scholarly journals miRNA targeting and alternative splicing in the stress response – events hosted by membrane-less compartments

2018 ◽  
Vol 131 (4) ◽  
pp. jcs202002 ◽  
Author(s):  
Mariya M. Kucherenko ◽  
Halyna R. Shcherbata
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Mirna Targeting

scholarly journals Genome-Wide Analysis of Alternative Splicing Provides Insights Into Stress Response of the Pacific White Shrimp Litopenaeus vanname

2019 ◽  
Vol 10 ◽  
Author(s):  
Xiaoxi Zhang ◽  
Jianbo Yuan ◽  
Xiaojun Zhang ◽  
Chengzhang Liu ◽  
Jianhai Xiang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Pacific White Shrimp ◽  
White Shrimp ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
The Pacific

scholarly journals MicroRNA miR-1002 Enhances NMNAT-Mediated Stress Response by Modulating Alternative Splicing

iScience ◽  
2019 ◽  
Vol 19 ◽  
pp. 1048-1064
Author(s):  
Joun Park ◽  
Yi Zhu ◽  
Xianzun Tao ◽  
Jennifer M. Brazill ◽  
Chong Li ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stress Response

scholarly journals MicroRNA miR-1002 enhances NMNAT-mediated stress response by modulating alternative splicing

2019 ◽  
Author(s):  
Joun Park ◽  
Yi Zhu ◽  
Xianzun Tao ◽  
Jennifer M. Brazill ◽  
Chong Li ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Stress Resistance ◽  
Stem Loop ◽  
Stress Protection ◽  
Stem Loop Structure ◽  
Nicotinamide Mononucleotide ◽  
Mrna Variants ◽  
Alternatively Spliced ◽  
Essential Enzyme

SUMMARYUnderstanding endogenous regulation of stress resistance and homeostasis maintenance is critical to developing neuroprotective therapies. Nicotinamide mononucleotide adenylyltransferase (NMNAT) is a conserved essential enzyme that confers extraordinary protection and stress resistance in many neurodegenerative disease models. Drosophila Nmnat is alternatively spliced to two mRNA variants, RA and RB. RB translates to protein isoform PD with robust protective activity and is upregulated upon stress to confer enhanced neuroprotection. The mechanisms regulating alternative splicing and stress response of NMNAT remain unclear. We have discovered a Drosophila microRNA, dme-miR-1002, which promotes the splicing of NMNAT pre-mRNA to RB by disrupting a pre-mRNA stem-loop structure. While NMNAT pre-mRNA is preferentially spliced to RA in basal conditions, miR-1002 enhances NMNAT PD-mediated stress protection by binding via RISC component Argonaute1 to the pre-mRNA, facilitating the splicing switch to RB. These results outline a new process for microRNAs in regulating alternative splicing and modulating stress resistance.

scholarly journals Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 182 ◽  
Author(s):  
Muthusamy ◽  
Yoon ◽  
Kim ◽  
Jeong ◽  
Lee
Keyword(s):  
Alternative Splicing ◽  
Drought Stress ◽  
Stress Response ◽  
Drought Tolerance ◽  
Brassica Rapa ◽  
Target Genes ◽  
Tolerance Index ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Splicing Patterns

The emerging evidence has shown that plant serine/arginine-rich (SR) proteins play a crucial role in abiotic stress responses by regulating the alternative splicing (AS) of key genes. Recently, we have shown that drought stress enhances the expression of SR45a (also known as SR-like 3) in Brassica rapa. Herein, we unraveled the hitherto unknown functions of BrSR45a in drought stress response by comparing the phenotypes, chlorophyll a fluorescence and splicing patterns of the drought-responsive genes of Arabidopsis BrSR45a overexpressors (OEs), homozygous mutants (SALK_052345), and controls (Col-0). Overexpression and loss of function did not result in aberrant phenotypes; however, the overexpression of BrSR45a was positively correlated with drought tolerance and the stress recovery rate in an expression-dependent manner. Moreover, OEs showed a higher drought tolerance index during seed germination (38.16%) than the control lines. Additionally, the overexpression of BrSR45a induced the expression of the drought stress-inducible genes RD29A, NCED3, and DREB2A under normal conditions. To further illustrate the molecular linkages between BrSR45a and drought tolerance, we investigated the AS patterns of key drought-tolerance and BrSR45a interacting genes in OEs, mutants, and controls under both normal and drought conditions. The splicing patterns of DCP5, RD29A, GOLS1, AKR, U2AF, and SDR were different between overexpressors and mutants under normal conditions. Furthermore, drought stress altered the splicing patterns of NCED2, SQE, UPF1, U4/U6-U5 tri-snRNP-associated protein, and UPF1 between OEs and mutants, indicating that both overexpression and loss of function differently influenced the splicing patterns of target genes. This study revealed that BrSR45a regulates the drought stress response via the alternative splicing of target genes in a concentration-dependent manner.

