A non-radioactive method for small RNA detection by northern blotting

Characterization of Argonaute-containing protein complexes in Leishmania-infected human macrophages

The intracellular protozoan parasite Leishmania causes leishmaniasis in humans, leading to serious illness and death in tropical and subtropical areas worldwide. Unfortunately, due to the unavailability of approved vaccines for humans and the limited efficacy of available drugs, leishmaniasis is on the rise. A comprehensive understanding of host-pathogen interactions at the molecular level could pave the way to counter leishmaniasis. There is growing evidence that several intracellular pathogens target RNA interference (RNAi) pathways in host cells to facilitate their persistence. The core elements of the RNAi system are complexes of Argonaute (Ago) proteins with small non-coding RNAs, also known as RNA-induced silencing complexes (RISCs). Recently, we have shown that Leishmania modulates Ago1 protein of host macrophages for its survival. In this study, we biochemically characterize the Ago proteins' interactome in Leishmania-infected macrophages compared to non-infected cells. For this, a quantitative proteomic approach using stable isotope labelling by amino acids in cell culture (SILAC) was employed, followed by purification of host Ago-complexes using a short TNRC6 protein-derived peptide fused to glutathione S-transferase beads as an affinity matrix. Proteomic-based detailed biochemical analysis revealed Leishmania modulated host macrophage RISC composition during infection. This analysis identified 51 Ago-interacting proteins with a broad range of biological activities. Strikingly, Leishmania proteins were detected as part of host Ago-containing complexes in infected cells. Our results present the first report of comprehensive quantitative proteomics of Ago-containing complexes isolated from Leishmania-infected macrophages and suggest targeting the effector complex of host RNAi machinery. Additionally, these results expand knowledge of RISC in the context of host-pathogen interactions in parasitology in general.

An electrochemical determination strategy for miRNA based on bimetallic nanozyme and toehold-mediated DNA replacement procedure

An electrochemical strategy based on bimetallic nanozyme in collaboration with toehold-mediated DNA replacement effect is proposed for the sensitive determination of miRNA-21. The AuPt nanoparticles (AuPt NPs) are prepared as a catalytic beacon; it shows favorable peroxidase properties with a Michaelis contant (K_m) of 0.072 mM for H₂O₂, which is capable of catalyzing H₂O₂ to induce an intense redox reaction, and causing a measurable electrochemical signal. To further enhance the strength of the signal response, a novel toehold-mediated DNA replacement strategy is employed. DNA strands with specific sequences are modified on electrodes and AuPt NPs, respectively. In the presence of miRNA-21, a cyclic substitution effect is subsequently activated via a specific toehold sequence and leads to a large accumulation of AuPt NPs on the electrodes. Subsequently, a strong signal depending on the amount of miRNA-21 is obtained after adding a small amount of H₂O₂. The analytical range of this determination method is from 0.1 pM to 1.0 nM, and the LOD is 84.1 fM. The spike recoveries for serum samples are 95.0 to 102.4% and the RSD values are 3.7 to 5.8%. The results suggests a promising application of the established method in clinical testing and disease diagnosis.

A high-throughput screening RT-qPCR assay for quantifying surrogate markers of immunity from PBMCs

Immunoassays that quantitate cytokines and other surrogate markers of immunity from peripheral blood mononuclear cells (PBMCs), such as flow cytometry or Enzyme-Linked Immunosorbent Spot (ELIspot), allow highly sensitive measurements of immune effector function. However, those assays consume relatively high numbers of cells and expensive reagents, precluding comprehensive analyses and high-throughput screening (HTS). To address this issue, we developed a sensitive and specific reverse transcription-quantitative PCR (RT-qPCR)-based HTS assay, specifically designed to quantify surrogate markers of immunity from very low numbers of PBMCs. We systematically evaluated the volumes and concentrations of critical reagents within the RT-qPCR protocol, miniaturizing the assay and ultimately reducing the cost by almost 90% compared to current standard practice. We assessed the suitability of this cost-optimized RT-qPCR protocol as an HTS tool and determined the assay exceeds HTS uniformity and signal variance testing standards. Furthermore, we demonstrate this technique can effectively delineate a hierarchy of responses from as little as 50,000 PBMCs stimulated with CD4⁺ or CD8⁺ T cell peptide epitopes. Finally, we establish that this HTS-optimized protocol has single-cell analytical sensitivity and a diagnostic sensitivity equivalent to detecting 1:10,000 responding cells (i.e., 100 Spot Forming Cells/10⁶ PBMCs by ELIspot) with over 90% accuracy. We anticipate this assay will have widespread applicability in preclinical and clinical studies, especially when samples are limited, and cost is an important consideration.

