scholarly journals Germline silencing of UASt depends on the piRNA pathway

2018 ◽  
Author(s):  
Yi-Chun Huang ◽  
Henry Moreno ◽  
Sarayu Row ◽  
Dongyu Jia ◽  
Wu-Min Deng
Keyword(s):  
Binary System ◽  
Small Rnas ◽  
Transgene Expression ◽  
Rna Seq ◽  
Somatic Tissues ◽  
Germline Expression ◽  
Germline Cells ◽  
Pirna Pathway ◽  
Nonsense Mediated Rna Decay

AbstractOne of the most extensively used techniques in Drosophila is the Gal4/UAS binary system, which allows tissue-specific misexpression or knockdown of specific genes of interest. The original UAS vector, UASt, can only be activated for transgene expression in somatic tissues and not in the germline cells. Rørth (1998) generated UASp, a modified UAS vector that is responsive to Gal4 in both somatic and germline tissues, by replacing both the hsp70 promoter and the SV40 3’UTR with the P transposase promoter and the K10 3’UTR respectively. At present, the mechanisms by which UASt is silenced in germline cells are not fully understood. Here, we report that the piRNA pathway is involved in suppressing UASt expression in ovarian germline cells. Individually knocking down or mutating components of the piRNA biogenesis pathway (e.g., Piwi, AGO3, Aub, Spn-E, and Vasa) resulted in the expression of the UASt-reporter (GFP or RFP) in the germline. An RNA-seq analysis of small RNAs revealed that the hsp70 promoter of UASt is targeted by piRNAs, and in the aub mutant ovary, the amount of piRNAs targeting the hsp70 promoter is reduced by around 40 folds. In contrast, the SV40 3’UTR of the UASt, which happens to be targeted by the Nonsense-mediated RNA decay (NMD) pathway, is not responsible for germline UASt suppression, as UASt-reporters with NMD-insensitive 3’UTRs fail to show germline expression. Taken together, our studies reveal a crucial role of the piRNA pathway, potentially via the suppression of the hsp70 promoter, in germline UASt silencing in Drosophila ovaries.

scholarly journals The role of the NMD factor UPF3B in olfactory sensory neurons

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Kun Tan ◽  
Samantha H Jones ◽  
Blue B Lake ◽  
Jennifer N Dumdie ◽  
Eleen Y Shum ◽  
...  
Keyword(s):  
Human Cognition ◽  
Cell Populations ◽  
Rna Seq ◽  
Wild Type ◽  
Single Cell Rna Sequencing ◽  
Nonsense Mediated Rna Decay ◽  
Different Levels ◽  
Selection Of

The UPF3B-dependent branch of the nonsense-mediated RNA decay (NMD) pathway is critical for human cognition. Here, we examined the role of UPF3B in the olfactory system. Single-cell RNA-sequencing (scRNA-seq) analysis demonstrated considerable heterogeneity of olfactory sensory neuron (OSN) cell populations in wild-type (WT) mice, and revealed that UPF3B loss influences specific subsets of these cell populations. UPF3B also regulates the expression of a large cadre of antimicrobial genes in OSNs, and promotes the selection of specific olfactory receptor (Olfr) genes for expression in mature OSNs (mOSNs). RNA-seq and Ribotag analyses identified classes of mRNAs expressed and translated at different levels in WT and Upf3b-null mOSNs. Integrating multiple computational approaches, UPF3B-dependent NMD target transcripts that are candidates to mediate the functions of NMD in mOSNs were identified in vivo. Together, our data provides a valuable resource for the olfactory field and insights into the roles of NMD in vivo.

scholarly journals Somatic piRNAs and Transposons are Differentially Expressed Coincident with Skeletal Muscle Atrophy and Programmed Cell Death

2021 ◽  
Vol 12 ◽  
Author(s):  
Junko Tsuji ◽  
Travis Thomson ◽  
Christine Brown ◽  
Subhanita Ghosh ◽  
William E. Theurkauf ◽  
...  
Keyword(s):  
Cell Death ◽  
Programmed Cell Death ◽  
Skeletal Muscle Atrophy ◽  
Rna Seq ◽  
Developmentally Regulated ◽  
Transposon Silencing ◽  
Ping Pong ◽  
Somatic Tissues ◽  
Oxidation Resistant ◽  
Pirna Pathway

