scholarly journals Stress Resets Transgenerational Small RNA Inheritance

2019 ◽  
Author(s):  
Leah Houri-Ze’evi ◽  
Guy Teichman ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Memory Trace ◽  
Mapk Pathway ◽  
Transgenerational Inheritance ◽  
Cultivation Conditions ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Basic Concepts

AbstractTransgenerational inheritance of small RNAs is challenging basic concepts of heredity and achieving control over such responses is of great interest. InC. elegansnematodes, small RNAs are transmitted across generations to establish a transgenerational memory trace of ancestral environments and distinguish self from non-self genes. Inheritance of small RNAs is regulated by dedicated machinery and carryover of aberrant heritable small RNA responses was shown to be maladaptive and to induce sterility. Here we show that various types of stress (starvation, high temperatures, and high osmolarity) but not non-stressful changes in cultivation conditions, lead to resetting of small RNA inheritance. We found that stress leads to a genome-wide reduction in heritable small RNA levels and that mutants defective in different stress pathways exhibit irregular RNAi inheritance dynamics. Moreover, we discovered that resetting of heritable RNAi is orchestrated by MAPK pathway factors, the transcription factor SKN-1, and the MET-2 methyltransferase. Termination of small RNA inheritance, and the fact that this process depends on stress, could protect from run-on of environment-irrelevant heritable gene regulation.

scholarly journals Stress resets ancestral heritable small RNA responses

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Leah Houri Zeevi ◽  
Guy Teichman ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Memory Trace ◽  
Mapk Pathway ◽  
Transgenerational Inheritance ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Basic Concepts ◽  
Stress Dependent

Transgenerational inheritance of small RNAs challenges basic concepts of heredity. In C. elegans nematodes, small RNAs are transmitted across generations to establish a transgenerational memory trace of ancestral environments and distinguish self-genes from non-self-elements. Carryover of aberrant heritable small RNA responses was shown to be maladaptive and to lead to sterility. Here we show that various types of stress (starvation, high temperatures, and high osmolarity) induce resetting of ancestral small RNA responses and a genome-wide reduction in heritable small RNA levels. We found that mutants that are defective in various stress pathways exhibit irregular RNAi inheritance dynamics even in the absence of stress. Moreover, we discovered that resetting of ancestral RNAi responses is specifically orchestrated by factors that function in the p38 MAPK pathway and the transcription factor SKN-1/Nrf2. Stress-dependent termination of small RNA inheritance could protect from run-on of environment-irrelevant heritable gene regulation.

scholarly journals A small RNA pathway mediates global allelic dosage in endosperm

2017 ◽  
Author(s):  
Robert M. Erdmann ◽  
P.R. V. Satyaki ◽  
Maja Klosinska ◽  
Mary Gehring
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Inverse Relationship ◽  
Paternal Genome ◽  
Pol Iv ◽  
Genome Wide ◽  
A Genome ◽  
Normal Seed ◽  
Wide Scale ◽  
Parent Of Origin

SummaryBalance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of genes in Arabidopsis endosperm are expressed in a 2:1 maternal:paternal ratio, reflecting endosperm genomic DNA content. Here we find that the 2:1 transcriptional ratio is not, unexpectedly, a passive default but is actively regulated. We describe an inverse relationship between the parent-of-origin of small RNAs and mRNAs in endosperm on a genome-wide scale. Disruption of the Pol IV small RNA pathway causes the entire transcriptome to become more maternally biased. Furthermore, paternal inheritance of a RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. These results indicate that maintenance of the maternal:paternal transcriptome ratio in endosperm is an active process and reveal a function for RNA Pol IV in mediating the global transcriptional balance between maternally and paternally inherited genomes in endosperm.

scholarly journals Comparative Profiling of Small RNAs Originated From Two Varieties of Chinese Cabbage (Brassica Rapa) With Distinct Leaf Traits

2021 ◽  
Author(s):  
XU XIN LIU ◽  
XIANG YU ◽  
HAN WANG ◽  
YU KE HE
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Small Rna ◽  
Small Rnas ◽  
Leaf Shape ◽  
Leaf Traits ◽  
Differentially Expressed ◽  
High Yield ◽  
Genome Wide ◽  
A Genome