The key micronutrient copper orchestrates broad-spectrum virus resistance in rice

Copper is a critical regulator of plant growth and development. However, the mechanisms by which copper responds to virus invasion are unclear. We previously showed that SPL9-mediated transcriptional activation of miR528 adds a previously unidentified regulatory layer to the established ARGONAUTE (AGO18)-miR528-L-ascorbate oxidase (AO) antiviral defense. Here, we report that rice promotes copper accumulation in shoots by inducing copper transporter genes, including HMA5 and COPT, to counteract viral infection. Copper suppresses the transcriptional activation of miR528 by inhibiting the protein level of SPL9, thus alleviating miR528-mediated cleavage of AO transcripts to strengthen the antiviral response. Loss-of-function mutations in HMA5, COPT1, and COPT5 caused a significant reduction in copper accumulation and plant viral resistance because of the increased SPL9-mediated miR528 transcription. Gain in viral susceptibility was mitigated when SPL9 was mutated in the hma5 mutant background. Our study elucidates the molecular mechanisms and regulatory networks of copper homeostasis and the SPL9-miR528-AO antiviral pathway.

Considerations and Suggestions for the Reliable Analysis of miRNA in Plasma Using qRT-PCR

MicroRNAs (miRNAs) are promising molecules that can regulate gene expression, and their expression level and type have been associated with early diagnosis, targeted therapy, and prognosis of various diseases. Therefore, analysis of miRNA in the plasma or serum is useful for the discovery of biomarkers and the diagnosis of implicated diseases to achieve potentially unprecedented progress in early treatment. Numerous methods to improve sensitivity have recently been proposed and confirmed to be valuable in miRNA detection. Specifically, quantitative reverse-transcription polymerase chain reaction (qRT-PCR) is an effective and common method for sensitive and specific analysis of miRNA from biological fluids, such as plasma or serum. Despite this, the application of qRT-PCR is limited, as it can be affected by various contaminants. Therefore, extraction studies have been frequently conducted to maximize the extracted miRNA amount while simultaneously minimizing contaminants. Moreover, studies have evaluated extraction efficiency and normalization of the extracted sample. However, variability in results among laboratories still exists. In this review, we aimed to summarize the factors influencing the qualification and quantification of miRNAs in the plasma using qRT-PCR. Factors influencing reliable analysis of miRNA using qRT-PCR are described in detail. Additionally, we aimed to describe the importance of evaluating extraction and normalization for reliable miRNA analysis and to explore how miRNA detection accuracy, especially from plasma, can be improved.

Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

The distinctive biology and unique evolutionary features of snakes make them fascinating model systems to elucidate how genomes evolve and how variation at the genomic level is interlinked with phenotypic-level evolution. Similar to other eukaryotic genomes, large proportions of snake genomes contain repetitive DNA, including transposable elements (TEs) and satellite repeats. The importance of repetitive DNA and its structural and functional role in the snake genome, remain unclear. This review highlights the major types of repeats and their proportions in snake genomes, reflecting the high diversity and composition of snake repeats. We present snakes as an emerging and important model system for the study of repetitive DNA under the impact of sex and microchromosome evolution. We assemble evidence to show that certain repetitive elements in snakes are transcriptionally active and demonstrate highly dynamic lineage-specific patterns as repeat sequences. We hypothesize that particular TEs can trigger different genomic mechanisms that might contribute to driving adaptive evolution in snakes. Finally, we review emerging approaches that may be used to study the expression of repetitive elements in complex genomes, such as snakes. The specific aspects presented here will stimulate further discussion on the role of genomic repeats in shaping snake evolution.

Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish

Yeast Rcl1 is a potential endonuclease that mediates pre-RNA cleavage at the A₂-site to separate 18S rRNA from 5.8S and 25S rRNAs. However, the biological function of Rcl1 in opisthokonta is poorly defined. Moreover, there is no information regarding the exact positions of 18S pre-rRNA processing in zebrafish. Here, we report that zebrafish pre-rRNA harbours three major cleavage sites in the 5′ETS, namely –477nt (A′-site), –97nt (A₀-site) and the 5′ETS and 18S rRNA link (A₁-site), as well as two major cleavage regions within the ITS1, namely 208–218nt (site 2) and 20–33nt (site E). We also demonstrate that depletion of zebrafish Rcl1 mainly impairs cleavage at the A₁-site. Phenotypically, rcl1^–/– mutants exhibit a small liver and exocrine pancreas and die before 15 days post-fertilization. RNA-seq analysis revealed that the most significant event in rcl1^–/– mutants is the up-regulated expression of a cohort of genes related to ribosome biogenesis and tRNA production. Our data demonstrate that Rcl1 is essential for 18S rRNA maturation at the A₁-site and for digestive organogenesis in zebrafish. Rcl1 deficiency, similar to deficiencies in other ribosome biogenesis factors, might trigger a common mechanism to upregulate the expression of genes responsible for ribosome biogenesis.

A Comprehensive Analysis of Northern versus Liquid Hybridization Assays for mRNAs, Small RNAs, and miRNAs Using a Non-Radiolabeled Approach

Northern blotting (NB), a gold standard for RNA detection, has lost its charm due to its hands-on nature, need for good quality RNA, and radioactivity. With the emergence of the field of microRNAs (miRNAs), the necessity for sensitive and quantitative NBs has again emerged. Here, we developed highly sensitive yet non-radiolabeled, fast, economical NB, and liquid hybridization (LH) assays without radioactivity or specialized reagents like locked nucleic acid (LNA)- or digoxigenin-labeled probes for mRNAs/small RNAs, especially miRNAs using biotinylated probes. An improvised means of hybridizing oligo probes along with efficient transfer, cross-linking, and signal enhancement techniques was employed. Important caveats of each assay were elaborated upon, especially issues related to probe biotinylation, use of exonuclease, and bioimagers not reported earlier. We demonstrate that, while the NBs were sensitive for mRNAs and small RNAs, our LH protocol could efficiently detect these and miRNAs using less than 10-100 times the total amount of RNA, a sensitivity comparable to radiolabeled probes. Compared to NBs, LH was a faster, more sensitive, and specific approach for mRNA/small RNA/miRNA detection. A comparison of present work with six seminal studies is presented along with detailed protocols for easy reproducibility. Overall, our study provides effective platforms to study large and small RNAs in a sensitive, efficient, and cost-effective manner.

Structural-profiling of low molecular weight RNAs by nanopore trapping/translocation using Mycobacterium smegmatis porin A

Folding of RNA can produce elaborate tertiary structures, corresponding to their diverse roles in the regulation of biological activities. Direct observation of RNA structures at high resolution in their native form however remains a challenge. The large vestibule and the narrow constriction of a Mycobacterium smegmatis porin A (MspA) suggests a sensing mode called nanopore trapping/translocation, which clearly distinguishes between microRNA, small interfering RNA (siRNA), transfer RNA (tRNA) and 5 S ribosomal RNA (rRNA). To further profit from the acquired event characteristics, a custom machine learning algorithm is developed. Events from measurements with a mixture of RNA analytes can be automatically classified, reporting a general accuracy of ~93.4%. tRNAs, which possess a unique tertiary structure, report a highly distinguishable sensing feature, different from all other RNA types tested in this study. With this strategy, tRNAs from different sources are measured and a high structural conservation across different species is observed in single molecule.

