scholarly journals Making a mark: the role of RNA modifications in plant biology

2020 ◽  
Vol 42 (4) ◽  
pp. 26-30
Author(s):  
Matthew T. Parker ◽  
Katarzyna Knop ◽  
Gordon G. Simpson
Keyword(s):  
Messenger Rna ◽  
Growth And Development ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Biological Significance ◽  
Plant Biology ◽  
Developmental Pathways ◽  
Rna Modifications ◽  
Feature Article

Plants coordinate their growth and development through complex regulatory networks involving changes in the expression of thousands of genes. Many developmental pathways are regulated at the level of messenger RNA (mRNA) through alternative choices in mRNA processing. These choices can have consequences for the localization, stability or translatability of mRNAs. One of the key ways in which RNAs are processed is by the methylation of the RNA base adenosine – a modification known as m6A. Even though it was first discovered in the 1970s, the biological significance of m6A marks has only recently become clear. In this feature article, we identify the factors controlling the writing and reading of m6A modifications in plants. We also highlight some of the features of plant development that depend on m6A and explore the recently discovered molecular mechanisms that use m6A to control development or response to environmental stress.

scholarly journals First person – Kim Landry-Truchon and Nicolas Houde

2020 ◽  
Vol 13 (12) ◽  
pp. dmm048199
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Early Career ◽  
Mouse Lung ◽  
Pleuropulmonary Blastoma ◽  
First Person ◽  
Research Assistant ◽  
Lung Epithelium ◽  
Mouse Development

ABSTRACTFirst Person is a series of interviews with the first authors of a selection of papers published in Disease Models & Mechanisms, helping early-career researchers promote themselves alongside their papers. Kim Landry-Truchon is first author on ‘Deletion of Yy1 in mouse lung epithelium unveils molecular mechanisms governing pleuropulmonary blastoma pathogenesis’, published in DMM. Kim is a research assistant in the lab of Lucie Jeannotte at Centre de recherche du CHU de Québec-Université Laval, Québec, Canada, investigating organ development and the regulatory networks involved. Nicolas is a research assistant in the same lab, investigating the role of master transcription factors during mouse development.

scholarly journals Molecular Events Involved in Influenza A Virus-Induced Cell Death

2022 ◽  
Vol 12 ◽  
Author(s):  
Rui Gui ◽  
Quanjiao Chen
Keyword(s):  
Cell Death ◽  
Influenza A Virus ◽  
Influenza A ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Tissue Destruction ◽  
Inflammatory Reactions ◽  
Molecular Events ◽  
Host Death

Viral infection usually leads to cell death. Moderate cell death is a protective innate immune response. By contrast, excessive, uncontrolled cell death causes tissue destruction, cytokine storm, or even host death. Thus, the struggle between the host and virus determines whether the host survives. Influenza A virus (IAV) infection in humans can lead to unbridled hyper-inflammatory reactions and cause serious illnesses and even death. A full understanding of the molecular mechanisms and regulatory networks through which IAVs induce cell death could facilitate the development of more effective antiviral treatments. In this review, we discuss current progress in research on cell death induced by IAV infection and evaluate the role of cell death in IAV replication and disease prognosis.

scholarly journals The Evolving Role of Ferroptosis in Breast Cancer: Translational Implications Present and Future

Cancers ◽  
2021 ◽  
Vol 13 (18) ◽  
pp. 4576
Author(s):  
Hung-Yu Lin ◽  
Hui-Wen Ho ◽  
Yen-Hsiang Chang ◽  
Chun-Jui Wei ◽  
Pei-Yi Chu
Keyword(s):  
Breast Cancer ◽  
Cell Death ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Drug Resistant ◽  
Therapeutic Targeting ◽  
The Past ◽  
Regulated Cell Death ◽  
Common Malignancy

Breast cancer (BC) is the most common malignancy among women worldwide. The discovery of regulated cell death processes has enabled advances in the treatment of BC. In the past decade, ferroptosis, a new form of iron-dependent regulated cell death caused by excessive lipid peroxidation has been implicated in the development and therapeutic responses of BC. Intriguingly, the induction of ferroptosis acts to suppress conventional therapy-resistant cells, and to potentiate the effects of immunotherapy. As such, pharmacological or genetic modulation targeting ferroptosis holds great potential for the treatment of drug-resistant cancers. In this review, we present a critical analysis of the current understanding of the molecular mechanisms and regulatory networks involved in ferroptosis, the potential physiological functions of ferroptosis in tumor suppression, its potential in therapeutic targeting, and explore recent advances in the development of therapeutic strategies for BC.

scholarly journals Linc00426 accelerates lung adenocarcinoma progression by regulating miR-455-5p as a molecular sponge

2020 ◽  
Vol 11 (12) ◽  
Author(s):  
Hongli Li ◽  
Qingjie Mu ◽  
Guoxin Zhang ◽  
Zhixin Shen ◽  
Yuanyuan Zhang ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Molecular Mechanisms ◽  
Epithelial Mesenchymal Transition ◽  
Ectopic Expression ◽  
Tumor Development ◽  
Biological Significance ◽  
Mesenchymal Transition

