Crossroads between transposons and gene regulation

Transposons are mobile genetic elements that have made a large contribution to genome evolution in a largely species-specific manner. A wide variety of different transposons have invaded genomes throughout evolution, acting in a first instance as ‘selfish’ elements, whose success was determined by their ability to self-replicate and expand within the host genome. However, their coevolution with the host has created many crossroads between transposons and the regulation of host gene expression. Transposons are an abundant source of transcriptional modulatory elements, such as gene promoters and enhancers, splicing and termination sites, and regulatory non-coding RNAs. Moreover, transposons have driven the evolution of host defence mechanisms that have been repurposed for gene regulation. However, dissecting the potential functional roles of transposons remains challenging owing to their evolutionary path, as well as their repetitive nature, which requires the development of specialized analytical tools. In this special issue, we present a collection of articles that lay out current paradigms in the field and discuss a vision for future research. This article is part of a discussion meeting issue ‘Crossroads between transposons and gene regulation’.

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Long Non-Coding RNAs: the New Horizon of Gene Regulation in Ovarian Cancer

Cellular Physiology and Biochemistry ◽

10.1159/000485395 ◽

2017 ◽

Vol 44 (3) ◽

pp. 948-966 ◽

Cited By ~ 28

Author(s):

Tesfaye Worku ◽

Dinesh Bhattarai ◽

Duncan Ayers ◽

Kai Wang ◽

Chen Wang ◽

...

Keyword(s):

Ovarian Cancer ◽

Gene Regulation ◽

Molecular Mechanisms ◽

Future Directions ◽

Diagnostic Biomarkers ◽

Functional Roles ◽

Gene Therapies ◽

Wide Range ◽

Recent Developments ◽

Non Coding Rnas

Long non-coding RNAs (lncRNAs), a class of non-coding transcripts, have recently been emerging with heterogeneous molecular actions, adding a new layer of complexity to gene-regulation networks in tumorigenesis. LncRNAs are considered important factors in several ovarian cancer histotypes, although few have been identified and characterized. Owing to their complexity and the lack of adapted molecular technology, the roles of most lncRNAs remain mysterious. Some lncRNAs have been reported to play functional roles in ovarian cancer and can be used as classifiers for personalized medicine. The intrinsic features of lncRNAs govern their various molecular mechanisms and provide a wide range of platforms to design different therapeutic strategies for treating cancer at a particular stage. Although we are only beginning to understand the functions of lncRNAs and their interactions with microRNAs (miRNAs) and proteins, the expanding literature indicates that lncRNA-miRNA interactions could be useful biomarkers and therapeutic targets for ovarian cancer. In this review, we discuss the genetic variants of lncRNAs, heterogeneous mechanisms of actions of lncRNAs in ovarian cancer tumorigenesis, and drug resistance. We also highlight the recent developments in using lncRNAs as potential prognostic and diagnostic biomarkers. Lastly, we discuss potential approaches for linking lncRNAs to future gene therapies, and highlight future directions in the field of ovarian cancer research.

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Extracellular Vesicle Associated Non-Coding RNAs in Lung Infections and Injury

Cells ◽

10.3390/cells10050965 ◽

2021 ◽

Vol 10 (5) ◽

pp. 965

Author(s):

Zhi Hao Kwok ◽

Kareemah Ni ◽

Yang Jin

Keyword(s):

Extracellular Vesicle ◽

Human Diseases ◽

Future Research ◽

Functional Roles ◽

Bodily Fluids ◽

Wide Range ◽

Novel Biomarkers ◽

Heterogenous Population ◽

Non Coding Rnas ◽

Functional Relevance

Extracellular vesicles (EVs) refer to a heterogenous population of membrane-bound vesicles that are released by cells under physiological and pathological conditions. The detection of EVs in the majority of the bodily fluids, coupled with their diverse cargo comprising of DNA, RNA, lipids, and proteins, have led to the accumulated interests in leveraging these nanoparticles for diagnostic and therapeutic purposes. In particular, emerging studies have identified enhanced levels of a wide range of specific subclasses of non-coding RNAs (ncRNAs) in EVs, thereby suggesting the existence of highly selective and regulated molecular processes governing the sorting of these RNAs into EVs. Recent studies have also illustrated the functional relevance of these enriched ncRNAs in a variety of human diseases. This review summarizes the current state of knowledge on EV-ncRNAs, as well as their functions and significance in lung infection and injury. As a majority of the studies on EV-ncRNAs in lung diseases have focused on EV-microRNAs, we will particularly highlight the relevance of these molecules in the pathophysiology of these conditions, as well as their potential as novel biomarkers therein. We also outline the current challenges in the EV field amidst the tremendous efforts to propel the clinical utility of EVs for human diseases. The lack of published literature on the functional roles of other EV-ncRNA subtypes may in turn provide new avenues for future research to exploit their feasibility as novel diagnostic and therapeutic targets in human diseases.

