Argonaute Research Articles

Arabidopsis AGO1 N-terminal extension acts as an essential hub for PRMT5 interaction and post-translational modifications.

Plant ARGONAUTE (AGO) proteins play pivotal roles regulating gene expression through smallRNA(sRNA)-guided mechanisms. Among the 10AGO proteins in Arabidopsis thaliana, AGO1 stands out as the main effector of post-transcriptional gene silencing. Intriguingly, a specific region of AGO1, its N-terminal extension (NTE), has garnered attention in recent studies due to its involvement in diverse regulatory functions, including subcellular localization, sRNA loadingand interactions with regulatory factors. In the field of post-translational modifications (PTMs), little is known about arginine methylation in Arabidopsis AGOs. In this study, we show that NTE of AGO1 (NTEAGO1) undergoes symmetric arginine dimethylation at specific residues. Moreover, NTEAGO1 interacts with the methyltransferase PRMT5, which catalyzes its methylation. Notably, we observed that the lack of symmetric dimethylarginine has no discernible impact on AGO1's subcellular localization or miRNA loading capabilities. However, the absence of PRMT5 significantly alters the loading of a subgroup of sRNAs into AGO1 and reshapes the NTEAGO1 interactome. Importantly, our research shows that symmetric arginine dimethylation of NTEs is a common process among Arabidopsis AGOs, with AGO1, AGO2, AGO3and AGO5 undergoing thisPTM. Overall, this work deepens our understanding of PTMs in the intricate landscape of RNA-associated gene regulation.

A role for the C. elegans Argonaute protein CSR-1 in small nuclear RNA 3' processing.

The Integrator is a multi-subunit protein complex that catalyzes the maturation of snRNA transcripts via 3' cleavage, a step required for snRNA incorporation with snRNP for spliceosome biogenesis. Here we developed a GFP based in vivo snRNA misprocessing reporter as a readout of Integrator function and performed a genome-wide RNAi screen for Integrator regulators. We found that loss of the Argonaute encoding csr-1 gene resulted in widespread 3' misprocessing of snRNA transcripts that is accompanied by a significant increase in alternative splicing. Loss of the csr-1 gene down-regulates the germline expression of Integrator subunits 4 and 6 and is accompanied by a reduced protein translation efficiency of multiple Integrator catalytic and non-catalytic subunits. Through isoform and motif mutant analysis, we determined that CSR-1's effect on snRNA processing is dependent on its catalytic slicer activity but does not involve the CSR-1a isoform. Moreover, mRNA-sequencing revealed high similarity in the transcriptome profile between csr-1 and Integrator subunit knockdown via RNAi. Together, our findings reveal CSR-1 as a new regulator of the Integrator complex and implicate a novel role of this Argonaute protein in snRNA 3' processing.

Phyllostachys edulis argonaute genes function in the shoot architecture

Argonaute (AGO) proteins are the core components of the RNA-induced silencing complexes (RISC) in the cytoplasm and nucleus, and are necessary for the development of plant shoot meristem, which gives rise to the above-ground plant body. In this study, we identified 23 Phyllostachys edulis AGO genes (PhAGOs) that were distributed unequally on the 14 unmapped scaffolds. Gene collinearity and phylogeny analysis showed that the innovation of PhAGO genes was mainly due to dispersed duplication and whole-genome duplication, which resulted in the enlarged PhAGO family. PhAGO genes were expressed in a temporal-spatial expression pattern, and they encoded proteins differently localized in the cytoplasm and/or nucleus. Overexpression of the PhAGO2 and PhAGO4 genes increased the number of tillers or leaves in Oryza sativa and affected the shoot architecture of Arabidopsis thaliana. These results provided insight into the fact that PhAGO genes play important roles in plant development.

Polycomb proteins RING1A/B promote H2A monoubiquitination to regulate female gametophyte development in Arabidopsis.

