Modified Arabidopsis RootsmRNA FISH Protocol v1

To promote fidelity in nuclear pre-mRNA splicing, the spliceosome rejects and discards suboptimal splicing substrates after they have engaged the spliceosome. Although nuclear quality control mechanisms have been proposed to retain immature mRNPs, evidence indicates that discarded splicing substrates, including lariat intermediates, do export to the cytoplasm, as indicated by their translation and degradation by cytoplasmic nucleases. However, the mechanism for exporting these species has remained unknown. By single molecule (sm) RNA FISH in budding yeast, we have directly observed the nuclear export of lariat intermediates. Further, by crosslinking, export reporter assays, and smRNA FISH, we have demonstrated that the export of lariat intermediates requires the general mRNA export receptor Mex67p and three of its mRNA export adapter proteins, Nab2p, Yra1p, and Nlp3, establishing that mRNAs and lariat intermediates share the same export machinery. Unexpectedly, the export of lariat intermediates, but not mRNA, requires an interaction between Nab2p and Mlp1p, a nuclear basket component implicated in retaining immature mRNPs, including unspliced pre-mRNA, in the nucleus of budding yeast. Finally, the export of lariat intermediates, like mRNA, relies on the E3 ubiquitin ligase Tom1p and its target sites in Yra1p. Overall, our data indicate that the nuclear basket can promote, rather than antagonize, the export of an immature mRNP. Further, our data imply that the export of discarded lariat intermediates requires both Mlp1p-dependent docking onto the nuclear basket and subsequent Tom1p-mediated undocking, a mechanism our data suggests functions in the export of mRNA also but in a manner obscured by redundant pathways.

RNA molecules are localized to subcellular regions through interactions between localization-regulatory cis-elements and trans-acting RNA binding proteins (RBPs). However, the identities of RNAs whose localization is regulated by a specific RBP, as well as the impacts of that RNA localization on cell function, have generally remained unknown. Here, we demonstrate that the RBP HNRNPA2B1 acts to keep specific RNAs out of neuronal projections. Using subcellular fractionation, high-throughput sequencing, and single-molecule RNA FISH, we find that hundreds of RNAs demonstrate markedly increased abundance in neurites in HNRNPA2B1 knockout cells. These RNAs often encode motor proteins and are enriched for known HNRNPA2B1 binding sites and motifs in their 3' UTRs. The speed and processivity of microtubule-based transport are impaired in these cells. HNRNPA2B1 point mutations that increase its cytoplasmic abundance relative to wildtype lead to stronger suppression of RNA mislocalization defects than seen with wildtype HNRNPA2B1. We further find that the subcellular localizations of HNRNPA2B1 target RNAs are sensitive to perturbations of RNA decay machinery, suggesting that HNRNPA2B1's known role in regulating cytoplasmic RNA stability may explain these observations. These findings establish HNRNPA2B1 as a negative regulator of neurite RNA abundance and a necessary factor for efficient motor-dependent cargo transport.

Normal expression of the minor oncogene EIF5A2 in the hypusine pathway is restricted to brain and testis. However aberrant expression has been noted in multiple cancers, including ovarian gastric, colorectal and pancreatic, and artificial overexpression causes tumor growth in naked mice. Unlike cDNAs from the homologous gene EIF5A1, which are readily translated into protein upon transient transfection, EIF5A2-mRNAs only associate with monosomes without production of eIF5A-2 protein. Here we present data from multiple EIF5A2-positive cell lines on the steady state levels of the four different EIF5A2-mRNAs that arise through differential polyadenylation. While considering qPCR and RNA-Seq, we chose to apply Stellaris single molecule RNA fluorescence in situ hybridization with four unique probe sets, each reporting on the dependent A, B, C, or D segments. The probe sets were designed with multiple tiled singly labeled 18-22-mer oligonucleotides with balanced GC content, and hence similar hybridization characteristics, which in turn enabled the simultaneous quadruplex smRNA FISH. Stellaris RNA FISH leaves the cell intact, and also does not require RNA isolation or nucleic acid amplification that may introduce an otherwise hidden experimental bias. The single molecule spots revealed by widefield microscopy and subsequent image analysis co-localized with a high degree of confidence. Taking advantage of the added spatial dimension that RNA FISH affords, we also determined the localization of each mRNA variant and recorded the cell-to-cell variability and the actual range of mRNA copy numbers per cell. Our data is consistent with previous gene expression analysis data, but also provide actual counts of each mRNA variant. The results presented here have direct applications for the expression of the minor oncogene EIF5A2, and the regulated protein synthesis of its mRNAs, as well as of other mRNAs in polyamine and hypusine pathways. Further, the techniques and probes developed here can be directly transferred to the analysis of other mRNA variants that may arise through alternative transcription start site use, alternative splicing or alternative 3’ end processing in normal and aberrant cells. Citation Format: Hans E. Johansson, Raymund H. Yin, Swati Mandal, Myung-Hee Park. Alternative polyadenylation of eukaryotic initiation factor 5A-2 (eIF5A-2) mRNAs examined by quadruplex single molecule RNA fluorescence in situ hybridization (smRNA-FISH). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1998.