PIWI-interacting RNAs (piRNAs) are small single-stranded RNAs that can repress transposon expression via epigenetic silencing and transcript degradation. They have been identified predominantly in the ovary and testis, where they serve essential roles in transposon silencing in order to protect the integrity of the genome in the germline. The potential expression of piRNAs in somatic cells has been controversial. In the present study we demonstrate the expression of piRNAs derived from both genic and transposon RNAs in the intersegmental muscles (ISMs) from the tobacco hawkmoth Manduca sexta. These piRNAs are abundantly expressed, ∼27 nt long, map antisense to transposons, are oxidation resistant, exhibit a 5’ uridine bias, and amplify via the canonical ping-pong pathway. An RNA-seq analysis demonstrated that 19 piRNA pathway genes are expressed in the ISMs and are developmentally regulated. The abundance of piRNAs does not change when the muscles initiate developmentally-regulated atrophy, but are repressed coincident with the commitment of the muscles undergo programmed cell death at the end of metamorphosis. This change in piRNA expression is correlated with the repression of several retrotransposons and the induction of specific DNA transposons. The developmentally-regulated changes in the expression of piRNAs, piRNA pathway genes, and transposons are all regulated by 20-hydroxyecdysone, the steroid hormone that controls the timing of ISM death. Taken together, these data provide compelling evidence for the existence of piRNA in somatic tissues and suggest that they may play roles in developmental processes such as programmed cell death.

scholarly journals Differential Response of Grapevine to Infection with ‘Candidatus Phytoplasma solani’ in Early and Late Growing Season Through Complex Regulation of mRNA and Small RNA Transcriptomes

2021 ◽  
Vol 22 (7) ◽  
pp. 3531
Author(s):  
Marina Dermastia ◽  
Blaž Škrlj ◽  
Rebeka Strah ◽  
Barbara Anžič ◽  
Špela Tomaž ◽  
...  
Keyword(s):  
Small Rnas ◽  
Interaction Network ◽  
Growing Season ◽  
Transcriptional Level ◽  
Rna Seq ◽  
Bois Noir ◽  
Growing Seasons ◽  
New Genes ◽  
Causal Pathogen

Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA-Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grapevines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed several new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma pathogenicity previously. These novel actors may present a new reference framework for research and diagnostics of phytoplasma diseases of grapevine.

scholarly journals Maternal RNA-directed DNA methylation is required for seed development in Brassica rapa

2017 ◽  
Author(s):  
Jeffrey W. Grover ◽  
Timmy Kendall ◽  
Abdul Baten ◽  
Graham J. King ◽  
Rebecca A. Mosher
Keyword(s):  
Dna Methylation ◽  
Brassica Rapa ◽  
Small Rna ◽  
Small Rnas ◽  
Parental Influence ◽  
Genome Integrity ◽  
Accessory Cells ◽  
Somatic Tissues ◽  
Common Strategy

AbstractSome organisms deploy small RNAs from accessory cells to maintain genome integrity in the zygote, a mechanism that has been proposed but not demonstrated in plants. Here we show that maternal mutations in the Pol IV-dependent small RNA pathway cause abortion of developing seeds in Brassica rapa. Surprisingly, small RNA production is required in maternal somatic tissues, but not in maternal gametes or the developing zygote. We propose that parental influence over zygotic genomes is a common strategy in eukaryotes and that outbreeding species such as B. rapa are key to understanding the role of small RNAs during reproduction.

scholarly journals Key role of piRNAs in telomeric chromatin maintenance and telomere nuclear positioning in Drosophila germline

2017 ◽  
Author(s):  
Elizaveta Radion ◽  
Valeriya Morgunova ◽  
Sergei Ryazansky ◽  
Natalia Akulenko ◽  
Sergey Lavrov ◽  
...  
Keyword(s):  
Small Rnas ◽  
Telomere Dysfunction ◽  
Specific Mechanism ◽  
Telomere Elongation ◽  
Histone 3 ◽  
Telomere Function ◽  
Telomere Homeostasis ◽  
End Capping ◽  
Pirna Pathway

AbstractTelomeric small RNAs related to PIWI-interacting RNAs (piRNAs) were discovered in different species, however, their role in germline-specific telomere function remains poorly understood. Using a Drosophila model, we show that the piRNA pathway provides a strong germline-specific mechanism of telomere homeostasis. We show that telomeric retrotransposon arrays belong to a unique class of dual-strand piRNA clusters whose transcripts, required for telomere elongation, serve simultaneously as piRNA precursors and their only targets. However, the ability to produce piRNAs and bind Rhino – a germline-specific homolog of heterochromatic protein 1 (HP1) – varies along telomeres. Most likely, this heterogeneity is determined by the peculiarities of telomeric retrotransposons themselves. piRNAs play a pivotal role in the establishment and maintenance of telomeric and subtelomeric chromatin in the germline facilitating loading of HP1 and histone 3 lysine 9 trimethylation mark – highly conservative telomere components – at different telomeric regions. piRNA pathway disruption results in telomere dysfunction characterized by a loss of heterochromatic components and translocation of telomeres from the periphery to the nuclear interior but does not affect the telomere end capping.