A functional female gametophyte is the basis of successful sexual reproduction in flowering plants. During female gametophyte development, the megaspore mother cell (MMC), which differentiates from a single subepidermal somatic cell in the nucellus, undergoes meiosis to produce four megaspores; only the one at the chalazal end, referred to as the functional megaspore (FM), then undergoes three rounds of mitosis and develops into a mature embryo sac. Here, we report that RING1A and RING1B (RING1A/B), two functionally redundant Polycomb proteins in Arabidopsis, are critical for female gametophyte development. Mutations of RING1A/B resulted in defects in the specification of the MMC and the FM, and in the subsequent mitosis of the FM, thereby leading to aborted ovules. Detailed analysis revealed that several genes essential for female gametophyte development were ectopically expressed in the ring1a ring1b mutant, including Argonaute (AGO) family genes and critical transcription factors. Furthermore, RING1A/B bound to some of these genes to promote H2A monoubiquitination (H2Aub). Taken together, our study shows that RING1A/B promote H2Aub modification at key genes for female gametophyte development, suppressing their expression to ensure that the development progresses correctly.

Unveiling microRNA-like small RNAs implicated in the initial infection of Fusarium oxysporum f. sp. cubense through small RNA sequencing

ABSTRACT Banana Fusarium wilt (BFW), caused by Fusarium oxysporum f. sp. cubense (Foc), poses a major challenge to the worldwide banana industry. Fungal microRNA-like small RNAs (milRNAs) play crucial roles in regulating fungal growth, conidiation, development, and pathogenicity. However, the milRNAs and their functions in the pathogenesis of Foc remain poorly understood. In this study, we employed high-throughput sequencing and bioinformatics to profile Foc sRNAs during both pure culture and early infection stages. Our analysis identified six milRNAs exhibiting significantly upregulated expression at the initial Foc infection. Of these, milR106’s biogenesis was found to be Dicer-dependent, whereas milR87, milR133, milR138, and milR148 were associated with Dicer and Argonaute proteins. Genetic manipulation and phenotype analysis confirmed that milR106 is crucial for Foc virulence by regulating conidiation, hydrogen peroxide sensitivity, and infective growth. Gene Ontology analysis of milRNA targets in the banana genome revealed enrichment in defence response to fungus and cellular response to hypoxia, implying the importance of these target genes in response to pathogen infection. In conclusion, our sRNA profiling of Foc identified several infection-induced milRNAs. The corresponding results provide valuable molecular targets for the development of an efficient strategy to control BFW.

Mime-seq 2.0: a method to sequence microRNAs from specific mouse cell types

Many microRNAs (miRNAs) are expressed with high spatiotemporal specificity during organismal development, with some being limited to rare cell types, often embedded in complex tissues. Yet, most miRNA profiling efforts remain at the tissue and organ levels. To overcome challenges in accessing the microRNomes from tissue-embedded cells, we had previously developed mime-seq (miRNome by methylation-dependent sequencing), a technique in which cell-specific miRNA methylation in C. elegans and Drosophila enabled chemo-selective sequencing without the need for cell sorting or biochemical purification. Here, we present mime-seq 2.0 for profiling miRNAs from specific mouse cell types. We engineered a chimeric RNA methyltransferase that is tethered to Argonaute protein and efficiently methylates miRNAs at their 3′-terminal 2′-OH in mouse and human cell lines. We also generated a transgenic mouse for conditional expression of this methyltransferase, which can be used to direct methylation of miRNAs in a cell type of choice. We validated the use of this mouse model by profiling miRNAs from B cells and bone marrow plasma cells.

Investigating the Interactions of the Cucumber Mosaic Virus 2b Protein with the Viral 1a Replicase Component and the Cellular RNA Silencing Factor Argonaute 1.