Abstract The species Brassica rapa includes many important vegetable crops. For a genome-wide survey of small RNAs in B. rapa, we performed massively parallel small RNA deep sequencing by using two representative varieties of non-heading Chinese cabbage (B. rapa ssp. chinensis) that are distinct in leaf shape, size, color and curvature. In total, 13.30 million small RNA reads were generated from Huaq, a variety with up-curved blades and wide petioles, and 14.69 million for Wut, a variety with down-curved blades and narrow petioles. After normalization, about half of small RNA reads in each variety were mapped to the published reference genome of B. rapa. In Huaq seedlings, unique small RNAs were much more than in Wut seedlings. Among them, 45 miRNAs were up-regulated or down-regulated in one variety, compared with those in another variety. Numbers of ta-siRNAs (trans-acting siRNAs) and ra-siRNAs (repeat-associated siRNAs) in Huaq seedlings were more than those detected in Wut seedlings, while gene-derived siRNAs (siRNAs derived from the sense and antisense strands of annotated genes regeion) in Huaq seedlings were less than in Wut seedlings. Especially, bra-miR156, bra-miR166 and bra-miR319 and one of ta-siRNAs that play important role in leaf shape, leaf size, leaf curvature and phase transition were differentially expressed between two varieties. In addition, total number of small RNAs derived from chloroplast genome of Wut was more than that of Huaq. The differentially-expressed small RNAs on genome-wide level provides the clue for the study of small-RNA-mediated morphology of leaves and is useful for developing of small RNA markers for leaf traits desirable for high yield and quality.

scholarly journals Crosstalk in oxygen homeostasis networks: SKN-1/NRF inhibits the HIF-1 hypoxia-inducible factor in Caenorhabditis elegans

2021 ◽  
Author(s):  
Dingxia Feng ◽  
Zhiwei Zhai ◽  
Zhiyong Shao ◽  
Yi Zhang ◽  
Jo Anne Powell-Coffman
Keyword(s):  
Oxidative Stress ◽  
Hypoxia Inducible Factor ◽  
Regulatory Sequences ◽  
Low Oxygen ◽  
Transcriptional Responses ◽  
C Elegans ◽  
Protein Levels ◽  
Oxygen Homeostasis ◽  
Genome Wide ◽  
A Genome

AbstractDuring development, homeostasis, and disease, organisms must balance responses that allow adaptation to low oxygen (hypoxia) with those that protect cells from oxidative stress. The evolutionarily conserved hypoxia-inducible factors are central to these processes, as they orchestrate transcriptional responses to oxygen deprivation. Here, we employ genetic strategies in C. elegans to identify stress-responsive genes and pathways that modulate the HIF-1 hypoxia-inducible factor and facilitate oxygen homeostasis. Through a genome-wide RNAi screen, we show that RNAi-mediated mitochondrial or proteasomal dysfunction increases the expression of hypoxia-responsive reporter Pnhr-57:GFP in C. elegans. Interestingly, only a subset of these effects requires hif-1. Of particular importance, we found that skn-1 RNAi increases the expression of hypoxia-responsive reporter Pnhr-57:GFP and elevates HIF-1 protein levels. The SKN-1/NRF transcription factor has been shown to promote oxidative stress resistance. We present evidence that the crosstalk between HIF-1 and SKN-1 is mediated by EGL-9, the prolyl hydroxylase that targets HIF-1 for oxygen-dependent degradation. Treatment that induces SKN-1, such as heat, increases expression of a Pegl-9:GFP reporter, and this effect requires skn-1 function and a putative SKN-1 binding site in egl-9 regulatory sequences. Collectively, these data support a model in which SKN-1 promotes egl-9 transcription, thereby inhibiting HIF-1. We propose that this interaction enables animals to adapt quickly to changes in cellular oxygenation and to better survive accompanying oxidative stress.

scholarly journals Small RNAs in parasitic nematodes – forms and functions

Parasitology ◽  
2019 ◽  
Vol 147 (8) ◽  
pp. 855-864
Author(s):  
Collette Britton ◽  
Roz Laing ◽  
Eileen Devaney
Keyword(s):  
Gene Expression ◽  
Small Rna ◽  
Small Rnas ◽  
Target Genes ◽  
Parasitic Nematodes ◽  
Small Rna Sequencing ◽  
Small Interfering Rnas ◽  
Rna Sequences ◽  
C Elegans

AbstractSmall RNAs are important regulators of gene expression. They were first identified in Caenorhabditis elegans, but it is now apparent that the main small RNA silencing pathways are functionally conserved across diverse organisms. Availability of genome data for an increasing number of parasitic nematodes has enabled bioinformatic identification of small RNA sequences. Expression of these in different lifecycle stages is revealed by small RNA sequencing and microarray analysis. In this review we describe what is known of the three main small RNA classes in parasitic nematodes – microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs) and small interfering RNAs (siRNAs) – and their proposed functions. miRNAs regulate development in C. elegans and the temporal expression of parasitic nematode miRNAs suggest modulation of target gene levels as parasites develop within the host. miRNAs are also present in extracellular vesicles released by nematodes in vitro, and in plasma from infected hosts, suggesting potential regulation of host gene expression. Roles of piRNAs and siRNAs in suppressing target genes, including transposable elements, are also reviewed. Recent successes in RNAi-mediated gene silencing, and application of small RNA inhibitors and mimics will continue to advance understanding of small RNA functions within the parasite and at the host–parasite interface.

scholarly journals A genome-wide RNAi screen identifies genes regulating the formation of P bodies in C. elegans and their functions in NMD and RNAi