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The Non-Coding Regulatory RNA Revolution in Archaea

10.20944/preprints201801.0232.v1 ◽

2018 ◽

Cited By ~ 2

Author(s):

Diego R. Gelsinger ◽

Jocelyne DiRuggiero

Keyword(s):

Gene Regulation ◽

Regulatory Networks ◽

Large Scale ◽

Rna Binding ◽

Cis Acting ◽

Functional Roles ◽

Domains Of Life ◽

Opposite Strand ◽

Non Coding Rnas ◽

Protein Components

Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing, and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3’ UTR, 5’ UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved, and how sRNAs integrate with complex regulatory networks.  

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Clues of in vivo nuclear gene regulation by mitochondrial short non-coding RNAs

Scientific Reports ◽

10.1038/s41598-020-65084-z ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Marco Passamonti ◽

Marco Calderone ◽

Manuel Delpero ◽

Federico Plazzi

Keyword(s):

Gene Regulation ◽

Nuclear Gene ◽

Non Coding Rnas ◽

Nuclear Gene Regulation

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Signatures of conserved and unique molecular features in Afrotheria

Scientific Reports ◽

10.1038/s41598-020-79559-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Arangasamy Yazhini ◽

Narayanaswamy Srinivasan ◽

Sankaran Sandhya

Keyword(s):

Ribosomal Proteins ◽

Individual Species ◽

Functional Domain ◽

Nucleic Acid Binding ◽

Uncharacterized Protein ◽

Homologous Proteins ◽

Functional Roles ◽

Molecular Features ◽

Specific Proteins ◽

Species Specific

AbstractAfrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.

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Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

BMC Plant Biology ◽

10.1186/s12870-021-03059-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Garima Bhatia ◽

Santosh K. Upadhyay ◽

Anuradha Upadhyay ◽

Kashmir Singh

Keyword(s):

Downy Mildew ◽

Plasmopara Viticola ◽

Defense Responses ◽

Protein Coding ◽

Functional Roles ◽

Real Time Quantitative Pcr ◽

Transcriptional Reprogramming ◽

Sequencing Technologies ◽

Non Coding Rnas ◽

Fungal Phytopathogens

Abstract Background Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide. Results Using computational approach based on RNA-seq data, 71 PM- and 83 DM-responsive V. vinifera lncRNAs were identified and comprehensively examined for their putative functional roles in plant defense response. V. vinifera protein coding sequences (CDS) were also profiled based on expression levels, and 1037 PM-responsive and 670 DM-responsive CDS were identified. Next, co-expression analysis-based functional annotation revealed their association with gene ontology (GO) terms for ‘response to stress’, ‘response to biotic stimulus’, ‘immune system process’, etc. Further investigation based on analysis of domains, enzyme classification, pathways enrichment, transcription factors (TFs), interactions with microRNAs (miRNAs), and real-time quantitative PCR of lncRNAs and co-expressing CDS pairs suggested their involvement in modulation of basal and specific defense responses such as: Ca2+-dependent signaling, cell wall reinforcement, reactive oxygen species metabolism, pathogenesis related proteins accumulation, phytohormonal signal transduction, and secondary metabolism. Conclusions Overall, the identified lncRNAs provide insights into the underlying intricacy of grapevine transcriptional reprogramming/post-transcriptional regulation to delay or seize the living cell-dependent pathogen growth. Therefore, in addition to defense-responsive genes such as TFs, the identified lncRNAs can be further examined and leveraged to candidates for biotechnological improvement/breeding to enhance fungal stress resistance in this susceptible fruit crop of economic and nutritional importance.