An integrated target recognition and polymerase primer probe for microRNA detection

Extremely sensitive and visual measurements of microRNA (miRNA) in situ for early detection and monitoring of diseases remains a major challenge. To address this issue, this work reports a rapid, highly sensitive and selective microRNA (miRNA) biosensing strategy based on isothermal circular strand-displacement polymerization (ICSDP), and miRNA imaging was performed inside cells. In this work, a double hairpin DNA probe (HP1/HP2 complex) embedded with a sensing region and polymerase primer region was designed. Briefly, after the specific binding of target miRNA with the HP1/HP2 probe, HP1/HP2 itself can function as a primer to initiate the ICSDP with the help of Klenow Fragment (KF), yielding target miRNA for new rounds of ICSDP. In this process, one target can produce multiple signal outputs (1: n), achieving low abundance of miRNA detection. Under optimized conditions, the proposed strategy showed high sensitivity with a detection limit of 5 pM within 15 min and can also easily distinguish the control miRNA from the target miRNA. This method can be further applied to image the intracellular miRNA of interest in situ inside the cancer cells.

Non-coding RNAs in cancer: platforms and strategies for investigating the genomic "dark matter"

The discovery of the role of non-coding RNAs (ncRNAs) in the onset and progression of malignancies is a promising frontier of cancer genetics. It is clear that ncRNAs are candidates for therapeutic intervention, since they may act as biomarkers or key regulators of cancer gene network. Recently, profiling and sequencing of ncRNAs disclosed deep deregulation in human cancers mostly due to aberrant mechanisms of ncRNAs biogenesis, such as amplification, deletion, abnormal epigenetic or transcriptional regulation. Although dysregulated ncRNAs may promote hallmarks of cancer as oncogenes or antagonize them as tumor suppressors, the mechanisms behind these events remain to be clarified. The development of new bioinformatic tools as well as novel molecular technologies is a challenging opportunity to disclose the role of the "dark matter" of the genome. In this review, we focus on currently available platforms, computational analyses and experimental strategies to investigate ncRNAs in cancer. We highlight the differences among experimental approaches aimed to dissect miRNAs and lncRNAs, which are the most studied ncRNAs. These two classes indeed need different investigation taking into account their intrinsic characteristics, such as length, structures and also the interacting molecules. Finally, we discuss the relevance of ncRNAs in clinical practice by considering promises and challenges behind the bench to bedside translation.

MicroRNA-like milR236, regulated by transcription factor MoMsn2, targets histone acetyltransferase MoHat1 to play a role in appressorium formation and virulence of the rice blast fungus Magnaporthe oryzae

MicroRNAs (miRNAs) play important roles in various cellular growth and developmental processes through post-transcriptional gene regulation via mRNA cleavage and degradation and the inhibition of protein translation. To explore if miRNAs play a role in appressoria formation and virulence that are also governed by the regulators of G-protein signaling (RGS) proteins in the rice blast fungus Magnaporthe oryzae, we have compared small RNA (sRNA) production between several ΔMorgs mutant and the wild-type strains. We have identified sRNA236 as a microRNA-like milR236 that targets the encoding sequence of MoHat1, a histone acetyltransferase type B catalytic subunit involved in appressorium function and virulence. We have also found that milR236 overexpression induces delayed appressorium formation and virulence attenuation, similar to those displayed by the ΔMohat1 mutant strain. Moreover, we have shown that the transcription factor MoMsn2 binds to the promoter sequence of milR236 to further suppress MoHAT1 transcription and MoHat1-regulated appressorium formation and virulence. In summary, by identifying a novel regulatory role of sRNA in the blast fungus, our studies reveal a new paradigm in the multifaceted regulatory pathways that govern the appressorium formation and virulence of M. oryzae.

Liquid biopsy: Circulating exosomal long noncoding RNAs in cancer

Despite many advances in diagnostics and multimodal treatment (surgery, radiotherapy, chemotherapy), cancer still remains one of the most important public health challenges worldwide because of the associated morbidity and mortality. Liquid biopsy has been developed to detect cancer at an early stage based on minimally invasive and serial body fluid tests with the advantage of following tumor evolution in real time. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating cell-free noncoding RNAs (cfRNAs) and circulating exosomes represent the major components of liquid biopsy analysis. Liquid biopsy already has been implemented in cancer management, and most studies thus far are mainly focused on CTCs and ctDNA. In fact, the circulating long noncoding RNAs (lncRNAs) in exosomes have been discovered and confirmed to be closely related to tumorigenesis, metastasis and therapy. Thus this review is mainly focused on the clinical potential of circulating exosomal lncRNAs as a source of liquid biopsy biomarkers in cancer diagnosis, prognosis, and response to treatment, offering novel insights into the precision medicine of oncology.