The cucumber mosaic virus (CMV) 2b protein is a suppressor of plant defenses and a pathogenicity determinant. Amongst the 2b protein's host targets is the RNA silencing factor Argonaute 1 (AGO1), which it binds to and inhibits. In Arabidopsis thaliana, if 2b-induced inhibition of AGO1 is too efficient, it induces reinforcement of antiviral silencing by AGO2 and triggers increased resistance against aphids, CMV's insect vectors. These effects would be deleterious to CMV replication and transmission, respectively, but are moderated by the CMV 1a protein, which sequesters sufficient 2b protein molecules into P-bodies to prevent excessive inhibition of AGO1. Mutant 2b protein variants were generated, and red and green fluorescent protein fusions were used to investigate subcellular colocalization with AGO1 and the 1a protein. The effects of mutations on complex formation with the 1a protein and AGO1 were investigated using bimolecular fluorescence complementation and co-immunoprecipitation assays. Although we found that residues 56-60 influenced the 2b protein's interactions with the 1a protein and AGO1, it appears unlikely that any single residue or sequence domain is solely responsible. In silico predictions of intrinsic disorder within the 2b protein secondary structure were supported by circular dichroism (CD) but not by nuclear magnetic resonance (NMR) spectroscopy. Intrinsic disorder provides a plausible model to explain the 2b protein's ability to interact with AGO1, the 1a protein, and other factors. However, the reasons for the conflicting conclusions provided by CD and NMR must first be resolved.

Achieving large negative electrocaloric effect in AgNbO3-based antiferroelectric ceramics based on dipole disordering

The electrocaloric effect (ECE) is considered as an environmentally friendly refrigeration technology, which can be used to replace vapor compression refrigeration. Lead-free antiferroelectric (AFE) ceramics are promising electrocaloric materials because of large saturation polarization and polarization change with temperature, which can generate large positive or negative ECE. In this work, the lead-free Ag(Nb1-0.8xHfx)O3 (x = 0, 0.001 and 0.003) AFE ceramics are fabricated through a conventional solid-state reaction method which shows a decreased the phase transition temperature of M1 - M2 toward room temperature (RT), and a large negative ECE (ΔT = −2.3 K under 130 kV cm−1) is obtained near the ambient temperature by using an indirect measurement in ANH0.001 AFE ceramic. The large negative ECE behavior is ascribed to dipole disordering (i.e. the anti-parallel dipoles are broken and gradually becomes disordered under an external electric field) resulting from the field-induced phase transition under a modest electric field. This work shows that AgNbO3-based AFE ceramics could be used in the refrigeration devices as an electrocaloric material.

Mammalian PIWI-piRNA-target complexes reveal features for broad and efficient target silencing.

The PIWI-interacting RNA (piRNA) pathway is an adaptive defense system wherein piRNAs guide PIWI family Argonaute proteins to recognize and silence ever-evolving selfish genetic elements and ensure genome integrity. Driven by this intensive host-pathogen arms race, the piRNA pathway and its targeted transposons have coevolved rapidly in a species-specific manner, but how the piRNA pathway adapts specifically to target silencing in mammals remains elusive. Here, we show that mouse MILI and human HILI piRNA-induced silencing complexes (piRISCs) bind and cleave targets more efficiently than their invertebrate counterparts from the sponge Ephydatia fluviatilis. The inherent functional differences comport with structural features identified by cryo-EM studies of piRISCs. In the absence of target, MILI and HILI piRISCs adopt a wider nucleic-acid-binding channel and display an extended prearranged piRNA seed as compared with EfPiwi piRISC, consistent with their ability to capture targets more efficiently than EfPiwi piRISC. In the presence of target, the seed gate-which enforces seed-target fidelity in microRNA RISC-adopts a relaxed state in mammalian piRISC, revealing how MILI and HILI tolerate seed-target mismatches to broaden the target spectrum. A vertebrate-specific lysine distorts the piRNA seed, shifting the trajectory of the piRNA-target duplex out of the central cleft and toward the PAZ lobe. Functional analyses reveal that this lysine promotes target binding and cleavage. Our study therefore provides a molecular basis for the piRNA targeting mechanism in mice and humans, and suggests that mammalian piRNA machinery can achieve broad target silencing using a limited supply of piRNA species.

