Separable roles for RNAi in regulation of transposable elements and viability in the fission yeast Schizosaccharomyces japonicus

Small Rnas ◽

Transcriptional Level ◽

Genome Maintenance ◽

Repeat Sequences ◽

Heterochromatin Assembly

RNA interference (RNAi) is a conserved mechanism of small RNA-mediated genome regulation commonly involved in suppression of transposable elements (TEs) through both post-transcriptional silencing, and transcriptional repression via heterochromatin assembly. The fission yeast Schizosaccharomyces pombe has been extensively utilised as a model for studying RNAi pathways. However, this species is somewhat atypical in that TEs are not major targets of RNAi, and instead small RNAs correspond primarily to non-coding pericentromeric repeat sequences, reflecting a specialised role for the pathway in promoting heterochromatin assembly in these regions. In contrast, in the related fission yeast Schizosaccharomyces japonicus, sequenced small RNAs correspond primarily to TEs. This suggests there may be fundamental differences in the operation of RNAi pathways in these two related species. To investigate these differences, we probed RNAi function in S. japonicus. Unexpectedly, and in contrast to S. pombe, we found that RNAi is essential in this species. Moreover, viability of RNAi mutants can be rescued by mutations implicated in enhanching RNAi-independent heterochromatin propagation. These rescued strains retain heterochromatic marks on TE sequences, but exhibit derepression of TEs at the post-transcriptional level. Our findings indicate that S. japonicus retains the ancestral role of RNAi in facilitating suppression of TEs via both post-transcriptional silencing and heterochromatin assembly, with specifically the heterochromatin pathway being essential for viability, likely due to a function in genome maintenance. The specialised role of RNAi in heterochromatin assembly in S. pombe appears to be a derived state that emerged after the divergence of S. japonicus.

A Recombinationally Repressed Region Between mat2 and mat3 Loci Shares Homology to Centromeric Repeats and Regulates Directionality of Mating-Type Switching in Fission Yeast

Genetics ◽

10.1093/genetics/146.4.1221 ◽

1997 ◽

Vol 146 (4) ◽

pp. 1221-1238 ◽

Cited By ~ 12

Author(s):

Shiv I S Grewal ◽

Amar J S Klar

Keyword(s):

Fission Yeast ◽

Mating Type ◽

Sequencing Analysis ◽

Cell Type ◽

Cloning And Sequencing ◽

Type Region ◽

Repeat Sequences ◽

Mating Type Switching ◽

Cell Type Specific

Cells of the fission yeast Schizosaccharomyces pombe switch mating type by replacing genetic information at the transcriptionally active mat1 locus with sequences copied from one of two closely linked silent loci, mat2-P or mat3-M. By a process referred to as directionality of switching, cells predominantly switch to the opposite mat1 allele; the mat1-P allele preferentially recombines with mat3, while mat1-M selects the mat2. In contrast to efficient recombination at mat1, recombination within the adjoining mat2-mat3 interval is undetectable. We defined the role of sequences between mat2 and mat3, designated the K-region, in directionality as well as recombinational suppression. Cloning and sequencing analysis revealed that a part of the K-region is homologous to repeat sequences present at centromeres, which also display transcriptional and recombinational suppression. Replacement of 7.5 kb of the K-region with the ura4 + gene affected directionality in a variegated manner. Analysis of the swi6-mod locus, which was previously shown to affect directionality, in KΔ::ura4 + strains suggested the existence of at least two overlapping directionality mechanisms. Our work furthers the model that directionality is regulated by cell-type-specific organization of the heterochromatin-like structure in the mating-type region and provides evidence that the K-region contributes to silencing of the mat2-mat3 interval.

The functional role of microRNAs in laryngeal carcinoma

Open Life Sciences ◽

10.1515/biol-2017-0054 ◽

2017 ◽

Vol 12 (1) ◽

pp. 460-464

Author(s):

Jinzhang Cheng ◽

Junjun Chen ◽

Zonggui Wang ◽

Dan Yu ◽

Yuanzhang Zu

Keyword(s):

Laryngeal Cancer ◽

Cancer Diagnosis ◽

Small Rnas ◽

Tumor Suppressor Genes ◽

Functional Role ◽

Recent Progress ◽

Transcriptional Level ◽

Diagnosis And Prognosis ◽

Potential Use

AbstractMicroRNAs are a class of non-coding, small RNAs, which modulate gene expression at the post-transcriptional level. Numerous studies have showed microRNAs are involved in the pathogenesis of laryngeal cancer through regulating tumor-related genes such as oncogenes or tumor suppressor genes. In this review, we summarize recent progress on the function of microRNAs in laryngeal cancer. We focus on potential use of microRNAs in laryngeal cancer diagnosis and prognosis.

