Journal: RNA Biology

Article Title: C-terminal tagging impairs AGO2 function

doi: 10.1080/15476286.2025.2534028

Figure Lengend Snippet: Creation and genomic characterisation of AGO2-HaloTag cell Lines(A) schematic of WT AGO2 and the C terminal AGO2-HaloTag fusion (including T2A site, puromycin resistant (PuroR) and Poly(A) sections) genotype to be generated by CRISPaint editing of A549 cells. Arrows indicate locations of forward and reverse primers designed to confirm editing. Blue = AGO2 WT last intron forward and reverse; Light Teal = HaloTag1 forward and reverse; Dark Teal = HaloTag2 forward and reverse.(B) agarose gel loaded with PCR products of A549 WT and two AGO2-HaloTag (AGO2-HaloTag C5 and AGO2-HaloTag C10) lines amplified with indicated combinations of AGO2 WT and HaloTag primers, as indicated in (A). Red arrows indicate gDNA containing HaloTag sequence which was purified and submitted for sequencing. Circled numbers 1–3 indicate gDNA containing C terminal non-HaloTagged AGO2 product which was purified and submitted for sequencing. (C) sequence (generated from TOPO-seq) alignments of WT and two AGO2-HaloTag clones at the AGO2-HaloTag junction. From several submitted TOPO clones, two variants of AGO2-HaloTag (one long and one short) were identified in AGO2-HaloTag cells. Asterisk (*) indicates STOP codon. (D) schematic to show known functionally important domains of AGO2, with a focus on C-terminal PIWI domain. CRISPaint mediated AGO2-HaloTag fusion generated a long and a short variant. (E) chromatograph of C terminal AGO2 sequence identified in WT, AGO2-HaloTag C5 and AGO2-HaloTag C10 cells (circled numbers 1–3 in (B)) showing the additional and premature STOP codon in both AGO2-HaloTag lines. (F) abundance of untagged AGO2 mRNA transcript in A549 WT, two UnTagged (UT C1 and UT C2) and two AGO2-HaloTag (AGO2-HaloTag C5 and AGO2-HaloTag C10) cells. AGO2 (non-HaloTagged) mRNA abundance normalized to B Actin mRNA abundance and made relative to levels in WT cells. Data represent mean ± SEM of experiments; n = 3 (* p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001). (G & H) Western blot of whole-cell lysates from A549 WT, two UnTagged (UT C1 and UT C2) and two AGO2-HaloTag (AGO2-HaloTag C5 and AGO2-HaloTag C10) cell lines probed with antibodies against AGO2, HaloTag, and beta Actin.

Article Snippet: Single-cell clones were screened for loss of AGO2 expression by immunoblotting using rabbit anti-AGO2 (Sino Biological 101,620-T36).

Techniques: Generated, Agarose Gel Electrophoresis, Amplification, Sequencing, Purification, Clone Assay, Variant Assay, Western Blot

Journal: RNA Biology

Article Title: C-terminal tagging impairs AGO2 function

doi: 10.1080/15476286.2025.2534028

Figure Lengend Snippet: Initial characterisation of AGO2-HaloTag cells Lines(A) doubling time of A549 WT, two UnTagged (UT C1 and UT C2) and two AGO2-HaloTag (AGO2-HaloTag C5 and AGO2-HaloTag C10) measured using IncucyteZoom over 108 hours. Data represent mean ± SEM; n = 3 (ns p > 0.05). (B) Representative Western blot of whole-cell lysates from indicated cell lines (harvested during log-phase) probed with antibodies against AGO1, AGO2, AGO3, AGO4, Vinculin. (C) Representative Western blot of whole-cell lysates from indicated cell lines (harvested during log-phase) probed with antibodies against DDX6, TNRC6A, LIMD1, and beta Actin. (D) densitometry of AGO1/2/3/4 (normalized to loading control (Vinculin)) in indicated cell lines. Data represents mean ± SEM; n = 3 (* p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001 according to one-way ANOVA test with Dunnett’s multiple comparisons). (E) densitometry analysis of drosha, exportin 5, Dicer, DGCR8, DDX6 andTNRC6A, (normalized to loading control (beta Actin or vinculin)) in indicated cell lines. Data represent mean ± SEM; n = 3 (* p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001).

