The microRNA pathway controls germ cell proliferation and differentiation in C. elegans

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 as miRISC. 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 Degron system, 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.

An Intricate Network Involving the Argonaute ALG-1 Modulates Organismal Resistance to Oxidative Stress

Cellular response to redox imbalance is crucial for organismal health. microRNAs are implicated in stress responses. ALG-1, the C. elegans ortholog of human AGO2, plays an essential role in microRNA processing and function. Here we investigated the mechanisms governing ALG-1 expression in C. elegans and the players controlling lifespan and stress resistance downstream of ALG-1. We show that upregulation of ALG-1 is a shared feature in conditions linked to increased longevity (e.g., germline-deficient glp-1 mutants). ALG-1 knockdown reduces lifespan and oxidative stress resistance, while overexpression enhances survival against pro-oxidant agents but not heat or reductive stress. R02D3.7 represses alg-1 expression, impacting oxidative stress resistance at least in part via ALG-1. microRNAs upregulated in glp-1 mutants (miR-87-3p, miR-230-3p, and miR-235-3p) can target genes in the protein disulfide isomerase pathway and protect against oxidative stress. This study unveils a tightly regulated network involving transcription factors and microRNAs which controls organisms' ability to withstand oxidative stress.

Recent advances in understanding microRNA function and regulation in C. elegans

MicroRNAs (miRNAs) were first discovered in C. elegans as essential post-transcriptional regulators of gene expression. Since their initial discovery, miRNAs have been implicated in numerous areas of physiology and disease in all animals examined. In recent years, the C. elegans model continues to contribute important advances to all areas of miRNA research. Technological advances in tissue-specific miRNA profiling and genome editing have driven breakthroughs in understanding biological functions of miRNAs, mechanism of miRNA action, and regulation of miRNAs. In this review, we highlight these new C. elegans findings from the past five to seven years.

Defining the contribution of microRNA-specific slicing Argonautes in animals

microRNAs regulate gene expression through interaction with an Argonaute protein family member. 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 slicing activity in the canonical microRNA pathway is still unclear in animals. To address the importance of slicing Argonautes in animals, we created Caenorhabditis elegans strains, carrying catalytically dead endogenous ALG-1 and ALG-2, the only two slicing Argonautes essential for the miRNA pathway in this animal model. We observe that the loss of ALG-1 and ALG-2 slicing activity 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 catalytic activity of ALG-1 and ALG-2 differentially regulate the level of specific subsets of miRNAs in young adults. We also demonstrate that altering the slicing activity of those miRNA-specific Argonautes does not result in any defect in the production of canonical miRNAs. Together, these data support that the slicing activity of miRNA-specific Argonautes function to maintain the levels of a set of miRNAs for optimal viability and fitness in animals particularly exposed to specific growing conditions.

Male gonad-enriched microRNAs function to control sperm production in C. elegans

Germ cell development and gamete production in animals require small RNA pathways. While studies indicate that microRNAs (miRNAs) are necessary for normal sperm production and function, the specific roles for individual miRNAs are largely unknown. Here, we use small RNA sequencing of dissected gonads and functional analysis of new loss of function alleles to identify functions for miRNAs in the control of fecundity and sperm production in Caenorhabditis elegans males and hermaphrodites. We describe a set of 29 male gonad-enriched miRNAs and identify a set of 3 individual miRNAs (mir-58.1, mir-83, and mir-235) and a miRNA cluster (mir-4807-4810.1) that are required for optimal sperm production at 20°C and 5 additional miRNAs (mir-49, mir-57, mir-261, and mir-357/358) that are required for sperm production at 25°C. We observed defects in meiotic progression in mir-58.1, mir-83, mir-235, and mir-4807-4810.1 mutants that may contribute to the reduced number of sperm. Further, analysis of multiple mutants of these miRNAs suggested complex genetic interactions between these miRNAs for sperm production. This study provides insights on the regulatory roles of miRNAs that promote optimal sperm production and fecundity in males and hermaphrodites.

Systematic characterization of small RNAs associated with C. elegans Argonautes

Argonaute proteins generally play regulatory roles by forming complexes with the corresponding small RNAs (sRNAs). An expanded Argonaute family with 20 potentially functional members has been identified in Caenorhabditis elegans. Canonical sRNAs in C. elegans are miRNAs, small interfering RNAs including 22G-RNAs and 26G-RNAs, and 21U-RNAs, which are C. elegans piRNAs. Previous studies have only covered some of these Argonautes for their sRNA partners, and thus, a systematic study is needed to reveal the comprehensive regulatory networks formed by C. elegans Argonautes and their associated sRNAs. We obtained in situ knockin (KI) strains of all C. elegans Argonautes with fusion tags by CRISPR/Cas9 technology. RNA immunoprecipitation against these endogenously expressed Argonautes and high-throughput sequencing acquired the sRNA profiles of individual Argonautes. The sRNA partners for each Argonaute were then analyzed. We found that there were 10 Argonautes enriched miRNAs, 17 Argonautes bound to 22G-RNAs, 8 Argonautes bound to 26G-RNAs, and 1 Argonaute PRG-1 bound to piRNAs. Uridylated 22G-RNAs were bound by four Argonautes HRDE-1, WAGO-4, CSR-1, and PPW-2. We found that all four Argonautes played a role in transgenerational epigenetic inheritance. Regulatory roles of the corresponding Argonaute-sRNA complex in managing levels of long transcripts and interspecies regulation were also demonstrated. In this study, we portrayed the sRNAs bound to each functional Argonaute in C. elegans. Bioinformatics analyses together with experimental investigations provided perceptions in the overall view of the regulatory network formed by C. elegans Argonautes and sRNAs. The sRNA profiles bound to individual Argonautes reported here will be valuable resources for further studies.

The alg-1 Gene Is Necessary for Orsay Virus Replication in Caenorhabditis elegans

The establishment of the Orsay virus-Caenorhabditis elegans infection model has enabled the identification of host factors essential for virus infection. Argonautes are RNA interacting proteins evolutionary conserved in the three domains of life that are key components of small RNA pathways. C. elegans encodes 27 argonautes or argonaute-like proteins. Here, we determined that mutation of the argonaute-like gene 1, alg-1, results in a greater than 10,000-fold reduction in Orsay viral RNA levels, which could be rescued by ectopic expression of alg-1. Mutation in ain-1, a known interactor of ALG-1 and component of the RNA-induced silencing complex, also resulted in a significant reduction in Orsay virus levels. Viral RNA replication from an endogenous transgene replicon system was impaired by the lack of ALG-1, suggesting that ALG-1 plays a role during the replication stage of the virus life cycle. Orsay virus RNA levels were unaffected by mutations in the ALG-1 RNase H-like motif that ablate the slicer activity of ALG-1. These findings demonstrate a novel function of ALG-1 in promoting Orsay virus replication in C. elegans. IMPORTANCE All viruses are obligate intracellular parasites that recruit the cellular machinery of the host they infect to support their own proliferation. We used Caenorhabditis elegans and its only known infecting virus, Orsay virus, to identify host proteins relevant for virus infection. We determined that ALG-1, a protein previously known to be important in influencing worm life span and the expression levels of thousands of genes, is required for Orsay virus infection of C. elegans. This is a new function attributed to ALG-1 that was not recognized before. In humans, it has been shown that AGO2, a close relative protein to ALG-1, is essential for hepatitis C virus replication. This demonstrates that through evolution from worms to humans, some proteins have maintained similar functions, and consequently, this suggests that studying virus infection in a simple worm model has the potential to provide novel insights into strategies used by viruses to proliferate.