A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses

PeerJ ◽

10.7717/peerj.6080 ◽

2019 ◽

Vol 7 ◽

pp. e6080

Author(s):

Clicia Grativol ◽

Flavia Thiebaut ◽

Sara Sangi ◽

Patricia Montessoro ◽

Walaci da Silva Santos ◽

...

Keyword(s):

Transposable Elements ◽

Transposable Element ◽

Small Rna ◽

Genome Assembly ◽

Inverted Repeat ◽

Small Rnas ◽

Distribution Patterns ◽

Plant Genomes ◽

Sugarcane Genome

Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.

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

International Journal of Molecular Sciences ◽

10.3390/ijms22073531 ◽

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.

Post-transcriptional regulation of several biological processes involved in latex production in Hevea brasiliensis

PeerJ ◽

10.7717/peerj.8932 ◽

2020 ◽

Vol 8 ◽

pp. e8932 ◽

Cited By ~ 1

Author(s):

Julie Leclercq ◽

Shuangyang Wu ◽

Benoît Farinas ◽

Stéphanie Pointet ◽

Bénédicte Favreau ◽

...

Keyword(s):

Transcriptional Regulation ◽

Small Rna ◽

Small Rnas ◽

Gene Families ◽

Transcriptional Level ◽

Rubber Biosynthesis ◽

Transcript Cleavage ◽

Post Transcriptional Regulation ◽

Latex Production

Background Small RNAs modulate plant gene expression at both the transcriptional and post-transcriptional level, mostly through the induction of either targeted DNA methylation or transcript cleavage, respectively. Small RNA networks are involved in specific plant developmental processes, in signaling pathways triggered by various abiotic stresses and in interactions between the plant and viral and non-viral pathogens. They are also involved in silencing maintenance of transposable elements and endogenous viral elements. Alteration in small RNA production in response to various environmental stresses can affect all the above-mentioned processes. In rubber trees, changes observed in small RNA populations in response to trees affected by tapping panel dryness, in comparison to healthy ones, suggest a shift from a transcriptional to a post-transcriptional regulatory pathway. This is the first attempt to characterise small RNAs involved in post-transcriptional silencing and their target transcripts in Hevea. Methods Genes producing microRNAs (MIR genes) and loci producing trans-activated small interfering RNA (ta-siRNA) were identified in the clone PB 260 re-sequenced genome. Degradome libraries were constructed with a pool of total RNA from six different Hevea tissues in stressed and non-stressed plants. The analysis of cleaved RNA data, associated with genomics and transcriptomics data, led to the identification of transcripts that are affected by 20–22 nt small RNA-mediated post-transcriptional regulation. A detailed analysis was carried out on gene families related to latex production and in response to growth regulators. Results Compared to other tissues, latex cells had a higher proportion of transcript cleavage activity mediated by miRNAs and ta-siRNAs. Post-transcriptional regulation was also observed at each step of the natural rubber biosynthesis pathway. Among the genes involved in the miRNA biogenesis pathway, our analyses showed that all of them are expressed in latex. Using phylogenetic analyses, we show that both the Argonaute and Dicer-like gene families recently underwent expansion. Overall, our study underlines the fact that important biological pathways, including hormonal signalling and rubber biosynthesis, are subject to post-transcriptional silencing in laticifers.

Clr4SUV39H1 and Bdf2BRD4 ubiquitination mediate transcriptional silencing via heterochromatic phase transitions

10.1101/2021.01.08.425919 ◽

2021 ◽

Author(s):

Hyun-Soo Kim ◽

Benjamin Roche ◽

Sonali Bhattacharjee ◽

Leila Todeschini ◽

An-Yun Chang ◽

...