High energy density in Ag0.5Na0.5(Nb1-xTax)O3 antiferroelectric ceramics

There has been significant interest in AgNbO3-based antiferroelectric ceramics, recently, due to their ability to achieve high energy storage density (Wrec). However, fabricating their commercial products faces challenges due to chemically unstable and expensive Ag2O. To reduce Ag2O contents, we fabricated (Ag0.5Na0.5)(Nb1-xTax)O3 (ANNT100x) ceramics. The results reveal that Ta-substitution plays a dual role: inducing chemical pressure to compress the unit cell along spontaneous polarization direction, enhancing antiferroelectric stability; and increasing the band gap (Eg), boosting intrinsic breakdown strength (Eb). These crucial factors contribute to the enhanced Wrec achieved in ANNT50. Notably, ANNT50 ceramics fabricated by the rolling process exhibit higher Eb (=578 kV/cm) than the conventional process, favoring the complete triggering of “double” polarization with significantly enhanced Wrec (= 6.5 J/cm3). Discharge results indicate that the ceramic displays high power density (Pavg = 78 MW/cm3) and discharge energy (Wdis = 5.86 J/cm3), which can rival currently reported Ag(Nb, Ta)O3 ceramics.

Genome-wide identification and expression analyses of the Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in onion (Allium cepa L.)

ABSTRACT RNA silencing is a highly conserved gene expression regulatory mechanism participating in plant development and stress responses. Dicer-like protein (DCL), Argonaute protein (AGO) and RNA-dependent RNA polymerase (RDR) are directly involved in RNA silencing. So far, the characterisation and expression analysis of RDR, AGO and DCL proteins have not been performed in onion. A genome-wide analysis identified eight AcAGO, four AcDCL and four AcRDR putative genes in onion. Their cis-acting elements were investigated. The transcript levels of genes in different onion tissues and response to abiotic stress were studied. The results demonstrated that AcAGOs, AcDCLs and AcRDRs showed various tissue expression patterns. AcAGO2 and AcAGO4b were highly expressed in onion bulbs. AcDCLs and AcRDRs showed the highest transcript levels in inflorescence. AcAGO1, AcAGO5 and AcDCL1 were constitutively expressed in leaf and bulb during onion bulb expansion. AcRDR1 and AcRDR6 were upregulated during bulb expansion. AcAGOs were upregulated with salinity treatment, whereas AcDCLs and AcRDRs showed different expression patterns in abiotic stress response. Our results provided a basis for further clarification of RNA silencing-mediated environment stimulation response and development in onion.

The clade-specific target recognition mechanisms of plant RISCs.

Eukaryotic Argonaut proteins (AGOs) assemble RNA-induced silencing complexes (RISCs) with guide RNAs that allow binding to complementary RNA sequences and subsequent silencing of target genes. The model plant Arabidopsis thaliana encodes 10 different AGOs, categorized into three distinct clades based on amino acid sequence similarity. While clade 1 and 2 RISCs are known for their roles in post-transcriptional gene silencing, and clade 3 RISCs are associated with transcriptional gene silencing in the nucleus, the specific mechanisms of how RISCs from each clade recognize their targets remain unclear. In this study, I conducted quantitative binding analyses between RISCs and target nucleic acids with mismatches at various positions, unveiling distinct target binding characteristics unique to each clade. Clade 1 and 2 RISCs require base pairing not only in the seed region but also in the 3' supplementary region for stable target RNA binding, with clade 1 exhibiting a higher stringency. Conversely, clade 3 RISCs tolerate dinucleotide mismatches beyond the seed region. Strikingly, they bind to DNA targets with an affinity equal to or surpassing that of RNA, like prokaryotic AGO complexes. These insights challenge existing views on plant RNA silencing and open avenues for exploring new functions of eukaryotic AGOs.

Identification of an active RNAi pathway in Candida albicans

RNA interference (RNAi) is a fundamental regulatory pathway with a wide range of functions, including regulation of gene expression and maintenance of genome stability. Although RNAi is widespread in the fungal kingdom, well-known species, such as the model yeast Saccharomyces cerevisiae, have lost the RNAi pathway. Until now evidence has been lacking for a fully functional RNAi pathway in Candida albicans, a human fungal pathogen considered critically important by the World Health Organization. Here, we demonstrated that the widely used C. albicans reference strain (SC5314) contains an inactivating missense mutation in the gene encoding for the central RNAi component Argonaute. In contrast, most other C. albicans isolates contain a canonical Argonaute protein predicted to be functional and RNAi-active. Indeed, using high-throughput small and long RNA sequencing combined with seamless CRISPR/Cas9-based gene editing, we demonstrate that an active C. albicans RNAi machinery represses expression of subtelomeric gene families. Thus, an intact and functional RNAi pathway exists in C. albicans, highlighting the importance of using multiple reference strains when studying this dangerous pathogen.