Biological effects of ionizing radiation on aquatic biota - A critical review

Ionizing radiation from radionuclides impacts marine aquatic biota and the scope of investigation must be wider than just invertebrates. We intend to detail and illustrate numerous biological effects that occur in both aquatic vertebrates and invertebrates, at various dose rates from all three kinds of ionizing radiation. The characteristics of radiation sources and dosages that would most effectively generate the intended effects in the irradiated organism were assessed once the biological differentiation between vertebrates and invertebrates was determined through multiple lines of evidence. We contend that invertebrates are still more radiosensitive than vertebrates, due to their small genome size, rapid reproduction rates and lifestyle, which help them to compensate for the effects of radiation induced declines in fecundity, life span and individual health. We also identified various research gaps in this field and suggest future directions to be investigated to remedy the lack of data available in this area.

A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions

Argonaute (AGO) proteins associate with small RNAs to direct their effector function on complementary transcripts. The nematode Caenorhabditis elegans contains an expanded family of 19 functional AGO proteins, many of which have not been fully characterized. In this work, we systematically analyzed every C. elegans AGO using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG tags. We have characterized the expression patterns of each AGO throughout development, identified small RNA binding complements, and determined the effects of ago loss on small RNA populations and developmental phenotypes. Our analysis indicates stratification of subsets of AGOs into distinct regulatory modules, and integration of our data led us to uncover novel stress-induced fertility and pathogen response phenotypes due to ago loss.

The role of RNA-binding proteins in orchestrating germline development in Caenorhabditis elegans

RNA passed from parents to progeny controls several aspects of early development. The germline of the free-living nematode Caenorhabditis elegans contains many families of evolutionarily conserved RNA-binding proteins (RBPs) that target the untranslated regions of mRNA transcripts to regulate their translation and stability. In this review, we summarize what is known about the binding specificity of C. elegans germline RNA-binding proteins and the mechanisms of mRNA regulation that contribute to their function. We examine the emerging role of miRNAs in translational regulation of germline and embryo development. We also provide an overview of current technology that can be used to address the gaps in our understanding of RBP regulation of mRNAs. Finally, we present a hypothetical model wherein multiple 3'UTR-mediated regulatory processes contribute to pattern formation in the germline to ensure the proper and timely localization of germline proteins and thus a functional reproductive system.

Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans

The heat shock response (HSR) is a highly conserved cellular process that promotes survival during stress. A hallmark of the HSR is the rapid induction of heat shock proteins (HSPs), such as HSP-70, by transcriptional activation. Once the stress is alleviated, HSPs return to near basal levels through incompletely understood mechanisms. Here, we show that the microRNA pathway acts during heat shock recovery in Caenorhabditis elegans. Depletion of the miRNA Argonaute, Argonaute Like Gene 1 (ALG-1), after an episode of heat shock resulted in decreased survival and perdurance of high hsp-70 levels. We present evidence that regulation of hsp-70 is dependent on miR-85 and sequences in the hsp-70 3’UTR that contain target sites for this miRNA. Regulation of hsp-70 by the miRNA pathway was found to be particularly important during recovery from HS, as animals that lacked miR-85 or its target sites in the hsp-70 3’UTR overexpressed HSP-70 and exhibited reduced viability. In summary, our findings show that down-regulation of hsp-70 by miR-85 after HS promotes survival, highlighting a previously unappreciated role for the miRNA pathway during recovery from stress.

In the natural world, organisms constantly face stressful conditions such as oxidative stress, pathogen infection, starvation and heat stress. While many studies have focused on the cellular response to stress, less is known about how gene expression re-sets after the stress has been ameliorated. Here, we show that the microRNA pathway plays a critical role during the recovery phase after an episode of heat shock in the nematode, Caenorhabditis elegans. Elevated temperatures induce high expression of heat shock proteins (HSPs), including HSP-70, that provide protection from the damaging effects of high heat. We found that restoration of basal levels of HSP-70 after heat shock depends on Argonaute Like Gene 1 and miR-85. Moreover, loss of miRNA-mediated repression of HSP-70 results in compromised survival following heat shock. Our study draws attention to the recovery phase of the heat shock response and highlights an important role for the microRNA pathway in re-establishing gene expression programs needed for organismal viability post stress.

Sperm fate is promoted by the mir-44 microRNA family in the Caenorhabditis elegans hermaphrodite germline

Posttranscriptional regulation of gene expression, typically effected by RNA-binding proteins, microRNAs (miRNAs), and translation initiation factors, is essential for normal germ cell function. Numerous miRNAs have been detected in the germline; however, the functions of specific miRNAs remain largely unknown. Functions of miRNAs have been difficult to determine as miRNAs often modestly repress target mRNAs and are suggested to sculpt or fine tune gene expression to allow for the robust expression of cell fates. In Caenorhabditis elegans hermaphrodites, cell fate decisions are made for germline sex determination during larval development when sperm are generated in a short window before the switch to oocyte production. Here, analysis of newly generated mir-44 family mutants has identified a family of miRNAs that modulate the germline sex determination pathway in C. elegans. Mutants with the loss of mir-44 and mir-45 produce fewer sperm, showing both a delay in the specification and formation of sperm as well as an early termination of sperm specification accompanied by a premature switch to oocyte production. mir-44 and mir-45 are necessary for the normal period of fog-1 expression in larval development. Through genetic analysis, we find that mir-44 and mir-45 may act upstream of fbf-1 and fem-3 to promote sperm specification. Our research indicates that the mir-44 family promotes sperm cell fate specification during larval development and identifies an additional posttranscriptional regulator of the germline sex determination pathway.

miR‑139‑5p enhances cisplatin sensitivity in non‑small cell lung cancer cells by inhibiting cell proliferation and promoting apoptosis via the targeting of Homeobox protein Hox‑B2

The development of chemotherapeutic dug resistance hinders the clinical treatment of cancer. MicroRNAs (miRNAs/miRs) have been revealed to serve essential roles in the drug resistance of numerous types of cancer. miR‑139‑5p was previously reported to be associated with cisplatin (DDP) sensitivity in human nasopharyngeal carcinoma cells and colorectal cancer cells. However, the effect and underlying mechanism of miR‑139‑5p in DDP sensitivity in non‑small cell lung cancer (NSCLC) cells has not yet been fully elucidated. In the present study, the expression of miR‑139‑5p and Homeobox protein Hox‑B2 (HOXB2) in NSCLC tissues was examined by reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) and western blotting. Subsequently, the effect of miR‑139‑5p on the DDP sensitivity of NSCLC cells in vitro was investigated. Cell proliferation was examined using a Cell Counting Kit‑8 assay. Western blotting was used to evaluate the protein expression of HOXB2, phosphorylated (p)‑PI3K, p‑AKT, caspase‑3 and cleaved‑caspase‑3, and RT‑qPCR was used to evaluate the expression of miR‑139‑5p, and the mRNA expression levels of HOXB2, PI3K, AKT and caspase‑3. The apoptotic rate of the cells was detected using flow cytometry. miR‑139‑5p expression in NSCLC tissues was shown to be significantly lower compared with that in adjacent tissues. Additionally, miR‑139‑5p increased cell apoptosis and inhibited NSCLC cell proliferation induced by DDP in vitro via modulating the PI3K/AKT/caspase‑3 signaling pathway. Furthermore, HOXB2 was identified to be a target of miR‑139‑5p, and miR‑139‑5p was revealed to sensitize NSCLC cells to DDP via the targeting of HOXB2. Taken together, the results of the present study demonstrated that regulating the expression of miR‑139‑5p could provide a novel approach to reverse DDP resistance and increase chemosensitivity in the treatment of NSCLC.

