scholarly journals Evolution of plasticity in production and transgenerational inheritance of small RNAs under dynamic environmental conditions

2019 ◽  
Author(s):  
Willian T.A.F. Silva ◽  
Sarah P. Otto ◽  
Simone Immler
Keyword(s):  
Phenotypic Plasticity ◽  
Environmental Conditions ◽  
Small Rnas ◽  
Regulation Of Gene Expression ◽  
Selective Advantage ◽  
Regulatory Elements ◽  
Optimal Level ◽  
Transgenerational Inheritance ◽  
Dual Nature ◽  
Post Transcriptional Regulation

AbstractIn a changing environment, small RNAs (sRNAs) play an important role in the post-transcriptional regulation of gene expression and can vary in abundance depending on the conditions experienced by an individual (phenotypic plasticity) and its parents (non-genetic inheritance). Many sRNAs are unusual in that they can be produced in two ways, either using genomic DNA as the template (primary sRNAs) or existing sRNAs as the template (secondary sRNAs). Thus, organisms can evolve rapid plastic responses to their current environment by adjusting the amplification rate of sRNA templates. sRNA levels can also be transmitted transgenerationally by the direct transfer of either sRNAs or the proteins involved in amplification. Theory is needed to describe the selective forces acting on sRNA levels, accounting for the dual nature of sRNAs as regulatory elements and templates for amplification and for the potential to transmit sRNAs and their amplification agents to offspring. Here, we develop a model to study the dynamics of sRNA production and inheritance in a fluctuating environment. We tested the selective advantage of mutants capable of sRNA-mediated phenotypic plasticity within resident populations with fixed levels of sRNA transcription. Even when the resident was allowed to evolve an optimal constant rate of sRNA production, plastic amplification rates capable of responding to environmental conditions were favored. By contrast, mechanisms allowing sRNA transcripts or amplification agents to be inherited were favored primarily when parents and offspring face similar environments and when selection acts before the optimal level of sRNA can be reached within the organism. Our study provides a clear set of testable predictions for the evolution of sRNA-related mechanisms of phenotypic plasticity and transgenerational inheritance.

scholarly journals Evolution of plasticity in production and transgenerational inheritance of small RNAs under dynamic environmental conditions

PLoS Genetics ◽  
2021 ◽  
Vol 17 (5) ◽  
pp. e1009581
Author(s):  
Willian T. A. F. Silva ◽  
Sarah P. Otto ◽  
Simone Immler
Keyword(s):  
Phenotypic Plasticity ◽  
Environmental Conditions ◽  
Small Rnas ◽  
Regulation Of Gene Expression ◽  
Selective Advantage ◽  
Regulatory Elements ◽  
Optimal Level ◽  
Transgenerational Inheritance ◽  
Dual Nature ◽  
Post Transcriptional Regulation

In a changing environment, small RNAs (sRNAs) play an important role in the post-transcriptional regulation of gene expression and can vary in abundance depending on the conditions experienced by an individual (phenotypic plasticity) and its parents (non-genetic inheritance). Many sRNAs are unusual in that they can be produced in two ways, either using genomic DNA as the template (primary sRNAs) or existing sRNAs as the template (secondary sRNAs). Thus, organisms can evolve rapid plastic responses to their current environment by adjusting the amplification rate of sRNA templates. sRNA levels can also be transmitted transgenerationally by the direct transfer of either sRNAs or the proteins involved in amplification. Theory is needed to describe the selective forces acting on sRNA levels, accounting for the dual nature of sRNAs as regulatory elements and templates for amplification and for the potential to transmit sRNAs and their amplification agents to offspring. Here, we develop a model to study the dynamics of sRNA production and inheritance in a fluctuating environment. We tested the selective advantage of mutants capable of sRNA-mediated phenotypic plasticity within resident populations with fixed levels of sRNA transcription. Even when the resident was allowed to evolve an optimal constant rate of sRNA production, plastic amplification rates capable of responding to environmental conditions were favored. Mechanisms allowing sRNA transcripts or amplification agents to be inherited were favored primarily when parents and offspring face similar environments and when selection acts before the optimal level of sRNA can be reached within the organism. Our study provides a clear set of testable predictions for the evolution of sRNA-related mechanisms of phenotypic plasticity and transgenerational inheritance.