Interaction between a J-domain co-chaperone and a specific Argonaute protein contributes to microRNA function in animals.

MicroRNAs (miRNAs) are essential regulators of several biological processes. They are loaded onto Argonaute (AGO) proteins to achieve their repressive function, forming the microRNA-Induced Silencing Complex known asmiRISC. While several AGO proteins are expressed in plants and animals, it is still unclear why specific AGOs are strictly binding miRNAs. Here, we identified the co-chaperone DNJ-12 as a new interactor of ALG-1, one of the two major miRNA-specific AGOs in Caenorhabditis elegans. DNJ-12 does not interact with ALG-2, the other major miRNA-specific AGO, and PRG-1 and RDE-1, two AGOs involved in other small RNA pathways, making it a specific actor in ALG-1-dependent miRNA-mediated gene silencing. The loss of DNJ-12 causes developmental defects associated with defective miRNA function. Using the Auxin Inducible Degronsystem, a powerful tool to acutely degrade proteins in specific tissues, we show that DNJ-12 depletion hampers ALG-1 interaction with HSP70, a chaperone required for miRISC loading in vitro. Moreover, DNJ-12 depletion leads to the decrease of several miRNAs and prevents their loading onto ALG-1. This study uncovers the importance of a co-chaperone for the miRNA function in vivo and provides insights to explain how different small RNAs associate with specific AGO in animals.

Functions of RNAi Pathways in Ribosomal RNA Regulation.

Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.

Casein kinase II promotes piRNA production through direct phosphorylation of USTC component TOFU-4

Piwi-interacting RNAs (piRNAs) are genomically encoded small RNAs that engage Piwi Argonaute proteins to direct mRNA surveillance and transposon silencing. Despite advances in understanding piRNA pathways and functions, how the production of piRNA is regulated remains elusive. Here, using a genetic screen, we identify casein kinase II (CK2) as a factor required for piRNA pathway function. We show that CK2 is required for the localization of PRG-1 and for the proper localization of several factors that comprise the ‘upstream sequence transcription complex’ (USTC), which is required for piRNA transcription. Loss of CK2 impairs piRNA levels suggesting that CK2 promotes USTC function. We identify the USTC component twenty-one-U fouled-up 4 (TOFU-4) as a direct substrate for CK2. Our findings suggest that phosphorylation of TOFU-4 by CK2 promotes the assembly of USTC and piRNA transcription. Notably, during the aging process, CK2 activity declines, resulting in the disassembly of USTC, decreased piRNA production, and defects in piRNA-mediated gene silencing, including transposons silencing. These findings highlight the significance of posttranslational modification in regulating piRNA biogenesis and its implications for the aging process. Overall, our study provides compelling evidence for the involvement of a posttranslational modification mechanism in the regulation of piRNA biogenesis.

Abstract 2991: Global analysis of miR-210 and miR-21 dysregulation and direct targeting in thyroid cancer during hypoxia