The multifaceted roles of microRNAs in differentiation

MicroRNAs (miRNAs) are major drivers of cell fate specification and differentiation. The post-transcriptional regulation of key molecular factors by microRNAs contributes to the progression of embryonic and postembryonic development in several organisms. Following the discovery of lin-4 and let-7 in Caenorhabditis elegans and bantam microRNAs in Drosophila melanogaster, microRNAs have emerged as orchestrators of cellular differentiation and developmental timing. Spatiotemporal control of microRNAs and associated protein machinery can modulate microRNA activity. Additionally, adaptive modulation of microRNA expression and function in response to changing environmental conditions ensures that robust cell fate specification during development is maintained. Herein, we review the role of microRNAs in the regulation of differentiation during development.

Concepts and functions of small RNA pathways in C. elegans

A diversity of gene regulatory mechanisms drives the changes in gene expression required for animal development. Here, we discuss the developmental roles of a class of gene regulatory factors composed of a core protein subunit of the Argonaute family and a 21-26-nucleotide RNA cofactor. These represent ancient regulatory complexes, originally evolved to repress genomic parasites such as transposons, viruses and retroviruses. However, over the course of evolution, small RNA-guided pathways have expanded and diversified, and they play multiple roles across all eukaryotes. Pertinent to this review, Argonaute and small RNA-mediated regulation has acquired numerous functions that affect all aspects of animal life. The regulatory function is provided by the Argonaute protein and its interactors, while the small RNA provides target specificity, guiding the Argonaute to a complementary RNA. C. elegans has 19 different, functional Argonautes, defining distinct yet interconnected pathways. Each Argonaute binds a relatively well-defined class of small RNA with distinct molecular properties. A broad classification of animal small RNA pathways distinguishes between two groups: (i) the microRNA pathway is involved in repressing relatively specific endogenous genes and (ii) the other small RNA pathways, which effectively act as a genomic immune system to primarily repress expression of foreign or "non-self" RNA while maintaining correct endogenous gene expression. microRNAs play prominent direct roles in all developmental stages, adult physiology and lifespan. The other small RNA pathways act primarily in the germline, but their impact extends far beyond, into embryogenesis and adult physiology, and even to subsequent generations. Here, we review the mechanisms and developmental functions of the diverse small RNA pathways of C. elegans.

Denervation drives skeletal muscle atrophy and induces mitochondrial dysfunction, mitophagy and apoptosis via miR-142a-5p/MFN1 axis

Rationale: Peripheral nerve injury is common in clinic, which leads to severe atrophy and dysfunction of the denervated muscles, but the underlying mechanism is not fully understood. Recent studies advanced the causative role of mitochondrial dysfunction in muscle atrophy, while the upstream triggers remained unclear. Methods: In the present study, Atrophy of gastrocnemius and tibialis anterior (TA) were evaluated in mice sciatic nerve transection model. Transmission electron microscopy (TEM) was then used to observe the microstructure of atrophic gastrocnemius and mitochondria. Subsequently, small RNA sequencing, luciferase reporter assay and Electrophoretic Mobility Shift (EMSA) were performed to explore the potential signaling pathway involved in skeletal muscle atrophy. The effects of the corresponding pathway on mitochondrial function, mitophagy, apoptosis and muscle atrophy were further determined in C2C12 cells and denervated gastrocnemius. Results: Gastrocnemius and TA atrophied rapidly after denervation. Obvious decrease of mitochondria number and activation of mitophagy was further observed in atrophic gastrocnemius. Further, miR-142a-5p/ mitofusin-1 (MFN1) axis was confirmed to be activated in denervated gastrocnemius, which disrupted the tubular mitochondrial network, and induced mitochondrial dysfunction, mitophagy and apoptosis. Furthermore, the atrophy of gastrocnemius induced by denervation was relieved through targeting miR-142a-5p/MFN1 axis. Conclusions: Collectively, our data revealed that miR-142a-5p was able to function as an important regulator of denervation-induced skeletal muscle atrophy by inducing mitochondrial dysfunction, mitophagy, and apoptosis via targeting MFN1. Our findings provide new insights into the mechanism of skeletal muscle atrophy following denervation and propose a viable target for therapeutic intervention in individuals suffering from muscle atrophy after peripheral nerve injury.

ALG-2/AGO-Dependent mir-35 Family Regulates DNA Damage-Induced Apoptosis Through MPK-1/ERK MAPK Signaling Downstream of the Core Apoptotic Machinery in Caenorhabditis elegans

MicroRNAs (miRNAs) associate with argonaute (AGO) proteins to post-transcriptionally modulate the expression of genes involved in various cellular processes. Herein, we show that loss of the Caenorhabditis elegans AGO gene alg-2 results in rapid and significantly increased germ cell apoptosis in response to DNA damage inflicted by ionizing radiation (IR). We demonstrate that the abnormal apoptosis phenotype in alg-2 mutant animals can be explained by reduced expression of mir-35 miRNA family members. We show that the increased apoptosis levels in IR-treated alg-2 or mir-35 family mutants depend on a transient hyperactivation of the C. elegans ERK1/2 MAPK ortholog MPK-1 in dying germ cells. Unexpectedly, MPK-1 phosphorylation occurs downstream of caspase activation and depends at least in part on a functional cell corpse-engulfment machinery. Therefore, we propose a refined mechanism, in which an initial proapoptotic stimulus by the core apoptotic machinery initiates the engulfment process, which in turn activates MAPK signaling to facilitate the demise of genomically compromised germ cells.

ALG-1 Influences Accurate mRNA Splicing Patterns in the Caenorhabditis elegans Intestine and Body Muscle Tissues by Modulating Splicing Factor Activities

MicroRNAs (miRNAs) are known to modulate gene expression, but their activity at the tissue-specific level remains largely uncharacterized. To study their contribution to tissue-specific gene expression, we developed novel tools to profile putative miRNA targets in the Caenorhabditis elegans intestine and body muscle. We validated many previously described interactions and identified ∼3500 novel targets. Many of the candidate miRNA targets curated are known to modulate the functions of their respective tissues. Within our data sets we observed a disparity in the use of miRNA-based gene regulation between the intestine and body muscle. The intestine contained significantly more putative miRNA targets than the body muscle highlighting its transcriptional complexity. We detected an unexpected enrichment of RNA-binding proteins targeted by miRNA in both tissues, with a notable abundance of RNA splicing factors. We developed in vivo genetic tools to validate and further study three RNA splicing factors identified as putative miRNA targets in our study (asd-2, hrp-2, and smu-2), and show that these factors indeed contain functional miRNA regulatory elements in their 3'UTRs that are able to repress their expression in the intestine. In addition, the alternative splicing pattern of their respective downstream targets (unc-60, unc-52, lin-10, and ret-1) is dysregulated when the miRNA pathway is disrupted. A reannotation of the transcriptome data in C. elegans strains that are deficient in the miRNA pathway from past studies supports and expands on our results. This study highlights an unexpected role for miRNAs in modulating tissue-specific gene isoforms, where post-transcriptional regulation of RNA splicing factors associates with tissue-specific alternative splicing.