ZC3H12D belongs to a recently discovered family of proteins containing four members of which the most studied and best described is the RNase ZC3H12A (MCPIP1/Regnase-1). ZC3H12A is a crucial negative regulator of inflammation. It accelerates the turnover of transcripts of a spectrum of proinflammatory cytokines, as well as its own mRNA. The biological role of ZC3H12D is less clear, although it was shown that this member of ZC3H12 family is also involved in the regulation of inflammation. Here, we show that ZC3H12A and ZC3H12D recognize a set of common target mRNAs encoding proteins that play important roles in the course of the inflammation. Similarly to ZC3H12A, ZC3H12D participates in the 3'UTR-dependent regulation of the turnover of mRNAs encoding interleukin-6 (IL-6), tumor necrosis factor (TNF), and immediate early response 3 gene (IER3). The ZC3H12A mRNA is also among the identified ZC3H12D targets. Using the combination of immunofluorescence with single molecule RNA fluorescence in situ hybridization (smRNA FISH) we have shown that ZC3H12D protein interacts with the ZC3H12A transcript. The direct binding of these two molecules in vivo was further confirmed by RNA immunoprecipitation. Simultaneously, overexpression of ZC3H12D increases the turnover rate of transcripts containing ZC3H12A 3'UTR. Using reporter gene assays we have confirmed that the Asp95 residue present in the NYN/PIN-like domain is crucial for ZC3H12D biological activity. We have also revealed that ZC3H12D recognizes the same structural elements present in the 3'UTRs of the investigated transcripts, as ZC3H12A. J. Cell. Biochem. 118: 487-498, 2017. © 2016 Wiley Periodicals, Inc.

Whole-mount single-molecule RNA fluorescence in situ hybridization (smRNA FISH) in combination with immunofluorescence (IF) offers great potential to study long non-coding RNAs (lncRNAs): their subcellular localization, their interactions with proteins, and their function. Here, we describe a step-by-step, optimized, and robust protocol that allows detection of multiple RNA transcripts and protein molecules in whole-mount preimplantation mouse embryos. Moreover, to simultaneously detect protein and enable RNA probe penetration for the combined IF/smRNA FISH technique, we performed IF before smRNA FISH. We removed the zona pellucida, used Triton X-100 to permeabilize the embryos, and did not use a proteinase digestion step so as to preserve the antigens. In addition, we modified the IF technique by using RNase-free reagents to prevent RNA degradation during the IF procedure. Using this modified sequential IF/smRNA FISH technique, we have simultaneously detected protein, lncRNA, and mRNA in whole-mount preimplantation embryos. This reliable and robust protocol will contribute to the developmental biology and RNA biology fields by providing information regarding 3D expression patterns of RNA transcripts and proteins, shedding light on their biological function.

Recent studies indicate that approximately 15% of couples worldwide are affected by infertility. The discovery of female germline stem cells (FGSCs) offers a promising new therapeutic strategy for infertility treatment.The objective of this study is to elucidate the regulatory role of epibrassinolide in the development of FGSCs and its underlying mechanism. We developed an in vitro FGSC culture system treated with 24-epibrassinolide (EBR, E1641, Sigma), a bioactive brassinosteroid. Proliferation was quantified via CCK-8 assays and EdU incorporation; apoptotic levels of cells following drug treatment were assessed by flow cytometry and TUNEL assay; differentiation status was assessed by western blotting, immunofluorescence, and qRT-PCR. For exploring mechanisms，we performed long-read RNA-seq, RNA in situ conformation sequencing (RIC-seq), tagged RNA affinity purification, LC-MS/MS proteomics, single-molecule RNA FISH, and RNA immunoprecipitation. EBR significantly enhanced FGSC development by coordinately regulating: (1) meiotic progression acceleration and (2) apoptotic pathway suppression. Integrative RIC-seq/longRNA-seq analysis revealed EBR reinforces spatial interactions between lncRNA Gm26624 and transporter gene Abcg2. Mechanistically, N-myristoyltransferase 1 (NMT1) functions as an RNA-binding scaffold facilitating this RNA-RNA interaction. Functional validation established the EBR-induced Gm26624-Abcg2 axis as both necessary and sufficient for meiotic entry initiation. We identify a phytohormonal signaling pathway orchestrating FGSC fate determination through an NMT1-mediated RNA interactome. These findings elucidate fundamental germline stem cell regulation principles and provide proof-of-concept for plant-derived compounds as promising reproductive therapeutics. Working model: 24-Epibrassinolide drives female germline stem cell development via NMT1-mediated in situ interaction between Gm26624 and Abcg2 • First evidence that EBR promotes FGSC development. • Gm26624–Abcg2 interaction identified as a key regulator via LongRNA-seq and RIC-seq. • EBR acts through NMT1-mediated Gm26624–Abcg2 interaction.