Abstract Introduction: Hypoxia is frequent in solid tumors and stabilizes Hypoxia Inducible Factor-1 (HIF-1). HIF-1, in turn, activates several cellular pathways that promote tumor growth and resistance to chemotherapy. MicroRNA (miRNA) miR-210 is a direct HIF-1 target. HIF-1 binds to a Hypoxia-Response Element (HRE) in the miR-210 promoter, up-regulating its expression. miR-21 is the most widely reported oncogenic miRNA in cancer. miRNAs complexed with Argonaute-2 (AGO2) bind target mRNAs to inhibit translation. Given that a single miRNA can have hundreds of predicted mRNA targets, we sought to identify mRNA targets of miR-210 and miR-21. Identifying dysregulated target genes of miR-210 and miR-21 may highlight new therapeutic targets. Methods: The SW1736 (anaplastic thyroid cancer) cell line was cultured at 2% (hypoxic) or atmospheric (normoxic) O2 for 24 or 48hrs. HIF-1α accumulation relative to normoxia was analyzed by Western blot. miR-210-3p expression was measured relative to normoxia by RT-qPCR. Small and total RNA-sequencing was performed to identify additional differentially expressed miRNAs and mRNAs in hypoxia after 48hrs. To identify direct miRNA targets, SW1736 cells were cross-linked by UV irradiation after 48hrs of normoxic or hypoxic conditions. AGO2 covalently cross-linked to miRNA and target mRNAs were purified by immunoprecipitation after DNA and RNA digestion. miRNA and target mRNAs protected by AGO2 were ligated to generate chimeric miRNA:mRNA molecules followed by sequencing. miRNA:mRNA chimeras were analyzed using the SCRAP bioinformatic pipeline. Results: miR-210-3p expression was up-regulated by ~11-fold at 24hrs and ~19-fold at 48hrs, which was consistent with increased HIF-1α protein levels assessed by Western blot. miR-210-3p and HIF-1α levels were highest after 48hr of hypoxia relative to normoxia. Small RNA-seq showed that miR-210-3p was the only miRNA significantly up-regulated (>2-fold) in hypoxia (48hr) in SW1736. Further, miRNA:mRNA chimeric sequencing results confirmed that miRNAs primarily interacted with the 3’UTRs and coding sequences of mRNA. miR-210-3p was most abundant in hypoxia and found in chimeras with HIF-1α mRNA as well as some oncogenic and tumor suppressor transcripts involved in metabolism and mRNA processing. miR-21-5p was the most abundant chimera miRNA in both normoxia and hypoxia and was primarily bound to tumor suppressor mRNAs associated with cell cycle arrest, TGFB signaling, and inhibition of tumor invasion and migration. Conclusions: miR-210-3p and miR-21-5p elevated levels and interactions indicate hypoxia and malignancy in solid tumors including breast, thyroid, prostate, and lung. Further analysis of other miRNA:mRNA interactions and functional validation may aid in identifying novel therapies for solid tumors. Citation Format: Bonita H. Powell, William T. Mills, Andrey Turchinovich, Yongchun Wang, Martha A. Zeiger, Christopher B. Umbricht, Mollie K. Meffert, Kenneth W. Witwer. Global analysis of miR-210 and miR-21 dysregulation and direct targeting in thyroid cancer during hypoxia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2991.

Abstract 5973: Targeting prolyl 4-hydroxylase subunit alpha 1 with a small molecule inhibitor, diethyl-pythiDC, reduces pancreatic ductal adenocarcinoma growth and metastasis