Keyword(s):

Small Rnas ◽

Genome Stability ◽

Centromeric Heterochromatin ◽

Deubiquitinating Enzyme ◽

Dynamic Activity ◽

Intrinsically Disordered ◽

Ubiquitin Conjugating Enzyme ◽

Liquid Liquid Phase Separation

Heterochromatin has crucial roles in genome stability by silencing repetitive DNA and by suppressing recombination. In the fission yeast Schizosaccharomyces pombe, Clr4 methylates histone H3 lysine 9 (H3K9) to maintain centromeric heterochromatin during the cell cycle, guided by RNA interference (RNAi). Clr4 interacts with a specialized ubiquitination complex CLRC, which is recruited in part by small RNA and the RNAi transcriptional silencing complex (RITS) but otherwise, the role of CLRC is unknown. Here we show that the E2 ubiquitin conjugating enzyme Ubc4 interacts with CLRC and targets Clr4 for mono-ubiquitination at an intrinsically disordered region. Mono-ubiquitination is essential for the transition from co-transcriptional (H3K9me2) to transcriptional (H3K9me3) gene silencing by transiently releasing Clr4 from centromeric heterochromatin, and is reversed by the deubiquitinating enzyme Ubp3. Addition of ubiquitin changes the liquid-liquid phase separation (LLPS) of Clr4 to enhance its dynamic activity. Ubc4-CLRC also poly-ubiquitinates Bdf2, the homologue of BET family double bromodomain protein BRD4 for degradation, which otherwise accumulates at centromeres to promote transcription and production of small RNAs.

Mkt1 is required for RNAi-mediated silencing and establishment of heterochromatin in fission yeast

Nucleic Acids Research ◽

10.1093/nar/gkz1157 ◽

2019 ◽

Vol 48 (3) ◽

pp. 1239-1253 ◽

Cited By ~ 2

Author(s):

Francesca Taglini ◽

Elliott Chapman ◽

Rob van Nues ◽

Emmanuelle Theron ◽

Elizabeth H Bayne

Keyword(s):

Fission Yeast ◽

Histone Methylation ◽

Small Rnas ◽

De Novo ◽

Yeast Genome ◽

Regulatory Factor ◽

Transcriptional Regulatory ◽

Non Coding Rnas ◽

Insight Into

Abstract Constitutive domains of repressive heterochromatin are maintained within the fission yeast genome through self-reinforcing mechanisms involving histone methylation and small RNAs. Non-coding RNAs generated from heterochromatic regions are processed into small RNAs by the RNA interference pathway, and are subject to silencing through both transcriptional and post-transcriptional mechanisms. While the pathways involved in maintenance of the repressive heterochromatin state are reasonably well understood, less is known about the requirements for its establishment. Here, we describe a novel role for the post-transcriptional regulatory factor Mkt1 in establishment of heterochromatin at pericentromeres in fission yeast. Loss of Mkt1 does not affect maintenance of existing heterochromatin, but does affect its recovery following depletion, as well as de novo establishment of heterochromatin on a mini-chromosome. Pathway dissection revealed that Mkt1 is required for RNAi-mediated post-transcriptional silencing, downstream of small RNA production. Mkt1 physically associates with pericentromeric transcripts, and is additionally required for maintenance of silencing and heterochromatin at centromeres when transcriptional silencing is impaired. Our findings provide new insight into the mechanism of RNAi-mediated post-transcriptional silencing in fission yeast, and unveil an important role for post-transcriptional silencing in establishment of heterochromatin that is dispensable when full transcriptional silencing is imposed.

H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

Genome Biology ◽

10.1186/s13059-021-02476-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Shujing Liu ◽

Minerva S. Trejo-Arellano ◽

Yichun Qiu ◽

D. Magnus Eklund ◽

Claudia Köhler ◽

...

Keyword(s):

Gene Regulation ◽

Transposable Elements ◽

Point Mutations ◽

Marchantia Polymorpha ◽

Transcriptional Level ◽

Polycomb Repressive Complex ◽

Direct Role ◽

Chromatin Regulators ◽

Polycomb Repressive Complex 1

Abstract Background Polycomb repressive complex 1 (PRC1) and PRC2 are chromatin regulators maintaining transcriptional repression. The deposition of H3 lysine 27 tri-methylation (H3K27me3) by PRC2 is known to be required for transcriptional repression, whereas the contribution of H2A ubiquitination (H2Aub) in the Polycomb repressive system remains unclear in plants. Results We directly test the requirement of H2Aub for gene regulation in Marchantia polymorpha by generating point mutations in H2A that prevent ubiquitination by PRC1. These mutants show reduced H3K27me3 levels on the same target sites as mutants defective in PRC1 subunits MpBMI1 and the homolog MpBMI1L, revealing that PRC1-catalyzed H2Aub is essential for Polycomb system function. Furthermore, by comparing transcriptome data between mutants in MpH2A and MpBMI1/1L, we demonstrate that H2Aub contributes to the PRC1-mediated transcriptional level of genes and transposable elements. Conclusion Together, our data demonstrates that H2Aub plays a direct role in H3K27me3 deposition and is required for PRC1-mediated transcriptional changes in both genes and transposable elements in Marchantia.