Apoptosis contributes to protect germ cells from the oogenic germline starvation response but is not essential for the gonad shrinking or recovery observed during adult reproductive diapause in C. elegans

When C. elegans hermaphrodites are deprived of food during the mid-L4 larval stage and throughout adulthood, they enter an alternative stage termed "adult reproductive diapause (ARD)" in which they halt reproduction and extend their lifespan. During ARD, germ cell proliferation stops; oogenesis is slowed; and the gonad shrinks progressively, which has been described as the "oogenic germline starvation response". Upon refeeding, the shrunken gonad is regenerated, and animals recover fertility and live out their remaining lifespan. Little is known about the effects of ARD on oocyte quality after ARD. Thus, the aim of this study was to determine how oocyte quality is affected after ARD by measuring brood size and embryonic lethality as a reflection of defective oocyte production. We found that ARD affects reproductive capacity. The oogenic germline starvation response protects oogenic germ cells by slowing oogenesis to prevent prolonged arrest in diakinesis. In contrast to a previous report, we found that germ cell apoptosis is not the cause of gonad shrinkage; instead, we propose that ovulation contributes to gonad shrinkage during the oogenic germline starvation response. We show that germ cell apoptosis increases and continues during ARD via lin-35/Rb and an unknown mechanism. Although apoptosis contributes to maintain germ cell quality during ARD, we demonstrated that apoptosis is not essential to preserve animal fertility. Finally, we show that IIS signaling inactivation partially participates in the oogenic germline starvation response.

MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans

Post-transcriptional control of mRNAs by RNA-binding proteins (RBPs) has a prominent role in the regulation of gene expression. RBPs interact with mRNAs to control their biogenesis, splicing, transport, localization, translation, and stability. Defects in such regulation can lead to a wide range of human diseases from neurological disorders to cancer. Many RBPs are conserved between Caenorhabditis elegans and humans, and several are known to regulate apoptosis in the adult C. elegans germ line. How these RBPs control apoptosis is, however, largely unknown. Here, we identify mina-1(C41G7.3) in a RNA interference-based screen as a novel regulator of apoptosis, which is exclusively expressed in the adult germ line. The absence of MINA-1 causes a dramatic increase in germ cell apoptosis, a reduction in brood size, and an impaired P granules organization and structure. In vivo crosslinking immunoprecipitation experiments revealed that MINA-1 binds a set of mRNAs coding for RBPs associated with germ cell development. Additionally, a system-wide analysis of a mina-1 deletion mutant compared with wild type, including quantitative proteome and transcriptome data, hints to a post-transcriptional regulatory RBP network driven by MINA-1 during germ cell development in C. elegans. In particular, we found that the germline-specific Argonaute WAGO-4 protein levels are increased in mina-1 mutant background. Phenotypic analysis of double mutant mina-1;wago-4 revealed that contemporary loss of MINA-1 and WAGO-4 strongly rescues the phenotypes observed in mina-1 mutant background. To strengthen this functional interaction, we found that upregulation of WAGO-4 in mina-1 mutant animals causes hypersensitivity to exogenous RNAi. Our comprehensive experimental approach allowed us to describe a phenocritical interaction between two RBPs controlling germ cell apoptosis and exogenous RNAi. These findings broaden our understanding of how RBPs can orchestrate different cellular events such as differentiation and death in C. elegans.

Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment

RNA interference (RNAi) related pathways are essential for germline development and fertility in metazoa and can contribute to inter- and trans-generational inheritance. In the nematode Caenorhabditis elegans, environmental double-stranded RNA provided by feeding can lead to heritable changes in phenotype and gene expression. Notably, transmission efficiency differs between the male and female germline, yet the underlying mechanisms remain elusive. Here we use high-throughput sequencing of dissected gonads to quantify sex-specific endogenous piRNAs, miRNAs and siRNAs in the C. elegans germline and the somatic gonad. We identify genes with exceptionally high levels of secondary 22G RNAs that are associated with low mRNA expression, a signature compatible with silencing. We further demonstrate that contrary to the hermaphrodite germline, the male germline, but not male soma, is resistant to environmental RNAi triggers provided by feeding, in line with previous work. This sex-difference in silencing efficacy is associated with lower levels of gonadal RNAi amplification products. Moreover, this tissue- and sex-specific RNAi resistance is regulated by the germline, since mutant males with a feminized germline are RNAi sensitive. This study provides important sex- and tissue-specific expression data of miRNA, piRNA and siRNA as well as mechanistic insights into sex-differences of gene regulation in response to environmental cues.

Effects of 60Co γ Irradiation on the Reproductive Function of Caenorhabditis elegans

The effects of ionizing radiation on the reproductive system have always been a matter of great interest. Both artificial and naturally occurring ionizing radiation can directly or indirectly affect the reproductive system via the introduction of DNA single-strand and double-strand breaks, the excitation of water molecules, and the generation of free radicals. In order to quantitatively investigate the effects of ionizing radiation on reproductive function, ⁶⁰Co γ irradiation was applied on a model organism, Caenorhabditis elegans (C. elegans). The egg-laying and embryo-hatching activities were observed for the parent (F0) and the first 2 progeny (F1 and F2) generations. The incidence rate of ovipositor malformation was also recorded. Acridine orange was used to detect the number of apoptotic germ cells. With the above metrics, the effects of ⁶⁰Co γ irradiation on the reproductive function of C. elegans were systematically evaluated. The results showed that the postirradiation egg-laying and embryo-hatching activities of the F0 generation were increasingly suppressed by increasing doses of ⁶⁰Co γ irradiation. Those of the F1 generation showed a trend toward recovery although also suppressed by the radiation to the F0 generation compared with the control. Those activities were restored to normal or near-normal levels for the F2 generation. The incidence rate of ovipositor malformation was greatly increased by ⁶⁰Co γ irradiation according to radiation doses. Gamma irradiation by ⁶⁰Co also substantially induced germ cell apoptosis, and the apoptosis rate increased with increasing radiation doses. Therefore, ⁶⁰Co γ irradiation affects the reproductive function of C. elegans. The suppression on its reproductive function increases with increasing radiation doses. The reproductive functions of progeny generations are also affected and weakened.

Functional genomic analysis identifies miRNA repertoire regulating C. elegans oocyte development

Oocyte-specific miRNA function remains unclear in mice and worms because loss of Dgcr8 and Dicer from mouse and worm oocytes, respectively, does not yield oogenic defects. These data lead to several models: (a) miRNAs are not generated in oocytes; (b) miRNAs are generated but do not perform an oogenic function; (c) functional oocyte miRNAs are generated in a manner independent of these enzymes. Here, we test these models using a combination of genomic, expression and functional analyses on the C. elegans germline. We identify a repertoire of at least twenty-three miRNAs that accumulate in four spatial domains in oocytes. Genetic tests demonstrate that oocyte-expressed miRNAs regulate key oogenic processes within their respective expression domains. Unexpectedly, we find that over half of the oocyte-expressed miRNAs are generated through an unknown Drosha independent mechanism. Thus, a functional miRNA repertoire generated via Drosha dependent and independent pathways regulates C. elegans oocyte development.

