scholarly journals Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure

PLoS Genetics ◽  
2021 ◽  
Vol 17 (3) ◽  
pp. e1009444
Author(s):  
Heinrich Bente ◽  
Andrea M. Foerster ◽  
Nicole Lettner ◽  
Ortrun Mittelsten Scheid
Keyword(s):  
Arabidopsis Thaliana ◽  
Small Rna ◽  
Small Rnas ◽  
Underlying Mechanism ◽  
Mendelian Inheritance ◽  
Epigenetic Mechanisms ◽  
Epigenetic Changes ◽  
F2 Population ◽  
Different Types ◽  
Allelic Interaction

Paramutation is a form of non-Mendelian inheritance in which the expression of a paramutable allele changes when it encounters a paramutagenic allele. This change in expression of the paramutable alleles is stably inherited even after segregation of both alleles. While the discovery of paramutation and studies of its underlying mechanism were made with alleles that change plant pigmentation, paramutation-like phenomena are known to modulate the expression of other traits and in other eukaryotes, and many cases have probably gone undetected. It is likely that epigenetic mechanisms are responsible for the phenomenon, as paramutation forms epialleles, genes with identical sequences but different expression states. This could account for the intergenerational inheritance of the paramutated allele, providing profound evidence that triggered epigenetic changes can be maintained over generations. Here, we use a case of paramutation that affects a transgenic selection reporter gene in tetraploid Arabidopsis thaliana. Our data suggest that different types of small RNA are derived from paramutable and paramutagenic epialleles. In addition, deletion of a repeat within the epiallele changes its paramutability. Further, the temperature during the growth of the epiallelic hybrids determines the degree and timing of the allelic interaction. The data further make it plausible why paramutation in this system becomes evident only in the segregating F2 population of tetraploid plants containing both epialleles. In summary, the results support a model for polyploidy-associated paramutation, with similarities as well as distinctions from other cases of paramutation.

scholarly journals Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure

2020 ◽  
Author(s):  
Heinrich Bente ◽  
Andrea M. Foerster ◽  
Nicole Lettner ◽  
Ortrun Mittelsten Scheid
Keyword(s):  
Arabidopsis Thaliana ◽  
Leaf Shape ◽  
Underlying Mechanism ◽  
Mendelian Inheritance ◽  
Early Observation ◽  
Epigenetic Changes ◽  
Epigenetic Switch ◽  
F2 Population ◽  
Leaf Phenotype ◽  
Copy Number Ratio

ABSTRACTParamutation is a form of non-Mendelian inheritance in which the expression of a paramutable allele changes when it encounters a paramutagenic allele. This change in expression of the paramutable alleles is stably inherited even after segregation of both alleles. While the discovery of paramutation and studies of its underlying mechanism were made with alleles that change plant pigmentation, paramutation-like phenomena are known to modulate the expression of other traits and in other eukaryotes, and many cases have probably gone undetected. It is likely that epigenetic mechanisms are responsible for the phenomenon, as paramutation forms epialleles, genes with identical sequences but different expression states. This could account for the intergenerational inheritance of the paramutated allele, providing profound evidence that triggered epigenetic changes can be maintained over generations. Here, we use a case of paramutation that affects a transgenic selection reporter gene in tetraploid Arabidopsis thaliana. Our data suggest that different types of small RNA are associated with paramutable and paramutagenic epialleles. In addition, deletion of a repeat within the epiallele changes its paramutability. Further, the temperature during the growth of the epiallelic hybrids determines the degree and timing of the allelic interaction. The data further make it plausible why paramutation in this system becomes evident only in the segregating F2 population of tetraploid plants containing both epialleles. In summary, the results support a model for polyploidy-associated paramutation, with similarities as well as distinctions from other cases of paramutation.AUTHOR SUMMARYA curiosity in the history of genetics is the fact that experiments with peas, Mendel’s most studied plants, resulted in one of the first observations of non-Mendelian genetics published already in 1915. Crossings with plants showing a “rogue” leaf phenotype made normal leaf shape disappear in all progeny, without recovery. This phenomenon was later demonstrated for more traits in other plants and termed paramutation. Paramutation is due to the epigenetic switch of aa active gene to a silenced version which is then maintained in the inactive state in later generations. This demonstrates that acquired epigenetic changes can become permanent. Despite its early observation and numerous studies in mainly maize and tomato, it is barely understood how paramutation is established and which parameters influence the process. We investigated a case of paramutation in Arabidopsis thaliana, crossing plants with genetically identical but epigenetically different alleles that result in resistance or sensitivity to hygromycin in the growth medium. Unexpectedly, paramutation did not become manifest in the hybrids but only in their progeny and only in plants with a doubled chromosome set. These features make this paramutation distinct from other cases and our studies revealed the involvement of several parameters: an important role for sRNAs to initiate silencing, the sequence of the allele itself, the environmental conditions during growth of the hybrids, the developmental stage, and the copy number ratio between the epialleles.