Article Snippet: Single-cell clones were screened for loss of AGO2 expression by immunoblotting using rabbit anti-AGO2 (Sino Biological 101,620-T36).

Techniques: Western Blot, Control

Journal: RNA Biology

Article Title: C-terminal tagging impairs AGO2 function

doi: 10.1080/15476286.2025.2534028

Figure Lengend Snippet: Characterising AGO2 interactions, AGO2 localization and miR-451a levels in AGO2-HaloTag clones. (A) endogenous co-immunoprecipitation of AGO2 with Dicer and TNRC6A in WT, UnTagged C1 , UnTagged C2, AGO2-HaloTag C5 and AGO2-HaloTag C10 cells. Note the increased AGO2-Dicer and decreased AGO2-TNRC6A co-immunoprecipitation in AGO2 HALO cells compared to in WT and UnTagged cells. Histogram shows mean densitometry for TNRC6A IP normalized to AGO2 IP densitometry relative to WT A549 cells. Data represents mean of four independent repeats with * indicating p ≤ 0.05 according to one-way ANOVA test with Dunnett’s multiple comparisons. (B) immunoblots of nuclear and cytoplasmic fractions from WT. UnTagged C1 , UnTagged C2, AGO2-HaloTag C5 and AGO2-HaloTag C10 cells. Whole cell lysate (WCL) from WT A549 was also blotted alongside. Beta tubulin and histone H3 were probed as loading controls for cytoplasmic and nuclear fractions, respectively. (C) MiR-451a abundance (normalized to U6 RNA and made relative to relevant WT) in indicated cell lines measured by RT-qPCR using the 2 –∆∆Ct method. Data represent mean ± SEM; n = 2 (* p ≤ 0.05 according to one-way ANOVA test with Dunnett’s multiple comparisons). (D) pri-miR-451 abundance (normalised to beta actin mRNA levels) in indicated cell lines measured by RT-qPCR using the standard curve method. Data represent mean ± SEM; n = 2 (ns = not significant according to one-way ANOVA test with Dunnett’s multiple comparisons).

Article Snippet: Single-cell clones were screened for loss of AGO2 expression by immunoblotting using rabbit anti-AGO2 (Sino Biological 101,620-T36).

Techniques: Clone Assay, Immunoprecipitation, Western Blot, Quantitative RT-PCR

Journal: RNA Biology

Article Title: C-terminal tagging impairs AGO2 function

doi: 10.1080/15476286.2025.2534028

Figure Lengend Snippet: Creation of AGO2 knockout A549, firefly luciferase assays and comparison of N - and C-terminally tagged AGO2. (A) Generation of AGO2 knockout A549 cells. Immunoblot of two AGO2 −/− clones alongside two control clones for AGO2 and beta actin as a loading control. (B) Relative firefly/Renilla luciferase activity in indicated cell lines transfected with reporter plasmids expressing firefly and Renilla luciferase and a siRNA against firefly luciferase (esi FFLuc ) or ‘non-targeting’ control (esi GFP ). The ratio between firefly and Renilla luciferase activity was measured 24 h after transfection. Data represent mean ± SEM; n = 3 (ns p > 0.05, **** p ≤ 0.0001 according to two-way ANOVA test with Sidak’s multiple comparisons). (C) Plasmid constructs for expression of untagged AGO2, EGFP-AGO2 and AGO2-EGFP. EGFP-VO is a control. (D) Relative firefly/Renilla luciferase activity in AGO2 −/− A549 transfected with reporter plasmids, AGO2 plasmids and an siRNA against firefly luciferase (esi FFLuc ) or ‘non-targeting’ control (scr). The ratio between firefly and Renilla luciferase activity was measured 24 h after transfection. Data represent mean ± SEM; n = 3 (ns p > 0.05; *** p ≤ 0.001, **** p ≤ 0.0001 according to one-way ANOVA test with Dunnett’s multiple comparisons). (E) Relative Renilla/firefly luciferase activity of a miR-100 targeted (T) reporter relative to a non-targeted (NT) reporter in AGO2 −/− A549 transfected with reporter plasmid, 15 nM miR-100 mimic and the indicated AGO2 constructs or EGFP-VO. Data represent mean ± SEM; n = 3 (ns p > 0.05; ** p ≤ 0.01 according to one-way ANOVA test with Dunnett’s multiple comparisons). (F) Immunoblots of nuclear and cytoplasmic fractions from AGO2 −/− A549 transfected with EGFP-VO, AGO2 UT, EGFP-AGO2 or AGO2-EGFP. Beta tubulin and histone H3 were probed as loading controls for cytoplasmic and nuclear fractions, respectively. (G) Fluorescence microscopy images for AGO2 −/− A549 transfected with EGFP-VO, EGFP-AGO2 or AGO2-EGFP. Cell nuclei are stained with DAPI and merged images show DAPI and EGFP signal combined. Scale bars indicate 10 µm. (H) UnTagged C1 and AGO2-HaloTag C10 cells treated with 100 nM HaloTag-TMR ligand visualized using confocal microscopy.