Intracellular 2-keto-3-deoxy-6-phosphogluconate is the signal for carbon catabolite repression of phenylacetic acid metabolism in Pseudomonas putida KT2440

Microbiology ◽

10.1099/mic.0.027060-0 ◽

2009 ◽

Vol 155 (7) ◽

pp. 2420-2428 ◽

Cited By ~ 13

Author(s):

Juhyun Kim ◽

Jinki Yeom ◽

Che Ok Jeon ◽

Woojun Park

Keyword(s):

Pseudomonas Putida ◽

Catabolite Repression ◽

Phenylacetic Acid ◽

Carbon Catabolite Repression ◽

Transcriptional Level ◽

Pseudomonas Putida Kt2440 ◽

Coa Ligase ◽

Additional Support

The growth pattern of Pseudomonas putida KT2440 in the presence of glucose and phenylacetic acid (PAA), where the sugar is used in preference to the aromatic compound, suggests that there is carbon catabolite repression (CCR) of PAA metabolism by glucose or gluconate. Furthermore, CCR is regulated at the transcriptional level. However, this CCR phenomenon does not occur in PAA-amended minimal medium containing fructose, pyruvate or succinate. We previously identified 2-keto-3-deoxy-6-phosphogluconate (KDPG) as an inducer of glucose metabolism, and this has led to this investigation into the role of KDPG as a signal compound for CCR. Two mutant strains, the edd mutant (non-KDPG producer) and the eda mutant (KDPG overproducer), grew in the presence of PAA but not in the presence of glucose. The edd mutant utilized PAA even in the presence of glucose, indicating that CCR had been abolished. This observation has additional support from the finding that there is high phenylacetyl-CoA ligase activity in the edd mutant, even in the presence of glucose+PAA, but not in wild-type cells under the same conditions. Unlike the edd mutant, the eda mutant did not grow in the presence of glucose+PAA. Interestingly, there was no uptake and/or metabolism of PAA in the eda mutant cells under the same conditions. Targeted disruption of PaaX, a repressor of the PAA operon, had no effect on CCR of PAA metabolism in the presence of glucose, suggesting that there is another transcriptional repression system associated with the KDPG signal. This is the first study to demonstrate that KDPG is the true CCR signal of PAA metabolism in P. putida KT2440.

The SAGA Subunit Ada2 Functions in Transcriptional Silencing

Molecular and Cellular Biology ◽

10.1128/mcb.00542-09 ◽

2009 ◽

Vol 29 (22) ◽

pp. 6033-6045 ◽

Cited By ~ 20

Author(s):

Sandra Jacobson ◽

Lorraine Pillus

Keyword(s):

Histone Acetyltransferase ◽

Environmental Changes ◽

Histone H4 ◽

Nutrient Signaling ◽

Subtelomeric Regions ◽

Inducible Gene

ABSTRACT The cellular role of the Ada2 coactivator is currently understood in the context of the SAGA histone acetyltransferase (HAT) complex, where Ada2 increases the HAT activity of Gcn5 and interacts with transcriptional activators. Here we report a new function for Ada2 in promoting transcriptional silencing at telomeres and ribosomal DNA. This silencing function is the first characterized role for Ada2 distinct from its involvement with Gcn5. Ada2 binds telomeric chromatin and the silencing protein Sir2 in vivo. Loss of ADA2 causes the spreading of Sir2 and Sir3 into subtelomeric regions and decreased histone H4 K16 acetylation. This previously uncharacterized boundary activity of Ada2 is functionally similar to, but mechanistically distinct from, that of the MYST family HAT Sas2. Mounting evidence in the literature indicates that boundary activities create chromosomal domains important for regulating gene expression in response to environmental changes. Consistent with this, we show that upon nutritional changes, Ada2 occupancy increases at a subtelomeric region proximal to a SAGA-inducible gene and causes derepression of a silenced telomeric reporter gene. Thus, Ada2, likely in the context of SAGA, is positioned at chromosomal termini to participate in both transcriptional repression and activation in response to nutrient signaling.