Near-infrared fluorescent northern blot

Northern blot analysis detects RNA molecules immobilized on nylon membranes through hybridization with radioactive ³²P-labeled DNA or RNA oligonucleotide probes. Alternatively, nonradioactive northern blot relies on chemiluminescent reactions triggered by horseradish peroxidase (HRP) conjugated probes. The use of regulated radioactive material and the complexity of chemiluminescent reactions and detection have hampered the adoption of northern blot techniques by the wider biomedical research community. Here, we describe a sensitive and straightforward nonradioactive northern blot method, which utilizes near-infrared (IR) fluorescent dye-labeled probes (irNorthern). We found that irNorthern has a detection limit of ∼0.05 femtomoles (fmol), which is slightly less sensitive than ³²P-Northern. However, we found that the IR dye-labeled probe maintains the sensitivity after multiple usages as well as long-term storage. We also present alternative irNorthern methods using a biotinylated DNA probe, a DNA probe labeled by terminal transferase, or an RNA probe labeled during in vitro transcription. Furthermore, utilization of different IR dyes allows multiplex detection of different RNA species. Therefore, irNorthern represents a more convenient and versatile tool for RNA detection compared to traditional northern blot analysis.

tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner

tRNA related RNA fragments (tRFs), also known as tRNA-derived RNAs (tdRNAs), are abundant small RNAs reported to be associated with Argonaute proteins, yet their function is unclear. We show that endogenous 18 nucleotide tRFs derived from the 3' ends of tRNAs (tRF-3) post-transcriptionally repress genes in HEK293T cells in culture. tRF-3 levels increase upon parental tRNA overexpression. This represses target genes with a sequence complementary to the tRF-3 in the 3' UTR. The tRF-3-mediated repression is Dicer-independent, Argonaute-dependent, and the targets are recognized by sequence complementarity. Furthermore, tRF-3:target mRNA pairs in the RNA induced silencing complex associate with GW182 proteins, known to repress translation and promote the degradation of target mRNAs. RNA-seq demonstrates that endogenous target genes are specifically decreased upon tRF-3 induction. Therefore, Dicer-independent tRF-3s, generated upon tRNA overexpression, repress genes post-transcriptionally through an Argonaute-GW182 containing RISC via sequence matches with target mRNAs.

Resistance to CymMV and ORSV in artificial microRNA transgenic Nicotiana benthamiana plants

Transgenic plants expressing artificial microRNAs (amiRNAs) have been shown to confer specific resistance to corresponding viruses. Here, we generated Nicotiana benthamiana transgenic lines containing Oryza sativa miR528 as backbone, expressing amiRNAs targeting RNA-dependent RNA polymerase (RdRp) gene of Cymbidium mosaic virus (CymMV) and Odontoglossum ringspot virus (ORSV). The amiRNA transgenic lines could express amiR-CymMV and confer high percentage resistance to CymMV, while lack of detectable level of amiR-ORSV expression in amiR-ORSV transgenic N. benthamiana plants led to weak resistance to ORSV infection. In this project, we provide the first report of CymMV-resistant transgenic N. benthamiana plants based on amiRNA strategy. We believe that this amiRNA approach can be extended to generate CymMV-resistant transgenic orchids.

Comparative genome-wide analysis of extracellular small RNAs from the mucormycosis pathogen Rhizopus delemar

Rhizopus delemar is an emerging fungal pathogen causing devastating mucormycosis in immunocompromised individuals. The organism remains understudied and there are urgent needs for new methods of rapid disease diagnosis for timely therapy. Extracellular vesicles with encapsulated RNAs have recently been discovered to have great potential applications for disease diagnoses and treatments. To explore the utilization of ex-RNA in studies of mucormycosis, we have performed RNA-Seq of ex-sRNAs from two clinical strains of R. delemar. Approximately 3.3 and 3.2 million clean reads were obtained from FGSC-9543 and CDC-8219 strains, respectively. The median sequence length of the sRNAs was 22 nts, with a minimum of 18 and a maximum of 30 nts. Further annotation identified 560 and 526 miRNAs from FGSC-9543 and CDC-8219 strains, respectively. miRNA target prediction and analysis of GO and KEGG pathways have revealed that the regulation of metabolism, secondary metabolite biosynthesis, and two-component system signaling are important during growth. We have also validated RNA-Seq by qRT-PCR and Northern blotting analysis of randomly selected miRNAs. Our results show that R. delemar has a rich reservoir of secreted ex-sRNAs and our studies could facilitate the development of improved diagnostic methods as well as elucidating virulence mechanisms for R. delemar infection.