scholarly journals Gender- and stressor-specific microRNA expression in Tribolium castaneum

2012 ◽  
Vol 8 (5) ◽  
pp. 860-863 ◽  
Author(s):  
Dalial Freitak ◽  
Eileen Knorr ◽  
Heiko Vogel ◽  
Andreas Vilcinskas
Keyword(s):  
Immune Responses ◽  
Tribolium Castaneum ◽  
Natural Infection ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Immune Gene ◽  
Investment Strategies ◽  
Physiological Adaptations ◽  
Stress Related Genes ◽  
Post Transcriptional Regulation

MicroRNAs (miRNAs) are small non-coding RNAs mediating post-transcriptional regulation of gene expression in eukaryotes. Addressing their role in regulation of physiological adaptations to environmental stress in insects, we selected the red flour beetle Tribolium castaneum as a model. Beetles were fed with the bacterial entomopathogen Pseudomonas entomophila (to mimic natural infection), injected with peptidoglycan (experimental setting of strong immune responses) or subjected to either mild heat shock or starvation. Differential expression of selected immunity- and stress-related genes was quantified using real-time PCR, and expression and induction of 455 mature arthropod miRNAs were determined using proprietary microarrays. We found that Tribolium exhibits both gender- and stressor-specific adjustment of immune gene and miRNA expression. Strikingly, we discovered that the number of stressor-induced miRNAs in females is remarkably higher than in males. This observation could support the hypothesis called Bateman's principle in immunity that predicts gender-specific immune responses because females gain fitness through increased longevity, whereas males gain fitness by increasing mating rates. Our results suggest that Tribolium males and females display differential regulatory elements, both pre- and post-transcriptional, likely resulting from different investment strategies in life-history traits.

scholarly journals Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Sibo Wang ◽  
Hongping Liang ◽  
Yan Xu ◽  
Linzhou Li ◽  
Hongli Wang ◽  
...  
Keyword(s):  
Small Rna ◽  
Stress Responses ◽  
Small Rnas ◽  
Common Ancestor ◽  
Regulation Of Gene Expression ◽  
Mirna Biogenesis ◽  
Last Common Ancestor ◽  
Evolutionary Transitions ◽  
Genome Wide ◽  
Post Transcriptional Regulation

AbstractSmall RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small RNA (miRNA & siRNA) biosynthetic and degradation pathways. The results suggest that Viridiplantae started to evolve plant-like miRNA biogenesis and degradation after the divergence of the Mesostigmatophyceae in the streptophyte algae. We identified two major evolutionary transitions in small RNA metabolism in streptophyte algae; during the first transition, the origin of DCL-New, DCL1, AGO1/5/10 and AGO4/6/9 in the last common ancestor of Klebsormidiophyceae and all other streptophytes could be linked to abiotic stress responses and evolution of multicellularity in streptophytes. During the second transition, the evolution of DCL 2,3,4, and AGO 2,3,7 as well as DRB1 in the last common ancestor of Zygnematophyceae and embryophytes, suggests their possible contribution to pathogen defense and antibacterial immunity. Overall, the origin and diversification of DICER and AGO along with several other small RNA pathway-related genes among streptophyte algae suggested progressive adaptations of streptophyte algae during evolution to a subaerial environment.

scholarly journals In Silico Analysis of Osa-miR164 Gene Family in Rice (Oryza Sativa)