We developed a cost-effective genome-scale PCR-based method for high-definition DNA FISH (HD-FISH). We visualized gene loci with diffraction-limited resolution, chromosomes as spot clusters and single genes together with transcripts by combining HD-FISH with single-molecule RNA FISH. We provide a database of over 4.3 million primer pairs targeting the human and mouse genomes that is readily usable for rapid and flexible generation of probes.

Transcription activation of genes by estrogens is driven by enhancers, which are often located within the same Topologically Associating Domain (TAD) as non-targeted promoters. We investigated how acute enhancer-driven activation affects neighbouring non-target genes within the same TAD. Using single-molecule RNA FISH (smFISH), we tracked the transcription of TFF1 (enhancer-targeted) and TFF3 (non-targeted) during estrogen stimulation. We observed mutually exclusive expression patterns: TFF1 expression peaked at 1 hour, while TFF3 reached its peak at 3 hours, after TFF1’s activation had diminished. Chromatin looping data indicated that the enhancer loops with TFF1 but not TFF3, suggesting that TFF3 upregulation is not due to direct enhancer-promoter interactions. CRISPR deletion of the TFF1 enhancer and 1,6-hexanediol (HD) exposure revealed that the TFF1 enhancer:promoter undergo Liquid-Liquid Phase Separation (LLPS), which sequesters the transcriptional machinery and inhibits TFF3 expression. As estrogen signalling wanes or LLPS is disrupted, TFF1 expression declines while TFF3 expression increases. Our findings reveal that enhancer-driven activation can indirectly influence neighbouring genes, highlighting a dynamic shift in gene expression as signalling progresses.

We have compared the efflux of cholesterol from different cellular pools of human hepatoma cells HepG2 using intact cells or isolated membrane fractions. To label different pools, cells were incubated with either unesterified [14C]cholesterol that had been incorporated into high density lipoproteins ([14C]FC-HDL), low density lipoproteins ([14C]FC-LDL), or phosphatidylcholine liposomes ([14C]FC-PC), or with [14C]acetate. Cell fractionation revealed that labeling of cells with [14C]FC-PC resulted in the incorporation of [14C]cholesterol almost exclusively into the plasma membrane (PM), while incubation with [14C]FC-HDL resulted in the majority of [14C]cholesterol incorporation into the PM, but with a smaller component associated with lysosomes. Labeling with [14C]FC-LDL or [14C]acetate led to an accumulation of [14C]cholesterol predominantly in lysosomes or the endoplasmic reticulum (ER), respectively. When the kinetics of [14C]cholesterol efflux was analyzed after pulse-labeling of different cellular pools, half-times of cholesterol efflux from lysosomes and ER were significantly longer than that from PM. In another set of experiments, when both labeling and efflux times varied, efflux of [14C]cholesterol from the PM to human serum after 1.5 h pulse and chase incubations was double that from lysosomes and 8-fold that from ER. Extension of the incubation times from 1.5 to 3 h diminished the difference in cholesterol efflux from different membranes. Further incubation to 6 h almost abolished the different responses. Cell-free preparations of membranes, obtained from cells labeled with [14C]cholesterol, showed no differences in cholesterol efflux. No differences in the distribution of [14C]cholesterol released into serum among lipoprotein subfractions was observed. Pretreatment of the serum with Fab fragments of polyclonal rabbit anti-human apolipoprotein A-I antibodies reduced its ability to promote efflux of cholesterol from the ER by 77%, but had no effect on cholesterol efflux from the PM. Fab fragments of non-immune IgG had no effect on the efflux of both ER and PM cholesterol. We conclude that the availability of cellular cholesterol for efflux from HepG2 cells is strongly influenced by its subcellular location, and is regulated by apolipoprotein A-I.