Article Snippet: Single-cell clones were screened for loss of AGO2 expression by immunoblotting using rabbit anti-AGO2 (Sino Biological 101,620-T36).

Techniques: Knock-Out, Luciferase, Comparison, Western Blot, Clone Assay, Control, Activity Assay, Transfection, Expressing, Plasmid Preparation, Construct, Fluorescence, Microscopy, Staining, Confocal Microscopy

Journal: RNA Biology

Article Title: C-terminal tagging impairs AGO2 function

doi: 10.1080/15476286.2025.2534028

Figure Lengend Snippet: Structural insights of the C-terminal of AGO2 for an explanation of impaired function upon HaloTag insertion. (A) Schematic composition of AGO2 showing 7 main domains and motifs. (B) C-terminal residue A859 contributes to miRNA binding (PDB code: 4OLB). Residues shown in stick format and residue type and sequence number annotated. Dashed lines show inter-atom distances 5.0 Å. (C) Surface representation of AGO2 (4OLB) with domains coloured as in (A). Bound miRNA shown in spheres with 5ʹ-3ʹ direction indicated. The approximate location of the buried C-terminal residue A859 is indicated. (D) Surface representation of AGO2 (4OLB) showing sites of tryptophan binding and the N-terminal most residue (A22) seen in the electron density. Residues 1–21 were not observed in the data. (E) pLDDT values for predictions of native AGO2 (solid black line) and C-terminal halo-tagged AGO2 and relative solvent accessible surface area (QASA, Å 2 ; red line) calculated using PDB entry 4OLB .

Article Snippet: Single-cell clones were screened for loss of AGO2 expression by immunoblotting using rabbit anti-AGO2 (Sino Biological 101,620-T36).

Techniques: Residue, Binding Assay, Sequencing, Solvent

Journal: Nucleic Acids Research

Article Title: Nuclear Argonaute:miRNA complexes recognize target sequences within chromatin-associated RNA and silence gene expression

doi: 10.1093/nar/gkaf800

Figure Lengend Snippet: AGO2 and other protein factors involved in miRNA-mediated regulation can associate with chromatin. Western blots showing ( A ) AGO2 localization and purity of cytoplasm (CY), nucleoplasm (NP), and chromatin (CH) in wild-type samples ( N = 3), ( B ) purity [calnexin for endoplasmic reticulum (ER)] and localization of DROSHA, Dicer, TNRC6A, and AGO1–4 ( N = 3), and ( C ) AGO2 localization in the nuclear localization sequence (NLS)-AGO2 knock-in cell line ( N = 3).

Article Snippet: Western blot was visualized using anti-AGO2 primary antibody (50683-RP02, SinoBiological) at a 1:4000 dilution, with TrueBlot anti-rabbit secondary antibody (18-8816-31, Rockland) at 1:8000 dilution.