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Stoicism and Verbal Aggression in Serial Arguments: The Roles of Perceived Power, Perceived Resolvability, and Frequency of Arguments

Journal of Interpersonal Violence ◽

10.1177/0886260521994583 ◽

2021 ◽

pp. 088626052199458

Author(s):

Elle P. Johnson ◽

Jennifer A. Samp

Keyword(s):

Romantic Relationship ◽

Survey Design ◽

Romantic Partners ◽

Verbal Aggression ◽

Future Research ◽

Repetitive Nature ◽

Relational Partners ◽

The Relationship ◽

Significant Moderator ◽

Perceived Power

Impelled by a desire to control, suppress, and deny emotional response, stoic individuals may act out their pent-up emotions on relational partners by provoking conflict and/or engaging in partner-directed violent and aggressive behaviors. However, little is known regarding what factors can push stoics over the edge from remaining quiet or avoiding revealing frustrations to initiating aggressive behavior. This relationship between stoicism and aggression is important to consider in serial arguments, where the repetitive nature of a conflict may become increasingly difficult for stoics to manage internally. Here, we examined the influence of stoicism on verbal aggression in serial arguments between romantic partners. We additionally considered the effects of power, perceived resolvability, and argument frequency on the relationship between stoicism and verbal aggression. Using a survey design with a sample of 281 individuals involved in a romantic relationship, we observed that stoicism is positively associated with verbal aggression in serial arguments. While perceived power and resolvability did not moderate the relationship between stoicism and verbal aggression, argument frequency about a serial argument topic was a significant moderator. The results of this study imply that stoicism plays an important role in explaining aggressive tactics in conflict. A high argument frequency about a conflict topic may lead to a buildup of unexpressed emotions, particularly anger, in stoic individuals, resulting in an explosive release of violence and aggression toward a romantic partner. Unique results on the relationship between stoicism and power and directions for future research are discussed.

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Ferrous materials degradation: characterisation of rust by colour – an overview

Corrosion Reviews ◽

10.1515/corrrev-2021-0005 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Desmond E. P. Klenam ◽

Michael O. Bodunrin ◽

Stefania Akromah ◽

Emmanuel Gikunoo ◽

Anthony Andrews ◽

...

Keyword(s):

Yellow Rust ◽

Brown Rust ◽

Future Research ◽

Stable Form ◽

Low Oxygen ◽

High Moisture ◽

Oxygen Environment ◽

Causative Factors ◽

Analytical Tools

Abstract An overview of the characterisation of rust by colour is presented. Each distinct rust colour is caused by atmospheric impurities, high or low moisture content and high or low oxygen environment over time. Yellow rust is mainly due to the high moisture environment over a period of time, which drips. Brown rust is dry, crusty and due to water and oxygen contact with localised patches on component surfaces. Black rust, the most stable form, occurs in low moisture and low oxygen environment. The rust residue shows where the reaction started, especially in contact with chlorides. The causative factors of red rust are atmospheric and similar to black rust in a chloride-containing environment. The effect of packaging, manufacturing and environmental factors on rust colour is briefly discussed. Visual characterization of rust could pre-empt root causes and analytical tools for validation. The limitations of these concepts are mentioned and directions for future research highlighted.

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If things go South: The renewed policy of sport mega events allocation and its implications for future research

International Review for the Sociology of Sport ◽

10.1177/1012690220981342 ◽

2021 ◽

pp. 101269022098134

Author(s):

Billy Graeff ◽

Jorge Knijnik

Keyword(s):

21St Century ◽

Public Expenditure ◽

Global South ◽

International Olympic Committee ◽

Future Research ◽

Construction Costs ◽

Mega Events ◽

The Past ◽

Global North ◽

Analytical Tools

The past few decades have seen an increase of sport mega events (SMEs) held outside the Global North. This tendency has been accompanied by a growing public expenditure in these events. This paper employs selected Global South SMEs to discuss this trend. By critically analysing public documents, biddings and reports, the study traces comparisons between 21st-century Global South and Global North SMEs expenditures, in the revenue of franchise owners (FIFA and the International Olympic Committee), in construction costs within the budgets and in the costs related to security. This comprehensive and intertwined investigation shows the need for new analytical tools – such as the Renewed Policy of Sport Mega Events Allocation, a concept developed here - to better capture the central questions posed by the challenges of ‘SMEs going South’.

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