scholarly journals piRNAs mediate posttranscriptional retroelement silencing and localization to pi-bodies in the Drosophila germline

2009 ◽  
Vol 186 (3) ◽  
pp. 333-342 ◽  
Author(s):  
Ai Khim Lim ◽  
Liheng Tao ◽  
Toshie Kai
Keyword(s):  
Drosophila Melanogaster ◽  
Messenger Rna ◽  
Mrna Degradation ◽  
Full Length ◽  
Processing Bodies ◽  
Present Evidence ◽  
Maternal Expression ◽  
Germline Cells ◽  
Pirna Pathway

Nuage, a well-conserved perinuclear organelle found in germline cells, is thought to mediate retroelement repression in Drosophila melanogaster by regulating the production of Piwi-interacting RNAs (piRNAs). In this study, we present evidence that the nuage–piRNA pathway components can be found in cytoplasmic foci that also contain retroelement transcripts, antisense piRNAs, and proteins involved in messenger RNA (mRNA) degradation. These mRNA degradation proteins, decapping protein 1/2 (DCP1/2), Me31B (maternal expression at 31B), and pacman (PCM), are normally thought of as components of processing bodies. In spindle-E (spn-E) and aubergine (aub) mutants that lack piRNA production, piRNA pathway proteins no longer overlap the mRNA degradation proteins. Concomitantly, spn-E and aub mutant ovaries show an accumulation of full-length retroelement transcripts and prolonged stabilization of HeT-A mRNA, supporting the role of piRNAs in mediating posttranscriptional retroelement silencing. HeT-A mRNA is derepressed in mRNA degradation mutants twin, dcp1, and ski3, indicating that these enzymes also aid in removing full-length transcripts and/or decay intermediates.

scholarly journals Conserved and Widespread Expression of piRNA-Like Molecules and PIWI-Like Genes Reveal Dual Functions of Transposon Silencing and Gene Regulation in Pinctada fucata (Mollusca)

2021 ◽  
Vol 8 ◽  
Author(s):  
Songqian Huang ◽  
Yuki Ichikawa ◽  
Kazutoshi Yoshitake ◽  
Shigeharu Kinoshita ◽  
Md Asaduzzaman ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Pinctada Fucata ◽  
Locked Nucleic Acid ◽  
Regulatory Function ◽  
Insertion Mutagenesis ◽  
Transposon Silencing ◽  
Somatic Tissues ◽  
Endogenous Genes ◽  
Pirna Pathway

PIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus safeguarding the genome from detrimental insertion mutagenesis. Recent studies revealed additional targets and functions of piRNAs in various animals. piRNAs are ubiquitously expressed in somatic tissues of the pearl oyster Pinctada fucata, however, the role of somatic piRNAs has not well characterized. This study reports the PIWI/piRNA pathway, including piRNA biogenesis and piRNA-mediated transposon silencing, and gene regulation in P. fucata. The biogenesis factors of PIWI, Zucchini, and HEN1, which are ubiquitous in somatic and gonadal tissues, were first identified in P. fucata using transcriptome analysis. Bioinformatics analyses suggested that different populations of piRNAs participate in the ping-pong amplification loop in a tissue-specific manner. In addition, a total of 69 piRNA clusters were identified in the genome of P. fucata based on the expression of piRNAs, which contained 26% transposons and enhanced for DNA/Crypton, LINE/CR1, SINE/Deu, and DNA/Academ. The expression patterns of the piRNAs and piRNA clusters in somatic tissues were not substantially different, but varied significantly between the somatic and gonadal tissues. Furthermore, locked-nucleic-acid modified oligonucleotide (LNA-antagonist) was used to silence single piRNA (piRNA0001) expression in P. fucata. Hundreds of endogenous genes were differentially expressed after piRNA silencing in P. fucata. Target prediction showed that some endogenous genes were targeted by piRNA0001, including twelve upregulated and nine downregulated genes after piRNA0001 silencing. The results indicated that piRNAs from somatic tissues may be related to gene regulation, whereas piRNAs from gonadal tissues are more closely associated to transposon silencing. This study will enhance our understanding of the role of piRNAs in mollusks, transposon silencing, and the regulatory function of the PIWI/piRNA pathway on protein-coding genes outside of germ line cells in P. fucata.

scholarly journals MicroRNAs: Biological Regulators in Pathogen–Host Interactions

Cells ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 113 ◽  
Author(s):  
Stephanie Maia Acuña ◽  
Lucile Maria Floeter-Winter ◽  
Sandra Marcia Muxel
Keyword(s):  
Immune Response ◽  
Infectious Diseases ◽  
Small Rnas ◽  
Immune Cell ◽  
Fine Tuning ◽  
Biological Processes ◽  
Host Interactions ◽  
The Past ◽  
Biological Aspects