Spatiotemporal m(i)RNA Architecture and 3' UTR Regulation in the C. elegans Germline

In animal germlines, regulation of cell proliferation and differentiation is particularly important but poorly understood. Here, using a cryo-cut approach, we mapped RNA expression along the Caenorhabditis elegans germline and, using mutants, dissected gene regulatory mechanisms that control spatiotemporal expression. We detected, at near single-cell resolution, >10,000 mRNAs, >300 miRNAs, and numerous unannotated miRNAs. Most RNAs were organized in distinct spatial patterns. Germline-specific miRNAs and their targets were co-localized. Moreover, we observed differential 3' UTR isoform usage for hundreds of mRNAs. In tumorous gld-2 gld-1 mutants, gene expression was strongly perturbed. In particular, differential 3' UTR usage was significantly impaired. We propose that PIE-1, a transcriptional repressor, functions to maintain spatial gene expression. Our data also suggest that cpsf-4 and fipp-1 control differential 3' UTR usage for hundreds of genes. Finally, we constructed a "virtual gonad" enabling "virtual in situ hybridizations" and access to all data (https://shiny.mdc-berlin.de/spacegerm/).

Genes involved in miRNA biogenesis affect meiosis and fertility

MicroRNAs (miRNAs) are a class of small (containing about 22 nucleotides) single-stranded non-coding RNAs that regulate gene expression at the post-transcriptional level in plants and animals, being absent from unicellular organisms. They act on diverse key physiological and cellular processes, such as development and tissue differentiation, cell identity, cell cycle progression, and programmed cell death. They are also likely to be involved in a broad spectrum of human diseases. Particularly, this review examines and summarizes work characterizing the function of miRNAs in gametogenesis and fertility. Although numerous studies have elucidated the involvement of reproductive-specific small interfering RNAs (siRNAs) in regulating germ cell development and meiosis, less is known about the role of miRNAs in these processes. We focus on the study of hypomorphic and null alleles of genes encoding components of miRNA biogenesis in both plants (Arabidopsis thaliana) and mammals (Mus musculus). We compare the consequences of the presence of these mutations on male meiosis in both species.

Functional Interactions Between rsks-1/S6K, glp-1/Notch, and Regulators of Caenorhabditis elegans Fertility and Germline Stem Cell Maintenance

The proper accumulation and maintenance of stem cells is critical for organ development and homeostasis. The Notch signaling pathway maintains stem cells in diverse organisms and organ systems. In Caenorhabditis elegans, GLP-1/Notch activity prevents germline stem cell (GSC) differentiation. Other signaling mechanisms also influence the maintenance of GSCs, including the highly-conserved TOR substrate ribosomal protein S6 kinase (S6K). Although C. elegans bearing either a null mutation in rsks-1/S6K or a reduction-of-function (rf) mutation in glp-1/Notch produce half the normal number of adult germline progenitors, virtually all these single mutant animals are fertile. However, glp-1(rf) rsks-1(null) double mutant animals are all sterile, and in about half of their gonads, all GSCs differentiate, a distinctive phenotype associated with a significant reduction or loss of GLP-1 signaling. How rsks-1/S6K promotes GSC fate is unknown. Here, we determine that rsks-1/S6K acts germline-autonomously to maintain GSCs, and that it does not act through Cyclin-E or MAP kinase in this role. We found that interfering with translation also enhances glp-1(rf), but that regulation through rsks-1 cannot fully account for this effect. In a genome-scale RNAi screen for genes that act similarly to rsks-1/S6K, we identified 56 RNAi enhancers of glp-1(rf) sterility, many of which were previously not known to interact functionally with Notch. Further investigation revealed at least six candidates that, by genetic criteria, act linearly with rsks-1/S6K. These include genes encoding translation-related proteins, cacn-1/Cactin, an RNA exosome component, and a Hedgehog-related ligand. We found that additional Hedgehog-related ligands may share functional relationships with glp-1/Notch and rsks-1/S6K in maintaining germline progenitors.

Somatic and Germline MicroRNAs Form Distinct Silencing Complexes to Regulate Their Target mRNAs Differently

Animal germ cells possess a specific post-transcriptional regulatory context allowing the storage of maternal transcripts in the oocyte until their translation at a specific point in early development. As key regulators of gene expression, miRNAs repress translation mainly through mRNA destabilization. Thus, germline miRNAs likely use distinct ways to regulate their targets. Here, we use C. elegans to compare miRNA function within germline and somatic tissues. We show that the same miRNA displays tissue-specific gene regulatory mechanisms. While translational repression occurs in both tissues, targeted mRNAs are instead stabilized in the germline. Comparative analyses of miRNA silencing complexes (miRISC) demonstrate that their composition differs from germline to soma. We show that germline miRNA targets preferentially localize to perinuclear regions adjacent to P granules, and their repression is dependent on the core P granule component GLH-1. Together, our findings reveal the existence of different miRISC in animals that affect targeted mRNAs distinctively.

The Period protein homolog LIN-42 regulates germline development in C. elegans

Germline stem cells are maintained in the distal region of the C. elegans gonad. These cells undergo mitotic divisions, and GLP-1/Notch signaling dictates whether they remain in this state. The somatic distal tip cell (DTC) caps the end of the distal gonad and is essential for maintenance of the germline mitotic zone. As germ cells move away from the DTC they exit mitosis and enter early meiotic prophase. Here we identify the Period protein homolog LIN-42 as a new regulator of germline development in C. elegans. LIN-42 is expressed in almost all somatic cells including the DTC, and LIN-42 functions as a transcription factor in the heterochronic pathway and to regulate molting. We found that the mitotic proliferative zone size in the distal gonad was significantly reduced by ~25% in lin-42 mutants compared to WT N2 worms. A lin-42 mutation also reduced the mitotic proliferative zone size caused by glp-1 partial loss-of-function and gain-of-function alleles. LIN-42 mediates this effect, at least in part, by regulating expression of the GLP-1/Notch ligand LAG-2. We further show that lin-42 expression itself is regulated by ATX-2, which promotes germline proliferation and is the homolog of the RNA binding protein ataxin-2 that is implicated in human neurodegenerative diseases. Altogether our results establish a new role for the conserved, important Period protein homolog LIN-42 in regulating early germline development. These results also suggest that in addition to regulating behavioral rhythms, the circadian clock plays an important role in communicating environmental signals to essential reproductive pathways.

Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs

MicroRNAs are small, noncoding RNAs that regulate gene expression at the post-transcriptional level in essentially all aspects of Caenorhabditis elegans biology. More than 140 genes that encode microRNAs in C. elegans regulate development, behavior, metabolism, and responses to physiological and environmental changes. Genetic analysis of C. elegans microRNA genes continues to enhance our fundamental understanding of how microRNAs are integrated into broader gene regulatory networks to control diverse biological processes, including growth, cell division, cell fate determination, behavior, longevity, and stress responses. As many of these microRNA sequences and the related processing machinery are conserved over nearly a billion years of animal phylogeny, the assignment of their functions via worm genetics may inform the functions of their orthologs in other animals, including humans. In vivo investigations are especially important for microRNAs because in silico extrapolation of their functions using mRNA target prediction programs can easily assign microRNAs to incorrect genetic pathways. At this mezzanine level of microRNA bioinformatic sophistication, genetic analysis continues to be the gold standard for pathway assignments.

