sequencing techniques. Modern sequencing techniques enable the sequencing at realistic price of various cultivars of tiny plant genomes. Although many of the published genomes are deemed incomplete, they have nevertheless proven to be useful instruments for understanding significant plant characteristics such as fruit maturation, grain characteristics and adaptation of flowering time, here we review date palm genomic studies and determine its genomics element.

HDAC1-Smad3-mSin3Acomplex is required for Smad3-induced transcriptional inhibition of hepatocyte growth factor receptor in human lung cancers

2020 ◽  
Author(s):  
Hao-Xin Gui ◽  
Jun Peng ◽  
Ze-Ping Yang ◽  
Lu-Yao Chen ◽  
Hong Zeng ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
Molecular Mechanisms ◽  
Growth Factor Receptor ◽  
Mrna Levels ◽  
Lung Cancers ◽  
Transcriptional Inhibition ◽  
Transcriptional Suppression ◽  
Transcriptional Regulatory ◽  
Regulatory Complex ◽  
Cancer Tissues

Abstract c-Met hyperactivity has been observed in numerous neoplasms. Several researchers have shown that the abnormal activation of c-Met is mainly caused by transcriptional activation. However, the molecular mechanism behind this transcriptional regulation is poorly understood. Here, we suggest that Smad3 negatively regulates the expression and activation of c-Met via a transcriptional mechanism. We explore the molecular mechanisms that underlie Smad3-induced c-Met transcription inhibition. We found in contrast to the high expression of c-Met, Smad3 showed low protein and mRNA levels. Smad3 and c-Met expression was inconsistent between lung cancer tissues and cell lines. We also found that Smad3 overexpression suppresses whereas Smad3 knockdown significantly promotes EMT and production of the angiogenic factors VEGF, CTGF and COX-2 through the ERK1/2 pathway. In addition, Smad3 overexpression decreases whereas Smad3 knockdown significantly increases protein and mRNA levels of invasion related β-catenin and FAK through the PI3K/Akt pathway. Furthermore, using the ChIP analysis method, we demonstrate that a transcriptional regulatory complex consisting of HDAC1, Smad3 and mSin3A binds to the promoter of the c-Met gene. By either silencing endogenous mSin3A expression with siRNA or by pretreating cells with a specific HDAC1 inhibitor (MS-275), Smad3-induced transcriptional suppression of c-Met could be effectively attenuated. These results demonstrate that Smad3-induced inhibition of c-Met transcription depends on of a functional transcriptional regulatory complex that includes Smad3, mSin3A and HDAC1 at the c-Met promoter. Collectively, our findings reveal a new regulatory mechanism of c-Met signaling, and suggest a potential molecular target for the development of anticancer drugs.

scholarly journals Neurexin–Neuroligin 1 regulates synaptic morphology and functions via the WAVE regulatory complex in Drosophila neuromuscular junction

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Guanglin Xing ◽  
Moyi Li ◽  
Yichen Sun ◽  
Menglong Rui ◽  
Yan Zhuang ◽  
...  
Keyword(s):  
Neuromuscular Junction ◽  
Molecular Mechanisms ◽  
Postsynaptic Membrane ◽  
Synaptic Function ◽  
Actin Assembly ◽  
Actin Reorganization ◽  
Synaptic Structure ◽  
Structural And Functional Properties ◽  
Regulatory Complex ◽  
And Function

Neuroligins are postsynaptic adhesion molecules that are essential for postsynaptic specialization and synaptic function. But the underlying molecular mechanisms of neuroligin functions remain unclear. We found that Drosophila Neuroligin 1 (DNlg1) regulates synaptic structure and function through WAVE regulatory complex (WRC)-mediated postsynaptic actin reorganization. The disruption of DNlg1, DNlg2, or their presynaptic partner neurexin (DNrx) led to a dramatic decrease in the amount of F-actin. Further study showed that DNlg1, but not DNlg2 or DNlg3, directly interacts with the WRC via its C-terminal interacting receptor sequence. That interaction is required to recruit WRC to the postsynaptic membrane to promote F-actin assembly. Furthermore, the interaction between DNlg1 and the WRC is essential for DNlg1 to rescue the morphological and electrophysiological defects in dnlg1 mutants. Our results reveal a novel mechanism by which the DNrx-DNlg1 trans-synaptic interaction coordinates structural and functional properties at the neuromuscular junction.