2021 ◽  
Vol 37 (3) ◽  
Author(s):  
Vuong Quang Tien ◽  
Nguyen Huy Duong ◽  
Dao Trong Nhan ◽  
Phan Minh Vu ◽  
Do Thi Phuc
Keyword(s):  
Oryza Sativa ◽  
Expression Pattern ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Stress Conditions ◽  
Gene Promoters ◽  
Non Coding Rna ◽  
Post Transcriptional Regulation

MicroRNA (miRNA) is a small non-coding RNA molecule containing about 22- 24 nucleotides, which functions in post-transcriptional regulation of gene expression. Previous reports have shown that miRNA plays an important role on the resistance ability of plants to adverse conditions. Rice (Oryza sativa) is a major food crop. Climate change makes the situation of salinity and drought in Vietnam worse, significantly affects rice cultivation area, leading to the decrease of the quantity and the quality of rice grains. In this research, we focused on miR164 family in rice. By using bioinformatics approach, we analyzed sequences of all osa-miR164 belonging to rice miR164 family, evaluated the expression profile of osa-miR164 under different stress conditions, predicted cis-regulatory elements on osa-miR164 gene promoters, and simultaneously predicted miR164-targeted genes and their expressions. The results showed the high conserve in mature osa-miR164 sequences but not in the precursor sequences, different expression pattern of osa-miR164 gene members under stress conditions and various cis-regulatory elements present in osa-miR164 gene promoters which may explain for diverse expression pattern of osa-miR164 genes. Some potential target genes of osa-miR164 were identified and their expressions under different stress conditions were analyzed.

scholarly journals Prediction of Novel Bacterial Small RNAs From RIL-Seq RNA–RNA Interaction Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Amir Bar ◽  
Liron Argaman ◽  
Yael Altuvia ◽  
Hanah Margalit
Keyword(s):  
Small Rnas ◽  
Large Scale ◽  
Regulation Of Gene Expression ◽  
Untranslated Regions ◽  
Computational Framework ◽  
E Coli ◽  
Intergenic Regions ◽  
Rna Interaction ◽  
Genomic Regions ◽  
Post Transcriptional Regulation

The genomic revolution and subsequent advances in large-scale genomic and transcriptomic technologies highlighted hidden genomic treasures. Among them stand out non-coding small RNAs (sRNAs), shown to play important roles in post-transcriptional regulation of gene expression in both pro- and eukaryotes. Bacterial sRNA-encoding genes were initially identified in intergenic regions, but recent evidence suggest that they can be encoded within other, well-defined, genomic elements. This notion was strongly supported by data generated by RIL-seq, a RNA-seq-based methodology we recently developed for deciphering chaperon-dependent sRNA-target networks in bacteria. Applying RIL-seq to Hfq-bound RNAs in Escherichia coli, we found that ∼64% of the detected RNA pairs involved known sRNAs, suggesting that yet unknown sRNAs may be included in the ∼36% remaining pairs. To determine the latter, we first tested and refined a set of quantitative features derived from RIL-seq data, which distinguish between Hfq-dependent sRNAs and “other RNAs”. We then incorporated these features in a machine learning-based algorithm that predicts novel sRNAs from RIL-seq data, and identified high-scoring candidates encoded in various genomic regions, mostly intergenic regions and 3′ untranslated regions, but also 5′ untranslated regions and coding sequences. Several candidates were further tested and verified by northern blot analysis as Hfq-dependent sRNAs. Our study reinforces the emerging concept that sRNAs are encoded within various genomic elements, and provides a computational framework for the detection of additional sRNAs in Hfq RIL-seq data of E. coli grown under different conditions and of other bacteria manifesting Hfq-mediated sRNA-target interactions.