2011 ◽  
Vol 2 (11) ◽  
pp. 918-939 ◽  
Author(s):  
Yinyan Sun ◽  
Peiguo Yang ◽  
Yuxia Zhang ◽  
Xin Bao ◽  
Jun Li ◽  
...  
Keyword(s):  
Rnai Screen ◽  
P Bodies ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome

scholarly journals A stress-induced Tyrosine tRNA depletion response mediates codon-based translational repression and growth suppression

2018 ◽  
Author(s):  
Doowon Huh ◽  
Maria C. Passarelli ◽  
Jenny Gao ◽  
Shahnoza N Dusmatova ◽  
Clara Goin ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Small Rna ◽  
Small Rnas ◽  
Oxidative Stress Response ◽  
Translational Repression ◽  
Dependent Manner ◽  
Transfer Rnas ◽  
C Elegans ◽  
Metabolic Genes ◽  
Rna Fragments

SUMMARYEukaryotic transfer RNAs can become selectively fragmented upon various stresses, generating tRNA-derived small RNA fragments. Such fragmentation has been reported to impact a small fraction of the tRNA pool and thus presumed to not directly impact translation. We report that oxidative stress can rapidly generate tyrosine tRNAGUA fragments in human cells—causing significant depletion of the precursor tRNA. Tyrosine tRNAGUA depletion impaired translation of growth and metabolic genes enriched in cognate tyrosine codons. Depletion of tyrosine tRNAGUA or its translationally regulated targets USP3 and SCD repressed proliferation—revealing a dedicated tRNA-regulated growth suppressive pathway for oxidative stress response. Tyrosine fragments are generated in a DIS3L2 exoribonuclease-dependent manner and inhibit hnRNPA1-mediated transcript destabilization. Moreover, tyrosine fragmentation is conserved in C. elegans. Thus, tRNA fragmentation can coordinately generate trans-acting small-RNAs and functionally deplete a tRNA. Our findings reveal the existence of an underlying adaptive codon-based regulatory response inherent to the genetic code.

scholarly journals Removing bias against short sequences enables northern blotting to better complement RNA-seq for the study of small RNAs

2016 ◽  
Author(s):  
Yun S. Choi ◽  
Lanelle O. Edwards ◽  
Aubrey DiBello ◽  
Antony M. Jose
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Degradation Products ◽  
Northern Blotting ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Rna Integrity ◽  
C Elegans ◽  
Micro Rnas ◽  
Functional Rnas

ABSTRACTChanges in small non-coding RNAs such as micro RNAs (miRNAs) can serve as indicators of disease and can be measured using next-generation sequencing of RNA (RNA-seq). Here, we highlight the need for approaches that complement RNA-seq, discover that northern blotting of small RNAs is biased against short sequences, and develop a protocol that removes this bias. We found that multiple small RNA-seq datasets from the worm C. elegans had shorter forms of miRNAs that appear to be degradation products that arose during the preparatory steps required for RNA-seq. When using northern blotting during these studies, we discovered that miRNA-length probes can have a ~360-fold bias against detecting even synthetic sequences that are 8 nt shorter. By using shorter probes and by performing hybridization and washes at low temperatures, we greatly reduced this bias to enable equivalent detection of 24 nt to 14 nt RNAs. Our protocol can better discriminate RNAs that differ by a single nucleotide and can detect specific miRNAs present in total RNA from C. elegans. This improved northern blotting is particularly useful to obtain a measure of small RNA integrity, analyze products of RNA processing or turnover, and analyze functional RNAs that are shorter than typical miRNAs.

scholarly journals Horizontal and vertical transmission of transgenerational memories via the Cer1 transposon

2020 ◽  
Author(s):  
Rebecca S. Moore ◽  
Rachel Kaletsky ◽  
Chen Lesnik ◽  
Vanessa Cota ◽  
Edith Blackman ◽  
...  
Keyword(s):  
Adaptive Immunity ◽  
Vertical Transmission ◽  
Small Rna ◽  
Small Rnas ◽  
C Elegans ◽  
Common Pathogen ◽  
Transmission Of Information ◽  
Genomic Element ◽  
Pathogen Avoidance

AbstractAnimals face both external and internal dangers: pathogens threaten from the environment, and unstable genomic elements threaten from within. Previously, we discovered that C. elegans protects itself from pathogens by “reading” bacterial small RNAs and using this information to both induce avoidance and transmit memories for several generations. Here we found that these memories can be transferred to naïve animals via Cer1 retrotransposon-encoded capsids. Cer1 functions at the step of transmission of information from the germline to neurons, and is required for C. elegans’ learned avoidance ability and for mothers to pass this information on to progeny. The presence of the Cer1 retrotransposon in wild C. elegans strains correlates with the ability to learn and inherit small RNA-induced pathogen avoidance. Together, these results suggest that C. elegans has co-opted a potentially dangerous retrotransposon to instead protect itself and its progeny from a common pathogen through its inter-tissue signaling ability, hijacking this genomic element for its own adaptive immunity benefit.

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