Opposing roles of microRNA Argonautes during Caenorhabditis elegans aging

Argonaute (AGO) proteins partner with microRNAs (miRNAs) to target specific genes for post-transcriptional regulation. During larval development in Caenorhabditis elegans, Argonaute-Like Gene 1 (ALG-1) is the primary mediator of the miRNA pathway, while the related ALG-2 protein is largely dispensable. Here we show that in adult C. elegans these AGOs are differentially expressed and, surprisingly, work in opposition to each other; alg-1 promotes longevity, whereas alg-2 restricts lifespan. Transcriptional profiling of adult animals revealed that distinct miRNAs and largely non-overlapping sets of protein-coding genes are misregulated in alg-1 and alg-2 mutants. Interestingly, many of the differentially expressed genes are downstream targets of the Insulin/ IGF-1 Signaling (IIS) pathway, which controls lifespan by regulating the activity of the DAF-16/ FOXO transcription factor. Consistent with this observation, we show that daf-16 is required for the extended lifespan of alg-2 mutants. Furthermore, the long lifespan of daf-2 insulin receptor mutants, which depends on daf-16, is strongly reduced in animals lacking alg-1 activity. This work establishes an important role for AGO-mediated gene regulation in aging C. elegans and illustrates that the activity of homologous genes can switch from complementary to antagonistic, depending on the life stage.

Tiny non-coding RNAs called microRNAs (miRNAs) are broadly conserved across animal species and have established roles in regulating development, metabolism and behavior. In humans, aberrant expression or function of specific miRNAs has been associated with a wide variety of diseases, underscoring the critical role of these molecules in organismal viability. Argonaute (AGO) proteins are essential co-factors for miRNAs to regulate the expression of target genes. In C. elegans nematodes, two highly related AGOs (ALG-1 and ALG-2; Argonaute-Like Genes) play largely overlapping roles in the miRNA pathway during development. Here we report that the activities of these two AGOs diverge in aging animals, as loss of ALG-1 shortens lifespan, while loss of ALG-2 extends it. These opposite longevity phenotypes are associated with differential regulation of specific miRNAs and protein-coding genes that act in the Insulin/ IGF-1 Signaling (IIS) pathway. Furthermore, we present genetic evidence that alg-1 and alg-2 operate within this pathway to impact aging. In sum, our findings reveal that two related AGOs function antagonistically within the conserved insulin signaling pathway that regulates longevity.

A microRNA feedback loop regulates global microRNA abundance during aging

Expression levels of many microRNAs (miRNAs) change during aging, notably declining globally in a number of organisms and tissues across taxa. However, little is known about the mechanisms or the biological relevance for this change. We investigated the network of genes that controls miRNA transcription and processing during C. elegans aging. We found that miRNA biogenesis genes are highly networked with transcription factors and aging-associated miRNAs. In particular, miR-71, known to influence life span and itself up-regulated during aging, represses alg-1/Argonaute expression post-transcriptionally during aging. Increased ALG-1 abundance in mir-71 loss-of-function mutants led to globally increased miRNA expression. Interestingly, these mutants demonstrated widespread mRNA expression dysregulation and diminished levels of variability both in gene expression and in overall life span. Thus, the progressive molecular decline often thought to be the result of accumulated damage over an organism's life may be partially explained by a miRNA-directed mechanism of age-associated decline.

Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline

BACKGROUND

The 3' untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3' ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3'UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation.

RESULTS

We show that nearly half of germline transcripts are alternatively polyadenylated, that differential regulation of endogenous 3'UTR variants is common, and that alternative isoforms direct distinct spatiotemporal protein expression patterns in vivo. Dynamic expression profiling also reveals temporal regulation of X-linked gene expression, selective stabilization of transcripts, and strong evidence for a novel developmental program that promotes nucleolar dissolution in oocytes. We show that the RNA-binding protein NCL-1/Brat is a posttranscriptional regulator of numerous ribosome-related transcripts that acts through specific U-rich binding motifs to down-regulate mRNAs encoding ribosomal protein subunits, rRNA processing factors, and tRNA synthetases.

CONCLUSIONS

These results highlight the pervasive nature and functional potential of patterned gene and isoform expression during early animal development.

ALG-5 is a miRNA-associated Argonaute required for proper developmental timing in the Caenorhabditis elegans germline

Caenorhabditis elegans contains 25 Argonautes, of which, ALG-1 and ALG-2 are known to primarily interact with miRNAs. ALG-5 belongs to the AGO subfamily of Argonautes that includes ALG-1 and ALG-2, but its role in small RNA pathways is unknown. We analyzed by high-throughput sequencing the small RNAs associated with ALG-5, ALG-1 and ALG-2, as well as changes in mRNA expression in alg-5, alg-1 and alg-2 mutants. We show that ALG-5 defines a distinct branch of the miRNA pathway affecting the expression of genes involved in immunity, defense, and development. In contrast to ALG-1 and ALG-2, which associate with most miRNAs and have general roles throughout development, ALG-5 interacts with only a small subset of miRNAs and is specifically expressed in the germline where it localizes alongside the piRNA and siRNA machinery at P granules. alg-5 is required for optimal fertility and mutations in alg-5 lead to a precocious transition from spermatogenesis to oogenesis. Our results provide a near-comprehensive analysis of miRNA-Argonaute interactions in C. elegans and reveal a new role for miRNAs in the germline.

Functional analysis of microRNA pathway genes in the somatic gonad and germ cells during ovulation in C. elegans

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that play critical roles in animal development and physiology, though functions for most miRNAs remain unknown. Worms with reduced miRNA biogenesis due to loss of Drosha or Pasha/DGCR8 activity are sterile and fail to ovulate, indicating that miRNAs are required for the process of oocyte maturation and ovulation. Starting with this penetrant sterile phenotype and using new strains created to perform tissue specific RNAi, we characterized the roles of the C. elegans Pasha, pash-1, and two miRNA-specific Argonautes, alg-1 and alg-2, in somatic gonad cells and in germ cells in the regulation of ovulation. Conditional loss of pash-1 activity resulted in a reduced rate of ovulation and in basal and ovulatory sheath contractions. Similarly, knockdown of miRNA-specific Argonautes in the cells of the somatic gonad by tissue-specific RNAi results in a reduction of the ovulation rate and in basal and ovulatory sheath contractions. Reduced miRNA pathway gene activity resulted in a range of defects, including oocytes that were pinched upon entry of the oocyte into the distal end of the spermatheca in about 42% of the ovulation events observed following alg-1 RNAi. This phenotype was not observed on worms exposed to control RNAi. In contrast, knockdown of alg-1 and alg-2 in germ cells results in few defects in oocyte maturation and ovulation. These data identify specific steps in the process of ovulation that require miRNA pathway gene activity in the somatic gonad cells.

Regulation of the Balance Between Proliferation and Differentiation in Germ Line Stem Cells

In many animals, reproductive fitness is dependent upon the production of large numbers of gametes over an extended period of time. This level of gamete production is possible due to the continued presence of germ line stem cells. These cells can produce two types of daughter cells, self-renewing daughter cells that will maintain the stem cell population and differentiating daughter cells that will become gametes. A balance must be maintained between the proliferating self-renewing cells and those that differentiate for long-term gamete production to be maintained. Too little proliferation can result in depletion of the stem cell population, while too little differentiation can lead to a lack of gamete formation and possible tumor formation. In this chapter, we discuss our current understanding of how the balance between proliferation and differentiation is achieved in three well-studied germ line model systems: the Drosophila female, the mouse male, and the C. elegans hermaphrodite. While these three systems have significant differences in how this balance is regulated, including differences in stem cell population size, signaling pathways utilized, and the use of symmetric and/or asymmetric cell divisions, there are also similarities found between them. These similarities include the reliance on a predominant signaling pathway to promote proliferation, negative feedback loops to rapidly shutoff proliferation-promoting cues, close association of the germ line stem cells with a somatic niche, cytoplasmic connections between cells, projections emanating from the niche cell, and multiple mechanisms to limit the spatial influence of the niche. A comparison between different systems may help to identify elements that are essential for a proper balance between proliferation and differentiation to be achieved and elements that may be achieved through various mechanisms.