Techniques: Western Blot, Sequencing, Knock-In

Journal: Nucleic Acids Research

Article Title: Nuclear Argonaute:miRNA complexes recognize target sequences within chromatin-associated RNA and silence gene expression

doi: 10.1093/nar/gkaf800

Figure Lengend Snippet: AGO2 interacts with target RNAs in all cellular compartments. ( A ) Schematic outlining the chimeric eCLIP protocol used for the identification of AGO2-binding sites. Distribution of reproducible AGO2 ( B ) nonchimeric and ( C ) chimeric binding peaks across genomic features in cytoplasm ( N = 2), whole nucleus ( N = 2), and chromatin ( N = 2) fractions. Chimeric binding peaks only include chimeric reads that include miRNAs that map to the miRGeneDB database . ( D ) Percentage of chimeric miRNAs from the top eight miRNA families sharing the same seed sequence.

Article Snippet: Western blot was visualized using anti-AGO2 primary antibody (50683-RP02, SinoBiological) at a 1:4000 dilution, with TrueBlot anti-rabbit secondary antibody (18-8816-31, Rockland) at 1:8000 dilution.

Techniques: Binding Assay, Sequencing

Journal: Nucleic Acids Research

Article Title: Nuclear Argonaute:miRNA complexes recognize target sequences within chromatin-associated RNA and silence gene expression

doi: 10.1093/nar/gkaf800

Figure Lengend Snippet: HMGA2 RNA is bound by AGO2 in all compartments of the cell. Representative IGV browser images of chimeric eCLIP reads within the 3′-UTR of HMGA2 in the ( A ) cytoplasm, ( B ) nucleus, and ( C ) chromatin. HMGA2 is located on chromosome 12 (chr12). Peak height is defined as read density in reads per million (RPM). All AGO2 peaks are reproducible and meet the following criteria: log2FC > 3 (IP versus input) at least three reads per peak.

Article Snippet: Western blot was visualized using anti-AGO2 primary antibody (50683-RP02, SinoBiological) at a 1:4000 dilution, with TrueBlot anti-rabbit secondary antibody (18-8816-31, Rockland) at 1:8000 dilution.

Techniques:

Journal: Molecular Biology of the Cell

Article Title: Actin-dependent recruitment of AGO2 to the zonula adherens

doi: 10.1091/mbc.e22-03-0099-t

Figure Lengend Snippet: FIGURE 7: Contractile actin tension at the ZA is required for AGO2 junctional recruitment. (A–F) Immunofluorescence of Caco2 cells during a calcium switch assay in which DMSO or Blebbistatin (Blebb) were included in the calcium- containing recovery medium. Cells fixed at 30 and 60 min post Ca2+ reintroduction were stained for AGO2 (A), PLEKHA7 (B), E-cadherin (C), LMO7 (D), LIMCH1 (E), and PDLIM1 (F). Insets are marked by white rectangles and are 3× magnification of the original image. Fluorescence intensity of 6-µm line scans drawn perpendicular to cell–cell junctions was measured for each marker at the 60-min time point upon recovery from n = 30 cell–cell junctions (10 junctions/field) representative of three independent experiments; statistical analyses were performed using two-way ANOVA tests. Error bars represent mean ± SD. ****P < 0.0001; *P < 0.05; ns, non-significant. Scale bars = 20 µm.

Article Snippet: Antibodies The primary antibodies used in this study were PLEKHA7 (HPA038610; SigmaAldrich), Ecad (610182; BD Transduction Labs), AGO2 (ab57113; Abcam - optimal for immunoblotting), AGO2 (AP5281; ECM Biosciences - optimal for immunofluorescence), AGO2 (ab156870; Abcam - optimal for immunofluorescence and immunoprecipitation/RNA- immunoprecipitation); LMO7 (ab224113; Abcam), LIMCH1 (ab96178; Abcam), PDLIM1 (ab129015; Abcam), β-actin (4967L; Cell Signaling Technology), Myosin IIB (909901; Biolegend), Myosin IIA (909801; Biolegend), pS19-MRLC (3671; Cell Signaling Technology), α-catenin (610193; BD Transduction Labs), anti-Flag (clone M2, F1804; Sigma-Aldrich).