AbstractIncreasing lines of evidence indicate the role of long non-coding RNAs (LncRNAs) in gene regulation and tumor development. Hence, it is important to elucidate the mechanisms of LncRNAs underlying the proliferation, metastasis, and invasion of lung adenocarcinoma (LUAD). We employed microarrays to screen LncRNAs in LUAD tissues with and without lymph node metastasis and revealed their effects on LUAD. Among them, Linc00426 was selected for further exploration in its expression, the biological significance, and the underlying molecular mechanisms. Linc00426 exhibits ectopic expression in LUAD tissues and cells. The ectopic expression has been clinically linked to tumor size, lymphatic metastasis, and tumor differentiation of patients with LUAD. The deregulation of Linc00426 contributes to a notable impairment in proliferation, invasion, metastasis, and epithelial–mesenchymal transition (EMT) in vitro and in vivo. Mechanistically, the deregulation of Linc00426 could reduce cytoskeleton rearrangement and matrix metalloproteinase expression. Meanwhile, decreasing the level of Linc00426 or increasing miR-455-5p could down-regulate the level of UBE2V1. Thus, Linc00426 may act as a competing endogenous RNA (ceRNA) to abate miR-455-5p-dependent UBE2V1 reduction. We conclude that Linc00426 accelerates LUAD progression by acting as a molecular sponge to regulate miR-455-5p, and may be a potential novel tumor marker for LUAD.

scholarly journals The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis

2020 ◽  
Author(s):  
Hélène Scheer ◽  
Caroline de Almeida ◽  
Emilie Ferrier ◽  
Quentin Simonnot ◽  
Laure Poirier ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Growth And Development ◽  
Molecular Mechanisms ◽  
Tail Length ◽  
Mrna Degradation ◽  
In Planta ◽  
Rna Helicases ◽  
Eukaryotic Mrnas

AbstractUridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that the Arabidopsis TUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), the Arabidopsis ortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based on in vitro and in planta data, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3’ terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturb Arabidopsis growth and development.

scholarly journals Conservation and novelty in the microRNA genomic landscape of hyperdiverse cichlid fishes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Peiwen Xiong ◽  
Ralf F. Schneider ◽  
C. Darrin Hulsey ◽  
Axel Meyer ◽  
Paolo Franchini
Keyword(s):  
Messenger Rna ◽  
Regulatory Networks ◽  
Transcriptional Control ◽  
Protein Coding ◽  
Adaptive Diversification ◽  
Cichlid Fishes ◽  
Novel Mirna ◽  
Genomic Landscape ◽  
Target Sites

Abstract MicroRNAs (miRNAs) play crucial roles in the post-transcriptional control of messenger RNA (mRNA). These miRNA-mRNA regulatory networks are present in nearly all organisms and contribute to development, phenotypic divergence, and speciation. To examine the miRNA landscape of cichlid fishes, one of the most species-rich families of vertebrates, we profiled the expression of both miRNA and mRNA in a diverse set of cichlid lineages. Among these, we found that conserved miRNAs differ from recently arisen miRNAs (i.e. lineage specific) in average expression levels, number of target sites, sequence variability, and physical clustering patterns in the genome. Furthermore, conserved miRNA target sites tend to be enriched at the 5′ end of protein-coding gene 3′ UTRs. Consistent with the presumed regulatory role of miRNAs, we detected more negative correlations between the expression of miRNA-mRNA functional pairs than in random pairings. Finally, we provide evidence that novel miRNA targets sites are enriched in genes involved in protein synthesis pathways. Our results show how conserved and evolutionarily novel miRNAs differ in their contribution to the genomic landscape and highlight their particular evolutionary roles in the adaptive diversification of cichlids.

Role of Golgi Apparatus in the Formation of Plant Slimes, Cuticles and Extraneous Wall Material

1974 ◽  
Vol 32 ◽  
pp. 86-87
Author(s):  
Hilton H. Mollenhauer
Keyword(s):  
Cell Wall ◽  
Golgi Apparatus ◽  
Cell Walls ◽  
Growth And Development ◽  
Characteristic Property ◽  
Plant Cells ◽  
Plant Biology ◽  
Wall Material ◽  
Wall Properties

Cell walls are fundamentally involved in many aspects of plant biology including the morphology, growth, and development of plant cells and the interactions between plant hosts and their pathogens. Intuitively, one can recognize that these wall properties result from the sum total of the various components of which the wall is composed and that there are classes of substances each of which impart a characteristic property to the cell wall.