Discovering Numerical Differences between Animal and Plant microRNAs

Previous studies have confirmed that there are many differences between animal and plant microRNAs (miRNAs), and that numerical features based on sequence and structure can be used to predict the function of individual miRNAs. However, there is little research regarding numerical differences between animal and plant miRNAs, and whether a single numerical feature or combination of features could be used to distinguish animal and plant miRNAs or not. Therefore, in current study we aimed to discover numerical features that could be used to accomplish this. We performed a large-scale analysis of 132 miRNA numerical features, and identified 17 highly significant distinguishing features. However, none of the features independently could clearly differentiate animal and plant miRNAs. By further analysis, we found a four-feature subset that included helix number, stack number, length of pre-miRNA, and minimum free energy, and developed a logistic classifier that could distinguish animal and plant miRNAs effectively. The precision of the classifier was greater than 80%. Using this tool, we confirmed that there were universal differences between animal and plant miRNAs, and that a single feature was unable to adequately distinguish the difference. This feature set and classifier represent a valuable tool for identifying differences between animal and plant miRNAs at a molecular level.

The Use of the Nematode Caenorhabditis elegans to Evaluate the Adverse Effects of Epoxiconazole Exposure on Spermatogenesis

There is increasing evidence that epoxiconazole exposure can affect reproductive function, but few studies have investigated adverse effects on spermatogenesis. The nematode Caenorhabditis elegans (C. elegans) was used in our study to assess effects of epoxiconazole on spermatogenesis in male nematodes after 48 h of exposure to concentrations of 0.1, 1.0, or 10.0 μg/L. The results demonstrated that epoxiconazole exposure affected spermatogenesis, decreasing the number of total germ cells, mitotic cells, meiotic cells and spermatids, spermatid diameter, and cross-sectional area, and inducing mitotic germ cell proliferation arrest, premature entry into meiosis, and sperm activation inhibition; however, sperm transfer showed no abnormal changes. In addition, the results showed that epoxiconazole activated the transforming growth factor-β (TGFβ) signaling pathway and increased the expression levels of gene daf-1, daf-3, daf-4, daf-5 and daf-7 in nematodes. We therefore propose that epoxiconazole acts by activating the TGFβ signaling pathway, leading to the impairment of spermatogenesis and the consequent decline in male fertility.

CREB1-driven expression of miR-320a promotes mitophagy by down-regulating VDAC1 expression during serum starvation in cervical cancer cells

The altered expression of miRNAs in response to stresses contributes to cancer pathogenesis. However, little is known regarding the mechanism by which cellular stresses drive alterations in miRNA expression. Here, we found that serum starvation enhanced mitophagy by downregulating the mitophagy-associated protein voltage-dependent anion channel 1 (VDAC1) and by inducing the expression of miR-320a and the transcription factor cAMP responsive element binding protein 1(CREB1). Furthermore, we cloned the promoter of miR-320a and identified the core promoter of miR-320a in the upstream -16 to -130 region of pre-miR-320a. Moreover, CREB1 was found to bind to the promoter of miR-320a to activate its expression and to induce mitophagy during serum starvation. Collectively, our results reveal a new mechanism underlying serum starvation-induced mitophagy in which serum starvation induces CREB1 expression, in turn activating miR-320a expression, which then down-regulates VDAC1 expression to facilitate mitophagy. These findings may provide new insights into cancer cell survival in response to environmental stresses.

The implication of microRNAs and endo-siRNAs in animal germline and early development

Germ cells provide maternal mRNAs that are stored in the oocyte, and later translated at a specific time of development. In this context, gene regulation depends mainly on post-transcriptional mechanisms that contribute to keep maternal transcripts in a stable and translationally silent state. In recent years, small non-coding RNAs, such as microRNAs have emerged as key post-transcriptional regulators of gene expression. microRNAs control the translation efficiency and/or stability of targeted mRNAs. microRNAs are present in animal germ cells and maternally inherited microRNAs are abundant in early embryos. However, it is not known how microRNAs control the stability and translation of maternal transcripts. In this review, we will discuss the implication of germline microRNAs in regulating animal oogenesis and early embryogenesis as well as compare their roles with endo-siRNAs, small RNA species that share key molecular components with the microRNA pathway.

MicroRNA-19a regulates lipopolysaccharide-induced endothelial cell apoptosis through modulation of apoptosis signal-regulating kinase 1 expression

Background

MicroRNAs, small non-encoding RNAs that post-transcriptionally modulate expression of their target genes, have been implicated as critical regulatory molecules in endothelial cells.

Results

In the present study, we found that overexpression of miR-19a protects endothelial cells from lipopolysaccharide (LPS)-induced apoptosis through the apoptosis signal-regulating kinase 1 (ASK1)/p38 pathway. Quantitative real-time PCR demonstrated that the expression of miR-19a in endothelial cell was markedly down-regulated by LPS stimulation. Furthermore, LPS-induced apoptosis was significantly inhibited by over-expression of miR-19a. Finally, both a luciferase reporter assay and western blot analysis showed that ASK1 is a direct target of miR-19a.

Conclusions

MiR-19a regulates ASK1 expression by targeting specific binding sites in the 3’ untranslated region of ASK1 mRNA. Overexpression of miR-19a is an effective method to protect against LPS-induced apoptosis of endothelial cells.

Electronic supplementary material

The online version of this article (doi:10.1186/s12867-015-0034-8) contains supplementary material, which is available to authorized users.

Dynamic evolution and biogenesis of small RNAs during sex reversal

Understanding origin, evolution and functions of small RNA (sRNA) genes has been a great challenge in the past decade. Molecular mechanisms underlying sexual reversal in vertebrates, particularly sRNAs involved in this process, are largely unknown. By deep-sequencing of small RNA transcriptomes in combination with genomic analysis, we identified a large amount of piRNAs and miRNAs including over 1,000 novel miRNAs, which were differentially expressed during gonad reversal from ovary to testis via ovotesis. Biogenesis and expressions of miRNAs were dynamically changed during the reversal. Notably, phylogenetic analysis revealed dynamic expansions of miRNAs in vertebrates and an evolutionary trajectory of conserved miR-17-92 cluster in the Eukarya. We showed that the miR-17-92 cluster in vertebrates was generated through multiple duplications from ancestor miR-92 in invertebrates Tetranychus urticae and Daphnia pulex from the Chelicerata around 580 Mya. Moreover, we identified the sexual regulator Dmrt1 as a direct target of the members miR-19a and -19b in the cluster. These data suggested dynamic biogenesis and expressions of small RNAs during sex reversal and revealed multiple expansions and evolutionary trajectory of miRNAs from invertebrates to vertebrates, which implicate small RNAs in sexual reversal and provide new insight into evolutionary and molecular mechanisms underlying sexual reversal.