Nonradioactive Plant Small RNA Detection Using Biotin-Labeled Probes

Small noncoding RNAs are essential for gene expression at transcriptional and posttranscriptional levels. Northern blot is the most used method for small RNA detection in tissues. Here we present an improved protocol for the Northern blot-based small RNA detection from plant tissues by using biotin-labeled probes. MicroRNAs and small interfering RNAs derived from Arabidopsis and Oryza sativa, respectively, have been detected with this methodology. Results suggest that this method is sensitive and efficient enough to detect small RNAs from plant tissues by using as low as 5 μg of total RNA. Furthermore, biotin-labeled probes are safer and easier to store for long term than radiolabeled probes.

Detection and Verification of Mammalian Mirtrons by Northern Blotting

microRNAs (miRNAs) have vital roles in regulating gene expression-contributing to major diseases like cancer and heart disease. Over the last decade, thousands of miRNAs have been discovered through high throughput sequencing-based annotation. Different classes have been described, as well as a great dynamic range of expression levels. While sequencing approaches provide insight into biogenesis and allow confident identification, there is a need for additional methods for validation and characterization. Northern blotting was one of the first techniques used for studying miRNAs, and remains one of the most valuable as it avoids enzymatic manipulation of miRNA transcripts. Blotting can also provide insight into biogenesis by revealing RNA processing intermediates. Compared to sequencing, however, northern blotting is a relatively insensitive technology. This creates a challenge for detecting low expressed miRNAs, particularly those produced by inefficient, non-canonical pathways. In this chapter, we describe a strategy to study such miRNAs by northern blotting that involves ectopic expression of both miRNAs and miRNA-binding Argonaute (Ago) proteins. Through use of epitope tags, this strategy also provides a convenient method for verification of small RNA competency to be loaded into regulatory complexes.

Genome-wide identification and characterization of small RNAs in Rhodobacter capsulatus and identification of small RNAs affected by loss of the response regulator CtrA

Small non-coding RNAs (sRNAs) are involved in the control of numerous cellular processes through various regulatory mechanisms, and in the past decade many studies have identified sRNAs in a multitude of bacterial species using RNA sequencing (RNA-seq). Here, we present the first genome-wide analysis of sRNA sequencing data in Rhodobacter capsulatus, a purple nonsulfur photosynthetic alphaproteobacterium. Using a recently developed bioinformatics approach, sRNA-Detect, we detected 422 putative sRNAs from R. capsulatus RNA-seq data. Based on their sequence similarity to sRNAs in a sRNA collection, consisting of published putative sRNAs from 23 additional bacterial species, and RNA databases, the sequences of 124 putative sRNAs were conserved in at least one other bacterial species; and, 19 putative sRNAs were assigned a predicted function. We bioinformatically characterized all putative sRNAs and applied machine learning approaches to calculate the probability of a nucleotide sequence to be a bona fide sRNA. The resulting quantitative model was able to correctly classify 95.2% of sequences in a validation set. We found that putative cis-targets for antisense and partially overlapping sRNAs were enriched with protein-coding genes involved in primary metabolic processes, photosynthesis, compound binding, and with genes forming part of macromolecular complexes. We performed differential expression analysis to compare the wild type strain to a mutant lacking the response regulator CtrA, an important regulator of gene expression in R. capsulatus, and identified 18 putative sRNAs with differing levels in the two strains. Finally, we validated the existence and expression patterns of four novel sRNAs by Northern blot analysis.