scholarly journals Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci

2017 ◽  
Author(s):  
Seth Polydore ◽  
Michael J. Axtell
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Small Rna ◽  
Small Rnas ◽  
Rna Seq ◽  
Triple Mutant ◽  
Physiological Mechanisms ◽  
Protein Coding ◽  
Regulate Gene Expression ◽  
Rna Biogenesis

SummaryPlant small RNAs regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that aren’t. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs and other hairpin-derived sRNAs. In this study, we produced and analyzed small RNA-seq libraries from rdr1/rdr2/rdr6 triple mutant plants. Only a small fraction of all sRNA loci were RDR1/RDR2/RDR6-independent; most of these were microRNA loci or associated with predicted hairpin precursors. We found 58 previously annotated microRNA loci that were reliant on RDR1, −2, or −6 function, casting doubt on their classification. We also found 38 RDR1/2/6-independent small RNA loci that are not MIRNAs or otherwise hairpin-derived, and did not fit into other known paradigms for small RNA biogenesis. These 38 small RNA-producing loci have novel biogenesis mechanisms, and are frequently located in the vicinity of protein-coding genes. Altogether, our analysis suggest that these 38 loci represent one or more new types of small RNAs in Arabidopsis thaliana.Significance StatementSmall RNAs regulate gene expression in plants and are produced through a variety of previously-described mechanisms. Here, we examine a set of previously undiscovered small RNA-producing loci that are produced by novel mechanisms.

scholarly journals Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 232 ◽  
Author(s):  
Lorena Pantano ◽  
Francisco Pantano ◽  
Eulalia Marti ◽  
Shannan Ho Sui
Keyword(s):  
Gene Regulation ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rnas ◽  
Model Organisms ◽  
Visualization Tool ◽  
Rna Seq ◽  
Small Noncoding Rnas ◽  
Different Types ◽  
Genomic Locations

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease.

scholarly journals Visualization of the small RNA transcriptome using seqclusterViz

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 232
Author(s):  
Lorena Pantano ◽  
Francisco Pantano ◽  
Eulalia Marti ◽  
Shannan Ho Sui
Keyword(s):  
Gene Regulation ◽  
Small Rna ◽  
Small Rnas ◽  
Noncoding Rnas ◽  
Model Organisms ◽  
Visualization Tool ◽  
Rna Seq ◽  
Small Noncoding Rnas ◽  
Different Types ◽  
Genomic Locations

The study of small RNAs provides us with a deeper understanding of the complexity of gene regulation within cells. Of the different types of small RNAs, the most important in mammals are miRNA, tRNA fragments and piRNAs. Using small RNA-seq analysis, we can study all small RNA types simultaneously, with the potential to detect novel small RNA types. We describe SeqclusterViz, an interactive HTML-javascript webpage for visualizing small noncoding RNAs (small RNAs) detected by Seqcluster. The SeqclusterViz tool allows users to visualize known and novel small RNA types in model or non-model organisms, and to select small RNA candidates for further validation. SeqclusterViz is divided into three panels: i) query-ready tables showing detected small RNA clusters and their genomic locations, ii) the expression profile over the precursor for all the samples together with RNA secondary structures, and iii) the mostly highly expressed sequences. Here, we show the capabilities of the visualization tool and its validation using human brain samples from patients with Parkinson’s disease .

scholarly journals Identification of PTBP1 responsible for caspase dependent YRNA cleavage