Mechanistic Role of MicroRNA in Cancer Chemoprevention by Nonsteroidal Anti-inflammatory Drugs

Over the past several decades, studies have documented the significance of nonsteroidal anti-inflammatory drugs (NSAIDs) on cancer chemoprevention by lowering incidence and slowing down progression of malignant disease, which consequently lead to decline of cancer-related mortality and improvement of disease progression free survival (PFS). Inhibition of cyclooxygenase (COX) has been primarily believed to be the key mechanism responsible for anticancer activity of NSAIDs, while the serious toxicity caused by COX inhibitory effect reduces the enthusiasm to use NSAIDs as chemoprevention agents in the clinic. Recently, more and more studies demonstrate that non-COX inhibitory mechanisms may account for anticancer properties of NSAIDs, at least partially, which potentially support the indication of NSAIDs on cancer chemoprevention. MicroRNAs (miRNAs) are a set of non-coding and small RNA molecules with master regulatory effect on over 30% human genes through the post-transcriptional and translational modulation. Although miRNAs have been reported to be involved in many normal and pathological processes including cell proliferation, apoptosis, differentiation, as well as tumorigenesis, their roles in NSAIDs' properties of cancer chemoprevention have not yet been studied exclusively. Here, we will review the prior studies reporting interactions between miRNAs and COX/non-COX pathways with intent to provide insights into better understanding molecular mechanisms of cancer chemoprevention by NSAIDs.

MicroRNA-145 directly targets the insulin-like growth factor receptor I in human bladder cancer cells

The insulin-like growth factor receptor I (IGF-IR) is a proto-oncogene with potent mitogenic and antiapoptotic activities. It has been reported that expression of IGF-IR is up-regulated in bladder cancer. Here, we assessed whether microRNA-145 (miR-145) regulates IGF-IR expression in bladder cancer. In our study, miR-145 was shown to directly target IGF-IR 3'-untranslated region (UTR) in human bladder cancer cells. Small interfering RNA (siRNA)- and miR-145-mediated IGF-IR knockdown experiments revealed that miR-145 promotes cell apoptosis, and suppresses cell proliferation and migration through suppression of IGF-IR expression. Taken together, our data suggest that miR-145 may inhibit bladder cancer initiation by affecting IGF-IR signaling.

Protein kinase CK2 both promotes robust proliferation and inhibits the proliferative fate in the C. elegans germ line

Stem cells are capable of both self-renewal (proliferation) and differentiation. Determining the regulatory mechanisms controlling the balance between stem cell proliferation and differentiation is not only an important biological question, but also holds the key for using stem cells as therapeutic agents. The Caenorhabditis elegans germ line has emerged as a valuable model to study the molecular mechanisms controlling stem cell behavior. In this study, we describe a large-scale RNAi screen that identified kin-10, which encodes the β subunit of protein kinase CK2, as a novel factor regulating stem cell proliferation in the C. elegans germ line. While a loss of kin-10 in an otherwise wild-type background results in a decrease in the number of proliferative cells, loss of kin-10 in sensitized genetic backgrounds results in a germline tumor. Therefore, kin-10 is not only necessary for robust proliferation, it also inhibits the proliferative fate. We found that kin-10's regulatory role in inhibiting the proliferative fate is carried out through the CK2 holoenzyme, rather than through a holoenzyme-independent function, and that it functions downstream of GLP-1/Notch signaling. We propose that a loss of kin-10 leads to a defect in CK2 phosphorylation of its downstream targets, resulting in abnormal activity of target protein(s) that are involved in the proliferative fate vs. differentiation decision. This eventually causes a shift towards the proliferative fate in the stem cell fate decision.

A new role for the GARP complex in microRNA-mediated gene regulation

Many core components of the microRNA pathway have been elucidated and knowledge of their mechanisms of action actively progresses. In contrast, factors with modulatory roles on the pathway are just starting to become known and understood. Using a genetic screen in Caenorhabditis elegans, we identify a component of the GARP (Golgi Associated Retrograde Protein) complex, vps-52, as a novel genetic interactor of the microRNA pathway. The loss of vps-52 in distinct sensitized genetic backgrounds induces the enhancement of defective microRNA-mediated gene silencing. It synergizes with the core microRNA components, alg-1 Argonaute and ain-1 (GW182), in enhancing seam cell defects and exacerbates the gene silencing defects of the let-7 family and lsy-6 microRNAs in the regulation of seam cell, vulva and ASEL neuron development. Underpinning the observed genetic interactions, we found that VPS-52 impinges on the abundance of the GW182 proteins as well as the levels of microRNAs including the let-7 family. Altogether, we demonstrate that GARP complex fulfills a positive modulatory role on microRNA function and postulate that acting through GARP, vps-52 participates in a membrane-related process of the microRNA pathway.

Functional analysis of the miRNA-mRNA interaction network in C. elegans

MicroRNAs (miRNAs) are conserved small non-coding RNAs that typically regulate gene expression by binding to the 3' untranslated region (UTR) of mRNAs. Developmental functions of miRNAs have been extensively studied, but additional roles in various cellular processes remain to be understood. The investigation of the biological importance of individual miRNA-target interactions and the miRNA-target interaction network as a whole has been an exciting and challenging field of study. Here we briefly discuss the contributions our lab has made to our understanding of the physiological impact of this miRNA-network in C. elegans, in the context of recent studies in this advancing field. These studies have advanced our knowledge of the role of miRNAs in ensuring a robust cellular response to different physiological conditions. We briefly outline the genetic, biochemical, and computational strategies utilized to understand miRNA functions and discuss our recent study of the miRNA-interaction network in neurons and potential directions for future studies.

Sexual polyploidization in plants--cytological mechanisms and molecular regulation

In the plant kingdom, events of whole genome duplication or polyploidization are generally believed to occur via alterations of the sexual reproduction process. Thereby, diploid pollen and eggs are formed that contain the somatic number of chromosomes rather than the gametophytic number. By participating in fertilization, these so-called 2n gametes generate polyploid offspring and therefore constitute the basis for the establishment of polyploidy in plants. In addition, diplogamete formation, through meiotic restitution, is an essential component of apomixis and also serves as an important mechanism for the restoration of F1 hybrid fertility. Characterization of the cytological mechanisms and molecular factors underlying 2n gamete formation is therefore not only relevant for basic plant biology and evolution, but may also provide valuable cues for agricultural and biotechnological applications (e.g. reverse breeding, clonal seeds). Recent data have provided novel insights into the process of 2n pollen and egg formation and have revealed multiple means to the same end. Here, we summarize the cytological mechanisms and molecular regulatory networks underlying 2n gamete formation, and outline important mitotic and meiotic processes involved in the ectopic induction of sexual polyploidization.

AGO4 regulates entry into meiosis and influences silencing of sex chromosomes in the male mouse germline

The four mammalian Argonaute family members are thought to share redundant functions in the microRNA pathway, yet only AGO2 possesses the catalytic "slicer" function required for RNAi. Whether AGO1, AGO3, or AGO4 possesses specialized functions remains unclear. Here we show that AGO4 localizes to spermatocyte nuclei during meiotic prophase I, specifically at sites of asynapsis and the transcriptionally silenced XY subdomain, the sex body. We generated Ago4 knockout mice and show that Ago4(-/-) spermatogonia initiate meiosis early, resulting from premature induction of retinoic acid-response genes. During prophase I, the sex body assembles incorrectly in Ago4(-/-) mice, leading to disrupted meiotic sex chromosome inactivation (MSCI). This is associated with a dramatic loss of microRNAs, >20% of which arises from the X chromosome. Thus, AGO4 regulates meiotic entry and MSCI in mammalian germ cells, implicating small RNA pathways in these processes.