Various studies have shown that various cell types can be labeled with iron oxide particles and visualized by magnetic resonance imaging (MRI). However, reported protocols for cell labeling show a large variation in terms of labeling dose and incubation time. It is therefore not clear how different labeling protocols may influence labeling efficiency. Systematic assessment of the effects of various labeling protocols on labeling efficiency of human umbilical vein endothelial cells (HUVEC) using two different types of iron oxide nanoparticles, i.e. super paramagnetic iron oxide particles (SPIOs) and microparticles of iron oxide (MPIOs), demonstrated that probe concentration, incubation time and particle characteristics all influence the efficiency of label incorporation, label distribution, label retention and cell behavior. For SPIO the optimal labeling protocol consisted of a dose of 12.5 µg iron/2 ml/9.5 cm(2) and an incubation time of 24 h, resulting in an average iron load of 12.0 pg iron/per cell (uptake efficiency of 9.6%). At 4 h many SPIOs are seen sticking to the outside of the cell instead of being taken up by the cell. For MPIO optimal labeling was obtained with a dose of 50 µg iron/2 ml/9.5 cm(2). Incubation time was of less importance since most of the particles were already incorporated within 4 h with a 100% labeling efficiency, resulting in an intracellular iron load of 626 pg/cell. MPIO were taken up more efficiently than SPIO and were also better tolerated. HUVEC could be exposed to and contain higher amounts of iron without causing significant cell death, even though MPIO had a much more pronounced effect on cell appearance. Using optimal labeling conditions as found for HUVEC on other cell lines, we observed that different cell types react differently to identical labeling conditions. Consequently, for each cell type separately an optimal protocol has to be established.

A simple cell labeling technique by means of lectins linked to fluorochromes for the detection of cells on tissue sections

The radiolabelling of blood cellular elements with PET radionuclides offers a higher sensitivity and resolution than conventional imaging, but short-lived PET radionuclides have limited clinical use in cell labelling. Medium half-life PET radionuclides, such as 55Co (t1/2 = 18.2 h), 52Fe (t1/2 = 8.3 h) and 66Ga (t1/2 = 9.4 h), enable quantitative uptake and cell kinetic studies with radiolabelled blood cellular elements. Co(II) oxine, Co(III) tropolonate, Fe(III) oxine, Ga(III) oxine and Ga(III) MPO were prepared using gamma-emitting radionuclides and a number of cell labelling parameters were investigated. The uptake of 57Co(II) oxine into erythrocytes was only 37%, and 65% of the activity eluted from the cells in cell-free plasma within 30 min. In contrast, high leukocyte and erythrocyte labelling efficiencies (> 90%) were obtained with 57Co(III) tropolonate containing cobalt carrier and the elution in cell-free plasma over 4 h was < 8%. High labelling efficiencies were also observed with 59Fe(III) oxine and 67Ga-MPO and the elution from leukocytes over 4 h was < 25%. We conclude that Co(III) tropolonate, Fe(III) oxine and Ga-MPO may be useful for radiolabelling leukocytes for PET investigations.

Versatility of merocyanine 540 for the flow cytometric detection of apoptosis in human and murine cells

Advances in computer vision have substantially improved our ability to analyze the structure and mechanics of the heart. In comparison, our ability to observe and analyze cardiac electrical activities is much limited. The progress to computationally reconstruct cardiac current sources from noninvasive voltage data sensed on the body surface has been hindered by the ill-posedness and the lack of a unique solution of the reconstruction problem. Common L2- and L1-norm regularizations tend to produce a solution that is either too diffused or too scattered to reflect the complex spatial structure of current source distribution in the heart. In this work, we propose a general regularization with Lp-norm (1 < p < 2) constraint to bridge the gap and balance between an overly smeared and overly focal solution in cardiac source reconstruction. In a set of phantom experiments, we demonstrate the superiority of the proposed Lp-norm method over its L1 and L2 counterparts in imaging cardiac current sources with increasing extents. Through computer-simulated and real-data experiments, we further demonstrate the feasibility of the proposed method in imaging the complex structure of excitation wavefront, as well as current sources distributed along the postinfarction scar border. This ability to preserve the spatial structure of source distribution is important for revealing the potential disruption to the normal heart excitation.

A flow-cytometry based cytotoxicity assay using stained effector cells in combination with native target cells