The Genetics of Evolutionary Novelties

2014 ◽  
Author(s):  
Günter P. Wagner
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Regulatory Elements ◽  
Complex Problem ◽  
Micro Rnas ◽  
Sex Comb ◽  
Gene Regulatory ◽  
Transcription Factor Proteins ◽  
Evolutionary Novelties

This chapter examines the molecular genetics of evolutionary novelties. In particular, it investigates which molecular mechanisms might be involved in the origination of novel gene regulatory networks (and, thus, character identity networks) and what these mechanisms imply for the origin of novel characters. The chapter begins with a discussion of the complex problem of the evolution of transcriptional regulation by focusing on the evolution of cis-regulatory elements (CREs) and the evolution of transcription factor proteins. It then asks whether novel pigment spots, such as the Drosophila wing spots, are novelties. It also explores an evolutionary novelty known as sex comb and the role of transposable elements in the origin of novel CREs. Finally, it considers the role of gene duplications, the evolution of micro-RNAs (miRNAs), and the possibility of a mechanistic difference between adaptation and innovation.

scholarly journals Postsynaptic regulation of synaptic plasticity by synaptotagmin 4 requires both C2 domains

2009 ◽  
Vol 187 (2) ◽  
pp. 295-310 ◽  
Author(s):  
Cynthia F. Barber ◽  
Ramon A. Jorquera ◽  
Jan E. Melom ◽  
J. Troy Littleton
Keyword(s):  
Synaptic Plasticity ◽  
Messenger Rna ◽  
Molecular Mechanisms ◽  
Neuromuscular Junctions ◽  
Vesicle Fusion ◽  
Synaptic Growth ◽  
Synaptotagmin 1 ◽  
Presynaptic Vesicle ◽  
Activity Dependent

Ca2+ influx into synaptic compartments during activity is a key mediator of neuronal plasticity. Although the role of presynaptic Ca2+ in triggering vesicle fusion though the Ca2+ sensor synaptotagmin 1 (Syt 1) is established, molecular mechanisms that underlie responses to postsynaptic Ca2+ influx remain unclear. In this study, we demonstrate that fusion-competent Syt 4 vesicles localize postsynaptically at both neuromuscular junctions (NMJs) and central nervous system synapses in Drosophila melanogaster. Syt 4 messenger RNA and protein expression are strongly regulated by neuronal activity, whereas altered levels of postsynaptic Syt 4 modify synaptic growth and presynaptic release properties. Syt 4 is required for known forms of activity-dependent structural plasticity at NMJs. Synaptic proliferation and retrograde signaling mediated by Syt 4 requires functional C2A and C2B Ca2+–binding sites, as well as serine 284, an evolutionarily conserved substitution for a key Ca2+-binding aspartic acid found in other synaptotagmins. These data suggest that Syt 4 regulates activity-dependent release of postsynaptic retrograde signals that promote synaptic plasticity, similar to the role of Syt 1 as a Ca2+ sensor for presynaptic vesicle fusion.

scholarly journals Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huifen Cao ◽  
Dongyang Xu ◽  
Ye Cai ◽  
Xueer Han ◽  
Lu Tang ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Biological Significance ◽  
Genotoxic Stress ◽  
Cellular Adhesion ◽  
Negative Regulator ◽  
Chromatin Interactions ◽  
Multiple Genes ◽  
A Genome ◽  
Hidden Layer

Abstract Background The majority of the human genome is transcribed in the form of long non-coding (lnc) RNAs. While these transcripts have attracted considerable interest, their molecular mechanisms of function and biological significance remain controversial. One of the main reasons behind this lies in the significant challenges posed by lncRNAs requiring the development of novel methods and concepts to unravel their functionality. Existing methods often lack cross-validation and independent confirmation by different methodologies and therefore leave significant ambiguity as to the authenticity of the outcomes. Nonetheless, despite all the caveats, it appears that lncRNAs may function, at least in part, by regulating other genes via chromatin interactions. Therefore, the function of a lncRNA could be inferred from the function of genes it regulates. In this work, we present a genome-wide functional annotation strategy for lncRNAs based on identification of their regulatory networks via the integration of three distinct types of approaches: co-expression analysis, mapping of lncRNA-chromatin interactions, and assaying molecular effects of lncRNA knockdowns obtained using an inducible and highly specific CRISPR/Cas13 system. Results We applied the strategy to annotate 407 very long intergenic non-coding (vlinc) RNAs belonging to a novel widespread subclass of lncRNAs. We show that vlincRNAs indeed appear to regulate multiple genes encoding proteins predominantly involved in RNA- and development-related functions, cell cycle, and cellular adhesion via a mechanism involving proximity between vlincRNAs and their targets in the nucleus. A typical vlincRNAs can be both a positive and negative regulator and regulate multiple genes both in trans and cis. Finally, we show vlincRNAs and their regulatory networks potentially represent novel components of DNA damage response and are functionally important for the ability of cancer cells to survive genotoxic stress. Conclusions This study provides strong evidence for the regulatory role of the vlincRNA class of lncRNAs and a potentially important role played by these transcripts in the hidden layer of RNA-based regulation in complex biological systems.

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