An inflammatory response is essential for combating invading pathogens. Several effector components, as well as immune cell populations, are involved in mounting an immune response, thereby destroying pathogenic organisms such as bacteria, fungi, viruses, and parasites. In the past decade, microRNAs (miRNAs), a group of noncoding small RNAs, have emerged as functionally significant regulatory molecules with the significant capability of fine-tuning biological processes. The important role of miRNAs in inflammation and immune responses is highlighted by studies in which the regulation of miRNAs in the host was shown to be related to infectious diseases and associated with the eradication or susceptibility of the infection. Here, we review the biological aspects of microRNAs, focusing on their roles as regulators of gene expression during pathogen–host interactions and their implications in the immune response against Leishmania, Trypanosoma, Toxoplasma, and Plasmodium infectious diseases.

scholarly journals FOXO1 mitigates the SMAD3/FOXL2C134W transcriptomic effect in a model of human adult granulosa cell tumor

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Christian Secchi ◽  
Paola Benaglio ◽  
Francesca Mulas ◽  
Martina Belli ◽  
Dwayne Stupack ◽  
...  
Keyword(s):  
Granulosa Cell ◽  
Chromatin Remodeling ◽  
Granulosa Cell Tumor ◽  
Cell Tumor ◽  
Rna Seq ◽  
Pathogenic Role ◽  
Rare Type ◽  
Cellular Models ◽  
Genome Wide

Abstract Background Adult granulosa cell tumor (aGCT) is a rare type of stromal cell malignant cancer of the ovary characterized by elevated estrogen levels. aGCTs ubiquitously harbor a somatic mutation in FOXL2 gene, Cys134Trp (c.402C < G); however, the general molecular effect of this mutation and its putative pathogenic role in aGCT tumorigenesis is not completely understood. We previously studied the role of FOXL2C134W, its partner SMAD3 and its antagonist FOXO1 in cellular models of aGCT. Methods In this work, seeking more comprehensive profiling of FOXL2C134W transcriptomic effects, we performed an RNA-seq analysis comparing the effect of FOXL2WT/SMAD3 and FOXL2C134W/SMAD3 overexpression in an established human GC line (HGrC1), which is not luteinized, and bears normal alleles of FOXL2. Results Our data shows that FOXL2C134W/SMAD3 overexpression alters the expression of 717 genes. These genes include known and novel FOXL2 targets (TGFB2, SMARCA4, HSPG2, MKI67, NFKBIA) and are enriched for neoplastic pathways (Proteoglycans in Cancer, Chromatin remodeling, Apoptosis, Tissue Morphogenesis, Tyrosine Kinase Receptors). We additionally expressed the FOXL2 antagonistic Forkhead protein, FOXO1. Surprisingly, overexpression of FOXO1 mitigated 40% of the altered genome-wide effects specifically related to FOXL2C134W, suggesting it can be a new target for aGCT treatment. Conclusions Our transcriptomic data provide novel insights into potential genes (FOXO1 regulated) that could be used as biomarkers of efficacy in aGCT patients.

scholarly journals Targeting HSPA1A in ARID2-deficient lung adenocarcinoma

2021 ◽  
Author(s):  
Xue Wang ◽  
Yuetong Wang ◽  
Zhaoyuan Fang ◽  
Hua Wang ◽  
Jian Zhang ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Lung Adenocarcinoma ◽  
Genetically Engineered ◽  
Malignant Progression ◽  
Murine Models ◽  
Rna Seq ◽  
Potential Therapeutic Target ◽  
Lung Cancers ◽  
Integrative Analyses

Abstract Somatic mutations of the chromatin remodeling gene ARID2 are observed in about 7% of human lung adenocarcinoma (LUAD). However, the role of ARID2 in the pathogenesis of LUAD remains largely unknown. Here we find that ARID2 expression is decreased during the malignant progression of both human and mice LUAD. Using two KrasG12D-based genetically engineered murine models (GEMM), we demonstrate that ARID2 knockout significantly promotes lung cancer malignant progression and shortens the overall survival. Consistently, ARID2 knockdown significantly promotes cell proliferation in human and mice lung cancer cells. Through integrative analyses of Chip-Seq and RNA-Seq data, we find that Hspa1a is up-regulated by Arid2 loss. Knockdown of Hspa1a specifically inhibits malignant progression of Arid2-deficient but not Arid2-wt lung cancers in both cell lines as well as animal models. Treatment with Hspa1a inhibitor could significantly inhibit the malignant progression of lung cancer with Arid2 deficiency. Together, our findings establish ARID2 as an important tumor suppressor in LUAD with novel mechanistic insights, and further identify HSPA1A as a potential therapeutic target in ARID2-deficient LUAD.

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