2018 ◽  
Author(s):  
Jun Ogata ◽  
Yuki Sugiura ◽  
Akinori Kanai ◽  
Masafumi Tanaka ◽  
Hirotaka Matsui ◽  
...  
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Caspase 3 ◽  
Biological Significance ◽  
Underlying Mechanism ◽  
Rna Degradation ◽  
Rna Cleavage ◽  
28S Rrna ◽  
U1 Snrna ◽  
Non Coding Rnas

ABSTRACTSome RNAs such as 28S rRNA, U1 snRNA, and Y RNAs are known to be cleaved during apoptosis. As the underlying mechanism is yet unclear, the functions and biological significance of RNA degradation in apoptosis remain elusive. We previously identified novel, functional small RNAs named AGO-taxis small RNA (ASR) that are specifically bound to AGO1. Here, we investigated ASR biogenesis, which appears to be non-canonical. Y RNAs, non-coding RNAs degraded during apoptosis, were identified as the precursors of several ASRs. Cell-free analysis combined with fractionation methods revealed that the apoptosis-specific biogenesis of ASRs or Y RNA degradation was induced by PTBP1—an endoribonuclease inhibitor of Y RNAs. PTBP1, a splicing factor, was truncated by caspase 3, which subsequently activated endoribonuclease to induce biogenesis of ASRs and Y RNA cleavage.

EPEGENTIC TOXICOLOGY: PERSPECTIVES OF THE DEVELOPMENT

2018 ◽  
pp. 2-7
Author(s):  
G. A. Sofronov ◽  
E. L. Patkin
Keyword(s):  
Public Health ◽  
Life Cycle ◽  
Human Health ◽  
Chronic Exposure ◽  
Environmental Pollutants ◽  
Epigenetic Mechanisms ◽  
Epigenetic Changes ◽  
Mechanism Of Formation ◽  
Health Disorders ◽  
Time Periods

One of the complex problems of modern experimental toxicology remains the molecular mechanism of formation of human health disorders separated at different time periods from acute or chronic exposure to toxic environmental pollutants (ecotoxicants). Identifying and understanding what epigenetic changes are induced by the environment, and how they can lead to unfavorable outcome, are vital for protecting public health. Therefore, we consider it important a modern understanding of epigenetic mechanisms involved in the life cycle of mammals and assess available data on the environmentally caused epigenetic toxicity and, accordingly fledging epigenenomic (epigenetic) regulatory toxicology.

Epigenetics, Nutrition, Disease and Drug Development

2019 ◽  
Vol 16 (4) ◽  
pp. 386-391 ◽  
Author(s):  
Kenneth Lundstrom
Keyword(s):  
Dna Methylation ◽  
Drug Discovery ◽  
Rna Interference ◽  
Nutritional Requirements ◽  
Signal Pathways ◽  
Disease Development ◽  
Epigenetic Mechanisms ◽  
Epigenetic Changes ◽  
Health And Disease ◽  
Novel Drug

Epigenetic mechanisms comprising of DNA methylation, histone modifications and gene silencing by RNA interference have been strongly linked to the development and progression of various diseases. These findings have triggered research on epigenetic functions and signal pathways as targets for novel drug discovery. Dietary intake has also presented significant influence on human health and disease development and nutritional modifications have proven important in prevention, but also the treatment of disease. Moreover, a strong link between nutrition and epigenetic changes has been established. Therefore, in attempts to develop novel safer and more efficacious drugs, both nutritional requirements and epigenetic mechanisms need to be addressed.

COVID-19 Epigenetics and Implications for Public Health

Coronaviruses ◽  
2020 ◽  
Vol 01 ◽  
Author(s):  
Verda Tunalıgil ◽  
Gülsen Meral ◽  
Ahmet Katı ◽  
Dhrubajyoti Chattopadhyay ◽  
Amit Kumar Mandal
Keyword(s):  
Chronic Conditions ◽  
Empirical Investigation ◽  
Age Groups ◽  
Infectious Agent ◽  
Well Being ◽  
Epigenetic Mechanisms ◽  
Age Group ◽  
Epigenetic Changes ◽  
Patient Groups ◽  
Epigenetic Processes