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease that has a 5-yearrelative survival rate of less than 9%. It is the fourth leading cause of cancer-associated mortality,and is projected to become the second leading cause of cancer-related deaths by 2030. Since most(~80%) PDACs are diagnosed at late stages (metastasized), there is an urgent need to identifymolecular determinants that regulate PDAC progression and serve as candidates for therapeutictargeting. Prolyl 4-hydroxylase subunit alpha 1 (P4HA1) is the major isoform overexpressed inmost cancers, including PDAC. In PDAC, high expression of P4HA1 is associated with tumorprogression and poor clinical outcomes. Thus, we investigated if targeting P4HA1 in PDAC witha small molecule inhibitor; diethyl-pythiDC, had an inhibitory effect on cell proliferation, tumorprogression/growth, and metastasis. Methods: To demonstrate the therapeutic efficacy of diethyl-pythiDC, we performed MTT, colonyformation, wound healing, Transwell, and western blot assays in various PDAC cell lines. Tumorgrowth and metastasis was evaluated with xenografts in NOD/SCID/IL2γ receptor-null (NSG)mice. Additionally, expression of P4HA1 in human PDAC and in adjacent normal pancreatictissues was assessed. Results: In human PDACs, there was elevated expression of P4HA1 protein relative to adjacentnormal pancreatic tissues. Treatment of various PDAC cells (S2VP10, MIA PaCa2, BxPC-3, andPANC-1) with diethyl-pythiDC reduced cell proliferation and colony formation, and inducedG2/M cell cycle arrest. Diethyl-pythiDC reduced migration and invasion of PDAC cells bymodulating epithelial-mesenchymal transition (EMT) markers (N-cadherin, E-cadherin, andvimentin). In addition, diethyl-pythiDC reduced the expression of argonaute-2 (AGO2), acomponent of microRNA biogenesis implicated in tumorigenesis, and its downstream target,matrix metalloproteinase (MMP1). In preclinical animal models of PDAC, diethyl-pythiDCreduced tumor growth and metastasis. Furthermore, in xenograft tumors, diethyl-pythiDCtreatment reduced the expression of AGO2, MMP1, and the proliferative marker, PCNA, andmodulated proteins of the EMT. Conclusions: Treatment with diethyl-pythiDC reduces PDAC progression by decreasing cellproliferation, arresting cells in the G2/M phase, downregulating AGO2/MMP1 expression, andmodulating the EMT. These findings suggest that targeting P4HA1 by diethyl-pythiDC could be aviable strategy to improve treatment for PDACs, particularly those expressing high levels ofP4HA1. They also provide a basis to conduct clinical trials to assess the utility of targeting P4HA1by diethyl-pythiDC. Citation Format: Farrukh Afaq, Mohd Khushman, Prachi Bajpai, Sameer Al Diffalha, Dennis Otali, Sooryanarayana Varambally, Upender Manne. Targeting prolyl 4-hydroxylase subunit alpha 1 with a small molecule inhibitor, diethyl-pythiDC, reduces pancreatic ductal adenocarcinoma growth and metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5973.

SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway.

RNA-directed DNA methylation (RdDM) is driven by small RNAs (sRNAs) complementary to the nascent transcript of RNA polymerase V (Pol V). sRNAs associated with ARGONAUTE (AGO) proteins are tethered to Pol V mainly by the AGO-hook domain of its subunit NRPE1. We found, by in silico analyses, that Pol V strongly colocalizes on chromatin with another AGO-hook protein, SPT6-like (SPT6L), which is a known essential transcription elongation factor of Pol II. Our phylogenetic analysis revealed that SPT6L acquired its AGO-binding capacity already in the most basal streptophyte algae, even before the emergence of Pol V, suggesting that SPT6L might be a driving force behind the RdDM evolution. Since its emergence, SPT6L with the AGO-hook represents the only conserved SPT6 homolog in Viridiplantae, implying that the same protein is involved in both Pol II and Pol V complexes. To better understand the role of SPT6L in the Pol V complex, we characterized genomic loci where these two colocalize and uncovered that DNA methylation there is more dynamic, driven by higher levels of sRNAs often from non-canonical RdDM pathways and more dependent on chromatin modifying and remodeling proteins like MORC. Pol V loci with SPT6L are highly depleted in helitrons but enriched in gene promoters for which locally and temporally precise methylation is necessary. In view of these results, we discuss potential roles of multiple AGO-hook domains present in the Pol V complex and speculate that SPT6L mediates de novo methylation of naïve loci by interconnecting Pol II and Pol V activities.

Defining the contribution of microRNA-specific Argonautes with slicer capability in animals.

microRNAs regulate gene expression through interaction with an Argonaute protein. While some members of this protein family retain an enzymatic activity capable of cleaving RNA molecules complementary to Argonaute-bound small RNAs, the role of the slicer residues in the canonical microRNA pathway is still unclear in animals. To address this, we created Caenorhabditis elegans strains with mutated slicer residues in the endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the mutation in ALG-1 and ALG-2 catalytic residues affects overall animal fitness and causes phenotypes reminiscent of miRNA defects only when grown and maintained at restrictive temperature. Furthermore, the analysis of global miRNA expression shows that the slicer residues of ALG-1 and ALG-2 contribute differentially to regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the catalytic tetrad of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicer residues of miRNA-specific Argonautes contribute to maintaining levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.