Nonradioactive Detection of Small RNAs Using Digoxigenin-Labeled Probes

Small RNAs have been traditionally detected and quantified using small RNA blots, a modified Northern blot technique. The small RNAs are size-fractionated from the rest of the cellular RNA molecules by polyacrylamide gel electrophoresis and transferred by blotting onto a positively charged membrane. A radiolabeled probe was then traditionally used to detect a specific small RNA in the cellular pool. Small RNA blotting is a relatively simple, inexpensive approach to visualize small RNAs without artifacts. However, the radioactive labeling of the probe is sometimes an impediment, especially due to the requirement of specialized facilities. Here we describe a sensitive and simple method to detect and quantify small RNAs using digoxigenin-based nonradioactive RNA blots.

PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice

Phased small-interfering RNAs (phasiRNAs) are a special class of small RNAs, which are generated in 21- or 24-nt intervals from transcripts of precursor RNAs. Although phasiRNAs have been found in a range of organisms, their biological functions in plants have yet to be uncovered. Here we show that phasiRNAs generated by the photopheriod-sensetive genic male sterility 1 (Pms1) locus were associated with photoperiod-sensitive male sterility (PSMS) in rice, a germplasm that started the two-line hybrid rice breeding. The Pms1 locus encodes a long-noncoding RNA PMS1T that was preferentially expressed in young panicles. PMS1T was targeted by miR2118 to produce 21-nt phasiRNAs that preferentially accumulated in the PSMS line under long-day conditions. A single nucleotide polymorphism in PMS1T nearby the miR2118 recognition site was critical for fertility change, likely leading to differential accumulation of the phasiRNAs. This result suggested possible roles of phasiRNAs in reproductive development of rice, demonstrating the potential importance of this RNA class as regulators in biological processes.

Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview

The assessment of gene expression levels is an important step toward elucidating gene functions temporally and spatially. Decades ago, typical studies were focusing on a few genes individually, whereas now researchers are able to examine whole genomes at once. The upgrade of throughput levels aided the introduction of systems biology approaches whereby cell functional networks can be scrutinized in their entireties to unravel potential functional interacting components. The birth of systems biology goes hand-in-hand with huge technological advancements and enables a fairly rapid detection of all transcripts in studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in research laboratories. The objective here is to highlight key approaches used in gene expression analysis in plant responses to environmental stresses, or, more generally, any other condition of interest. Northern blots, RNase protection assays, and qPCR are described for their targeted detection of one or a few transcripts at a once. Differential display and serial analysis of gene expression represent non-targeted methods to evaluate expression changes of a significant number of gene transcripts. Finally, microarrays and RNA-seq (next-generation sequencing) contribute to the ultimate goal of identifying and quantifying all transcripts in a cell under conditions or stages of study. Recent examples of applications as well as principles, advantages, and drawbacks of each method are contrasted. We also suggest replacing the term “Next-Generation Sequencing (NGS)” with another less confusing synonym such as “RNA-seq”, “high throughput sequencing”, or “massively parallel sequencing” to avoid confusion with any future sequencing technologies.

Perturbations in actin dynamics reconfigure protein complexes that modulate GCN2 activity and promote an eIF2 response

Genetic and pharmacological interventions in yeast and mammalian cells have suggested a cross-talk between the actin cytoskeleton and protein synthesis. Regulation of the activity of the translation initiation factor 2 (eIF2) is a paramount mechanism for cells to rapidly adjust the rate of protein synthesis and to trigger reprogramming of gene expression to adapt in response to internal and external cues. Here we show that disruption of F-actin in mammalian cells inhibits translation in a GCN2-dependent manner, correlating with increased levels of uncharged tRNA. GCN2 activation increased phosphorylation of its substrate eIF2α and the induction of the integrated stress response master regulator, ATF4. GCN2 activation by latrunculin is dependent on GCN1 and inhibited by IMPACT. Our data suggest that GCN2 occurs in two different complexes, GCN2-eEF1A and GCN2-GCN1. Depolymerization of F-actin shifts GCN2 to favor the complex with GCN1, concomitant with GCN1 being released from its binding to IMPACT, which is sequestered by G-actin. These events may further contribute to GCN2 activation. Our findings indicate that GCN2 is an important sensor of the state of the actin cytoskeleton.