scholarly journals The Role of Canonical and Noncanonical Pre-mRNA Splicing in Plant Stress Responses

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
A. S. Dubrovina ◽  
K. V. Kiselev ◽  
Yu. N. Zhuravlev
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Stress Responses ◽  
Regulatory Networks ◽  
Plant Stress ◽  
Mrna Splicing ◽  
Plant Stress Response ◽  
Plant Stress Responses ◽  
Alternative Splicing Events ◽  
Stress Responsive Genes

Plants are sessile organisms capable of adapting to various environmental constraints, such as high or low temperatures, drought, soil salinity, or pathogen attack. To survive the unfavorable conditions, plants actively employ pre-mRNA splicing as a mechanism to regulate expression of stress-responsive genes and reprogram intracellular regulatory networks. There is a growing evidence that various stresses strongly affect the frequency and diversity of alternative splicing events in the stress-responsive genes and lead to an increased accumulation of mRNAs containing premature stop codons, which in turn have an impact on plant stress response. A number of studies revealed that some mRNAs involved in plant stress response are spliced counter to the traditional conception of alternative splicing. Such noncanonical mRNA splicing events includetrans-splicing, intraexonic deletions, or variations affecting multiple exons and often require short direct repeats to occur. The noncanonical alternative splicing, along with common splicing events, targets the spliced transcripts to degradation through nonsense-mediated mRNA decay or leads to translation of truncated proteins. Investigation of the diversity, biological consequences, and mechanisms of the canonical and noncanonical alternative splicing events will help one to identify those transcripts which are promising for using in genetic engineering and selection of stress-tolerant plants.

scholarly journals The evolution and diversity of the nonsense-mediated mRNA decay pathway

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1299 ◽  
Author(s):  
James P. B. Lloyd
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Driving Force ◽  
Mrna Decay ◽  
Common Ancestor ◽  
Last Eukaryotic Common Ancestor ◽  
Eukaryotic Evolution ◽  
Premature Termination Codons ◽  
Upstream Orf ◽  
Nonsense Mediated Mrna Decay

Nonsense-mediated mRNA decay is a eukaryotic pathway that degrades transcripts with premature termination codons (PTCs). In most eukaryotes, thousands of transcripts are degraded by NMD, including many important regulators of development and stress response pathways. Transcripts can be targeted to NMD by the presence of an upstream ORF or by introduction of a PTC through alternative splicing. Many factors involved in the recognition of PTCs and the destruction of NMD targets have been characterized. While some are highly conserved, others have been repeatedly lost in eukaryotic lineages. Here, I outline the factors involved in NMD, our current understanding of their interactions and how they have evolved. I outline a classification system to describe NMD pathways based on the presence/absence of key NMD factors. These types of NMD pathways exist in multiple different lineages, indicating the plasticity of the NMD pathway through recurrent losses of NMD factors during eukaryotic evolution. By classifying the NMD pathways in this way, gaps in our understanding are revealed, even within well studied organisms. Finally, I discuss the likely driving force behind the origins of the NMD pathway before the appearance of the last eukaryotic common ancestor: transposable element expansion and the consequential origin of introns.

scholarly journals PacBio and Illumina RNA Sequencing Identify Alternative Splicing Events in Response to Cold Stress in Two Poplar Species