T-cells require post-transcriptional regulation for accurate immune responses

2015 ◽  
Vol 43 (6) ◽  
pp. 1201-1207 ◽  
Author(s):  
Fiamma Salerno ◽  
Monika C. Wolkers
Keyword(s):  
T Cells ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cytotoxic T Cells ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Effector Molecules ◽  
Specific Mrnas ◽  
Infected Cells ◽  
Post Transcriptional Regulation

Cytotoxic T-cells are crucial to protect us from intracellular pathogens and malignant cells. When T-cells become activated, they rapidly secrete cytokines, chemokines and cytotoxic granules that are critical to clear infected cells. However, when not properly regulated, these toxic effector molecules become one of the key mediators of autoimmune diseases. Therefore, a tight and multi-layered regulation of gene expression and protein production is required to ensure a protective yet balanced immune response. In this review, we describe how post-transcriptional events modulate the production of effector molecules in T-cells. In particular, we will focus on the role of cis-regulatory elements within the 3′-UTR of specific mRNAs and on RNA-binding proteins (RBPs) and non-coding RNAs that control the initiation and resolution of T-cell responses.

The Role of microRNAs in the Viral Infections

2019 ◽  
Vol 24 (39) ◽  
pp. 4659-4667 ◽  
Author(s):  
Mona Fani ◽  
Milad Zandi ◽  
Majid Rezayi ◽  
Nastaran Khodadad ◽  
Hadis Langari ◽  
...  
Keyword(s):  
Viral Infections ◽  
Rna Viruses ◽  
Regulation Of Gene Expression ◽  
Molecular Structures ◽  
Main Function ◽  
Cellular Functions ◽  
Viral Genes ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

MicroRNAs (miRNAs) are non-coding RNAs with 19 to 24 nucleotides which are evolutionally conserved. MicroRNAs play a regulatory role in many cellular functions such as immune mechanisms, apoptosis, and tumorigenesis. The main function of miRNAs is the post-transcriptional regulation of gene expression via mRNA degradation or inhibition of translation. In fact, many of them act as an oncogene or tumor suppressor. These molecular structures participate in many physiological and pathological processes of the cell. The virus can also produce them for developing its pathogenic processes. It was initially thought that viruses without nuclear replication cycle such as Poxviridae and RNA viruses can not code miRNA, but recently, it has been proven that RNA viruses can also produce miRNA. The aim of this articles is to describe viral miRNAs biogenesis and their effects on cellular and viral genes.

scholarly journals Novel Antarctic yeast adapts to cold by switching energy metabolism and increasing small RNA synthesis

2021 ◽  
Author(s):  
D. Touchette ◽  
I. Altshuler ◽  
C. Gostinčar ◽  
P. Zalar ◽  
I. Raymond-Bouchard ◽  
...  
Keyword(s):  
Ethanol Production ◽  
Ethanol Fermentation ◽  
Phylogenetic Analyses ◽  
Regulation Of Gene Expression ◽  
Pentose Phosphate ◽  
Metabolic Switch ◽  
Antarctic Yeast ◽  
Fungal Adaptation ◽  
Pentose Phosphate Pathways ◽  
Post Transcriptional Regulation

AbstractThe novel extremophilic yeast Rhodotorula frigidialcoholis, formerly R. JG1b, was isolated from ice-cemented permafrost in University Valley (Antarctic), one of coldest and driest environments on Earth. Phenotypic and phylogenetic analyses classified R. frigidialcoholis as a novel species. To characterize its cold-adaptive strategies, we performed mRNA and sRNA transcriptomic analyses, phenotypic profiling, and assessed ethanol production at 0 and 23 °C. Downregulation of the ETC and citrate cycle genes, overexpression of fermentation and pentose phosphate pathways genes, growth without reduction of tetrazolium dye, and our discovery of ethanol production at 0 °C indicate that R. frigidialcoholis induces a metabolic switch from respiration to ethanol fermentation as adaptation in Antarctic permafrost. This is the first report of microbial ethanol fermentation utilized as the major energy pathway in response to cold and the coldest temperature reported for natural ethanol production. R. frigidialcoholis increased its diversity and abundance of sRNAs when grown at 0 versus 23 °C. This was consistent with increase in transcription of Dicer, a key protein for sRNA processing. Our results strongly imply that post-transcriptional regulation of gene expression and mRNA silencing may be a novel evolutionary fungal adaptation in the cryosphere.