Field Application of Glyphosate Induces Molecular Changes Affecting Vegetative Growth Processes in Leafy Spurge (Euphorbia esula)

Weed Science ◽  
2016 ◽  
Vol 64 (1) ◽  
pp. 87-100 ◽  
Author(s):  
Münevver Doğramacı ◽  
Greta G. Gramig ◽  
James V. Anderson ◽  
Wun S. Chao ◽  
Michael E. Foley
Keyword(s):  
Vegetative Growth ◽  
Molecular Mechanisms ◽  
Sublethal Effects ◽  
Vegetative Reproduction ◽  
Transcript Abundance ◽  
Leafy Spurge ◽  
Field Application ◽  
Limiting Factors ◽  
Molecular Processes ◽  
Perennial Plant

Recommended rates of glyphosate for noncultivated areas destroy the aboveground shoots of the perennial plant leafy spurge. However, such applications cause little or no damage to underground adventitious buds (UABs), and thus the plant readily regenerates vegetatively. High concentrations of glyphosate, applied under controlled environmental conditions, have been shown to cause sublethal effects in UABs of leafy spurge that produce stunted and bushy phenotypes in subsequent generations of shoots. We treated leafy spurge plants in the field with glyphosate (0, 1.1, 3.4, or 6.7 kg ai ha−1) to determine its effects on vegetative growth from UABs and on molecular processes. The number of shoots derived from UABs of glyphosate-treated plants was significantly increased compared to controls in subsequent years after application, and new shoots displayed various phenotypical changes, such as stunted and bushy phenotypes. Quantifying the abundance of a selected set of transcripts in UABs of nontreated vs. treated plants (0 vs. 6.7 kg ha−1) indicated that glyphosate impacted molecular processes involved in biosynthesis or signaling of tryptophan or auxin (ARF4,CYP79B2,PIN3,TAA1,TRP6,YUC4), gibberellic acid (GA1/CPS1,GA2/KS), ethylene (ACO1,ACS10), cytokinins (AHP1,AK2,CKX1), and the cell cycle (CDC2A,CDC2B,CYCD3;1). Glyphosate-induced effects on vegetative growth and transcript abundance were persistent for at least 2 yr after treatment. Determining the molecular mechanisms associated with vegetative reproduction in leafy spurge following foliar glyphosate-treatment could identify limiting factors or new targets for manipulation of plant growth and development in perennial weeds.

scholarly journals A Role of Ginseng and Its Constituents in the Treatment of Central Nervous System Disorders

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Natasya Trivena Rokot ◽  
Timothy Sean Kairupan ◽  
Kai-Chun Cheng ◽  
Joshua Runtuwene ◽  
Nova Hellen Kapantow ◽  
...  
Keyword(s):  
Central Nervous System ◽  
Nervous System ◽  
Molecular Mechanisms ◽  
Protective Effects ◽  
Pharmacological Effects ◽  
Intestinal Metabolism ◽  
Traditional Herbal Medicine ◽  
Perennial Plant ◽  
Enhanced Properties

Ginseng, a perennial plant belonging to thePanaxgenus of the Araliaceae family, has been used in China, Korea, and Japan as a traditional herbal medicine for thousands of years. Ginseng is recorded to have exhibited a wide variety of beneficial pharmacological effects and has become a popular and worldwide known health supplement and drug. The protective effects of ginseng on central nervous system are discussed in this review. Ginseng species and ginsenosides and their intestinal metabolism and bioavailability are concisely introduced. The molecular mechanisms of the effects of ginseng on central nervous system, mainly focused on the neuroprotection properties of ginseng, memory, and learning enhanced properties, and the effects on neurodegenerative disorders are presented. Thus, ginseng and its constituents are of potential merits in the treatment of cerebral disorders.

Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts

2014 ◽  
Vol 12 (05) ◽  
pp. 1450026 ◽  
Author(s):  
Harshal Inamdar ◽  
Avik Datta ◽  
Sunitha Manjari K ◽  
Rajendra Joshi
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Rna Seq ◽  
Cellular Functions ◽  
High Confidence ◽  
Rule Based ◽  
Profiling Techniques ◽  
Novel Transcripts ◽  
Different Levels ◽  
Sizable Number

Recent evidences suggest that a substantial amount of genome is transcribed more than that was anticipated, giving rise to a large number of unknown or novel transcripts. Identification of novel transcripts can provide key insights into understanding important cellular functions as well as molecular mechanisms underlying complex diseases like cancer. RNA-Seq has emerged as a powerful tool to detect novel transcripts, which previous profiling techniques failed to identify. A number of tools are available for enabling identification of novel transcripts at different levels. Read mappers such as TopHat, MapSplice, and SOAPsplice predict novel junctions, which are the indicators of novel transcripts. Cufflinks assembles novel transcripts based on alignment information and Oases performs de novo construction of transcripts. A common limitation of all these tools is prediction of sizable number of spurious or false positive (FP) novel transcripts. An approach that integrates information from all above sources and simultaneously scrutinizes FPs to correctly identify authentic novel transcripts of high confidence is proposed.

scholarly journals Genetic exploration of a nuclear receptor transcriptional regulatory complex

2020 ◽  
Author(s):  
Masako Asahina ◽  
Deborah Thurtle-Schmidt ◽  
Keith R. Yamamoto
Keyword(s):  
Nuclear Receptor ◽  
Molecular Mechanisms ◽  
Genetic Screen ◽  
Fluorescent Reporter ◽  
Response Elements ◽  
C Elegans ◽  
Transcriptional Regulatory ◽  
Regulatory Complex ◽  
Composition Structure ◽  
Context Specific

ABSTRACTMetazoan transcriptional regulatory factors (TFs) bind to genomic response elements and assemble with co-regulators into transcriptional regulatory complexes (TRCs) whose composition, structure and activities are gene-, cell- and physiological-context specific. Each TRC is a “regulatory logic module,” integrating incoming signaling information, which defines context and thereby recruits a distinct combination of co-regulators that together specify outgoing regulatory activity. Analyzing TRCs unique to every context is daunting, yet justified by their properties as self-contained regulatory modules. As proof-of-concept, we performed a forward genetic screen in C. elegans carrying a synthetic simple response element for nuclear receptor NHR-25 upstream of a fluorescent reporter gene. We isolated independent mutations in uba-2, a component of the sumoylation signaling machinery, and in lir-2, which we demonstrated to be a novel co-regulator, interacting with NHR-25 through LxxLL motifs and modulating target gene expression. Our studies establish that an unbiased genetic screen readily identifies both afferent and efferent components that specify TRC function, and suggest that screening natural response elements of interest could illuminate molecular mechanisms of both context-specificity and transcriptional regulation.

scholarly journals circ2GO: A Database Linking Circular RNAs to Gene Function

Cancers ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 2975
Author(s):  
Yanhong Lyu ◽  
Maiwen Caudron-Herger ◽  
Sven Diederichs
Keyword(s):  
Lung Cancer ◽  
Cell Lines ◽  
Molecular Mechanisms ◽  
Circular Rnas ◽  
Biological Functions ◽  
High Confidence ◽  
User Friendliness ◽  
Rrna Depletion ◽  
Transformed Cell Lines ◽  
Host Genes

Circular RNAs (circRNAs) play critical roles in a broad spectrum of physiological and pathological processes, including cancer. Here, we provide a comprehensive database—circ2GO—systematically linking circRNAs to the functions and processes of their linear counterparts. circ2GO contains 148,811 circular human RNAs originating from 12,251 genes, which we derived from deep transcriptomics after rRNA depletion in a panel of 60 lung cancer and non-transformed cell lines. The broad circRNA expression dataset is mapped to all isoforms of the respective gene. The data are visualized in transcript maps and in heatmaps, to intuitively display a comprehensive portrait for the abundance of circRNAs across transcripts and cell lines. By integrating gene ontology (GO) information for all genes in our dataset, circ2GO builds a connection between circRNAs and their host genes’ biological functions and molecular mechanisms. Additionally, circ2GO offers target predictions for circRNA—microRNA (miRNA) pairs for 25,166 highly abundant circRNAs from 6578 genes and 897 high-confidence human miRNAs. Visualization, user-friendliness, intuitive and advanced forward and reverse search options, batch processing and download options make circ2GO a comprehensive source for circRNA information to build hypotheses on their function, processes, and miRNA targets.

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