2021 ◽  
Vol 12 ◽  
Author(s):  
Jingli Yang ◽  
Wanqiu Lv ◽  
Liying Shao ◽  
Yanrui Fu ◽  
Haimei Liu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Stress Response ◽  
Cold Stress ◽  
Rna Sequencing ◽  
Single Molecule ◽  
Intron Retention ◽  
Global Analysis ◽  
Populus Trichocarpa ◽  
Rna Seq ◽  
Long Read

In eukaryotes, alternative splicing (AS) is a crucial regulatory mechanism that modulates mRNA diversity and stability. The contribution of AS to stress is known in many species related to stress, but the posttranscriptional mechanism in poplar under cold stress is still unclear. Recent studies have utilized the advantages of single molecular real-time (SMRT) sequencing technology from Pacific Bioscience (PacBio) to identify full-length transcripts. We, therefore, used a combination of single-molecule long-read sequencing and Illumina RNA sequencing (RNA-Seq) for a global analysis of AS in two poplar species (Populus trichocarpa and P. ussuriensis) under cold stress. We further identified 1,261 AS events in P. trichocarpa and 2,101 in P. ussuriensis among which intron retention, with a frequency of more than 30%, was the most prominent type under cold stress. RNA-Seq data analysis and annotation revealed the importance of calcium, abscisic acid, and reactive oxygen species signaling in cold stress response. Besides, the low temperature rapidly induced multiple splicing factors, transcription factors, and differentially expressed genes through AS. In P. ussuriensis, there was a rapid occurrence of AS events, which provided a new insight into the complexity and regulation of AS during cold stress response in different poplar species for the first time.

scholarly journals Stress-mediated convergence of splicing landscapes in male and female Rock Doves

2019 ◽  
Author(s):  
Andrew S Lang ◽  
Suzanne H Austin ◽  
Rayna M Harris ◽  
Rebecca M Calisi ◽  
Matthew D MacManes
Keyword(s):  
Sexual Behavior ◽  
Alternative Splicing ◽  
Stress Response ◽  
Drug Targets ◽  
Columba Livia ◽  
Hpg Axis ◽  
Behavioral Complexity ◽  
Coding Regions ◽  
Males And Females ◽  
And Control

AbstractBackgroundThe process of alternative splicing provides a unique mechanism by which eukaryotes are able to produce numerous protein products from the same gene. Heightened variability in the proteome has been thought to potentiate increased behavioral complexity and response flexibility to environmental stimuli, thus contributing to more refined traits on which natural and sexual selection can act. While it has been long known that various forms of environmental stress can negatively affect sexual behavior and reproduction, we know little of how stress can affect the alternative splicing associated with these events, and less still about how splicing may differ between sexes. Using the model of the rock dove (Columba livia), our team previously uncovered sexual dimorphism in the basal and stress-responsive gene transcription of a biological system necessary for facilitating sexual behavior and reproduction, the hypothlamic-pituitary-gonadal (HPG) axis. In this study, we delve further into understanding the mechanistic underpinnings of how changes in the environment can affect reproduction by testing the alternative splicing response of the HPG axis to an external stressor in both sexes.ResultsThis study reveals dramatic baseline differences in HPG alternative splicing between males and females. However, post submitting subjects to a restraint stress paradigm, we found a significant reduction in these differences between the sexes. In both stress and control treatments, we identified a higher incidence of splicing activity in the pituitary in both sexes as compared to other tissues. Of these splicing events, the core exon event is the most abundant form of splicing and more frequently occurs in the coding regions of the gene. Overall, we observed less splicing activity in the 3’UTR end of transcripts than the 5’UTR or coding regions.ConclusionsOur results provide vital new insight into sex-specific aspects of the stress response on the HPG axis at an unprecedented proximate level. Males and females uniquely respond to stress, yet exhibit splicing patterns suggesting a convergent, optimal splicing landscape for stress response. This information has the potential to inform evolutionary theory as well as the development of highly-specific drug targets for stress-induced reproductive dysfunction.

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