Abstract:: Epigenetic changes in COVID-19 host, a pandemic-causing infectious agent that globally incapacitated communities in varying complexities and capacities are discussed, proposing an analogy that epigenetic processes contribute to disease severity and elevate the risk for death from infection. Percentages of hospitalization, with and without intensive care, in the presence of diseases with increased ACE2 expression, were compared, based on the best available data. Further analysis compared two different age groups, 19-64 and ≥65 years of age. The COVID-19 disease is observed to be the most severe in the 65-and-higher-age group with preexisting chronic conditions. This observational study is a non-experimental empirical investigation of the outcomes of COVID-19 in different patient groups. Results are promising for conducting clinical trials with intervention groups. To ultimately succeed in disease prevention, researchers and clinicians must integrate epigenetic mechanisms to generate valid prescriptions for global well-being.

scholarly journals In Arabidopsis thaliana mitochondria 5′ end polymorphisms of nad4L-atp4 and nad3-rps12 transcripts are linked to RNA PROCESSING FACTORs 1 and 8

2021 ◽  
Author(s):  
Sarah Schleicher ◽  
Stefan Binder
Keyword(s):  
Arabidopsis Thaliana ◽  
Rna Processing ◽  
Degradation Products ◽  
Underlying Mechanism ◽  
Transcriptional Level ◽  
Pentatricopeptide Repeat ◽  
Repeat Proteins ◽  
P Type ◽  
Pentatricopeptide Repeat Proteins ◽  
Processing Factors

Abstract Key message RNA PROCESSING FACTORs 1 AND 8 (RPF1 and RPF8), both restorer of fertility like pentatricopeptide repeat proteins, are required for processing of dicistronic nad4L-atp4 and nad3-rps12 transcripts in Arabidopsis mitochondria. Abstract In mitochondria of Arabidopsis thaliana (Arabidopsis), the 5′ termini of many RNAs are generated on the post-transcriptional level. This process is still poorly understood in terms of both the underlying mechanism as well as proteins required. Our studies now link the generation of polymorphic 5′ extremities of the dicistronic nad3-rps12 and nad4L-atp4 transcripts to the function of the P-type pentatricopeptide repeat proteins RNA PROCESSING FACTORs 8 (RPF8) and 1 (RPF1). RPF8 is required to generate the nad3-rps12 -141 5′ end in ecotype Van-0 whereas the RPF8 allele in Col has no function in the generation of any 5′ terminus of this transcript. This observation strongly suggests the involvement of an additional factor in the generation of the -229 5′ end of nad3-rps12 transcripts in Col. RPF1, previously found to be necessary for the generation of the -228 5′ end of the major 1538 nucleotide-long nad4 mRNAs, is also important for the formation of nad4L-atp4 transcripts with a 5′ end at position -318 in Col. Many Arabidopsis ecotypes contain inactive RPF1 alleles resulting in the accumulation of various low abundant nad4L-atp4 RNAs which might represent precursor and/or degradation products. Some of these ecotypes accumulate major, but slightly smaller RNA species. The introduction of RPF1 into these lines not only establishes the formation of the major nad4L-atp4 dicistronic mRNA with the -318 5′ terminus, the presence of this gene also suppresses the accumulation of most alternative nad4L-atp4 RNAs. Beside RPF1, several other factors contribute to nad4L-atp4 transcript formation.

scholarly journals Mechanism of Stochastic Resonance in a Quorum Sensing Network Regulated by Small RNAs

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Ya-nan Zhu ◽  
Jianwei Shen ◽  
Yong Xu
Keyword(s):  
Quorum Sensing ◽  
Stochastic Resonance ◽  
Small Rna ◽  
Small Rnas ◽  
Cell Communication ◽  
The Other ◽  
Important Process ◽  
Positive Role ◽  
Bacterial Quorum Sensing ◽  
Bacterial Quorum

Bacterial quorum sensing (QS) is an important process of cell communication and more and more attention is paid to it. Moreover, the noises are ubiquitous in nature and often play positive role. In this paper, we investigate how the noise enhances the QS though the stochastic resonance (SR) and explain the mechanism of SR in this quorum sensing network. In addition, we also discuss the interaction between the small RNA and the other genes in this network and discover the biological importance.

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