scholarly journals The Impact of Different Environmental Conditions during Vegetative Propagation on Growth, Survival, and Biochemical Characteristics in Populus Hybrids in Clonal Field Trial

Forests ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 892
Author(s):  
Valda Gudynaitė-Franckevičienė ◽  
Alfas Pliūra
Keyword(s):  
Climate Change ◽  
Phenotypic Plasticity ◽  
Environmental Conditions ◽  
Vegetative Propagation ◽  
Genotypic Variation ◽  
Hybrid Poplar ◽  
Field Trials ◽  
Biochemical Traits ◽  
Suburban Areas ◽  
Growing Conditions

To have a cleaner environment, good well-being, and improve the health of citizens it is necessary to expand green urban and suburban areas using productive and adapted material of tree species. The quality of urban greenery, resistance to negative climate change factors and pollution, as well as efficiency of short-rotation forestry in suburban areas, depends primarily on the selection of hybrids and clones, suitable for the local environmental conditions. We postulate that ecogenetic response, phenotypic plasticity, and genotypic variation of hybrid poplars (Populus L.) grown in plantations are affected not only by the peculiarities of hybrids and clones, but also by environmental conditions of their vegetative propagation. The aim of the present study was to estimate growth and biochemical responses, the phenotypic plasticity, genotypic variation of adaptive traits, and genetically regulated adaptability of Populus hybrids in field trials which may be predisposed by the simulated contrasting temperature conditions at their vegetative propagation phase. The research was performed with the 20 cultivars and experimental clones of one intraspecific cross and four different interspecific hybrids of poplars propagated under six contrasting temperature regimes in phytotron. The results suggest that certain environmental conditions during vegetative propagation not only have a short-term effect on tree viability and growth, but also can help to adapt to climate change conditions and grow successfully in the long-term. It was found that tree growth and biochemical traits (the chlorophyll A and B, pigments content and the chlorophyll A/B ratio) of hybrid poplar clones grown in field trials, as well as their traits’ genetic parameters, were affected by the rooting-growing conditions during vegetative propagation phase. Hybrids P. balsamifera × P. trichocarpa, and P. trichocarpa × P. trichocarpa have shown the most substantial changes of biochemical traits across vegetative propagation treatments in field trial. Rooting-growing conditions during vegetative propagation had also an impact on coefficients of genotypic variation and heritability in hybrid poplar clones when grown in field trials.

scholarly journals Long non-coding RNAs in brain tumors

NAR Cancer ◽  
2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Keisuke Katsushima ◽  
George Jallo ◽  
Charles G Eberhart ◽  
Ranjan J Perera
Keyword(s):  
Gene Expression ◽  
Brain Tumors ◽  
Brain Cancer ◽  
Regulation Of Gene Expression ◽  
Therapeutic Targets ◽  
Diagnostic Biomarkers ◽  
Cancer Pathogenesis ◽  
Current State ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

Abstract Long non-coding RNAs (lncRNAs) have been found to be central players in the epigenetic, transcriptional and post-transcriptional regulation of gene expression. There is an accumulation of evidence on newly discovered lncRNAs, their molecular interactions and their roles in the development and progression of human brain tumors. LncRNAs can have either tumor suppressive or oncogenic functions in different brain cancers, making them attractive therapeutic targets and biomarkers for personalized therapy and precision diagnostics. Here, we summarize the current state of knowledge of the lncRNAs that have been implicated in brain cancer pathogenesis, particularly in gliomas and medulloblastomas. We discuss their epigenetic regulation as well as the prospects of using lncRNAs as diagnostic biomarkers and therapeutic targets in patients with brain tumors.

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