Techniques: Immunofluorescence, Staining, Fluorescence, Marker

Journal: Molecular Biology of the Cell

Article Title: Actin-dependent recruitment of AGO2 to the zonula adherens

doi: 10.1091/mbc.e22-03-0099-t

Figure Lengend Snippet: FIGURE 8: PLEKHA7, LMO7, LIMCH1, or PDLIM1 depletion each disrupt AGO2-Myosin IIB interaction at the ZA. (A) Immunoprecipitation (IP) of AGO2 and Myosin IIB from Caco2 cells, immunoblotted (IB) for the same markers; IgG is the negative control. Molecular masses (kD) are indicated on the right. (B–E) Wild type (WT) or PLEKHA7 KO Caco2 cells and control (NT) or LMO7, LIMCH1, and PDLIM1 knockdown (shLMO7, shLIMCH1, and shPDLIM1) cells stably expressing an AGO2-Flag construct (see Supplemental Figure S1, A–D) were subjected to PLA for AGO2-Flag, using an anti-Flag antibody, and Myosin IIB, followed by immunofluorescence staining for Ecad and confocal microscopy; DAPI was used to stain nuclei. Caco2 cells stably transduced with an empty vector were used as negative PLA control. Insets are marked by white rectangles and are 3× magnification of the original image. The ratio of junctional vs cytoplasmic PLA signals was quantified for each condition and from n = 30 cells (10 cells/field) representative of three independent experiments; statistical analyses were performed using either unpaired two-way t test (B–C) or one-way ANOVA test (D–E). Error bars represent mean ± SD. **P < 0.01; *P < 0.05. Scale bars = 20 µm.

Article Snippet: Antibodies The primary antibodies used in this study were PLEKHA7 (HPA038610; SigmaAldrich), Ecad (610182; BD Transduction Labs), AGO2 (ab57113; Abcam - optimal for immunoblotting), AGO2 (AP5281; ECM Biosciences - optimal for immunofluorescence), AGO2 (ab156870; Abcam - optimal for immunofluorescence and immunoprecipitation/RNA- immunoprecipitation); LMO7 (ab224113; Abcam), LIMCH1 (ab96178; Abcam), PDLIM1 (ab129015; Abcam), β-actin (4967L; Cell Signaling Technology), Myosin IIB (909901; Biolegend), Myosin IIA (909801; Biolegend), pS19-MRLC (3671; Cell Signaling Technology), α-catenin (610193; BD Transduction Labs), anti-Flag (clone M2, F1804; Sigma-Aldrich).

Techniques: Immunoprecipitation, Negative Control, Control, Knockdown, Stable Transfection, Expressing, Construct, Immunofluorescence, Staining, Confocal Microscopy, Transduction, Plasmid Preparation

Journal: Science Advances

Article Title: Enterovirus evolution reveals the mechanism of an RNA-targeted antiviral and determinants of viral replication

doi: 10.1126/sciadv.adg3060

Figure Lengend Snippet: ( A ) Single-point TROSY HSQC titration of A( 13 C)–selectively labeled SLII resist with DMA-135 at a fivefold excess. The black correlation peaks correspond to free SLII resist and the red to the (DMA-135)-SLII resist complex. The spectra were collected at 900 MHz in 10 mM K 2 HPO 4 (pH 6.5 before exchanging in D 2 O), 20 mM KCl, 0.5 mM EDTA, and 4 mM BME D 2 O buffer at 298 K. ( B ) Calorimetric titrations of A-RRM1,2 into SLII (left) and SLII resist (right). The A-RRM1,2-SLII data were fit to a 1:1 stoichiometric binding model in Affinimeter . ND, not determined. Reported values for K D and corresponding SD are from triplicate experiments. ( C ) RNA constructs used to assess determinants of specific and high-affinity AUF1-SLII interactions. Left, SLII CCC replaces the phylogenetically conserved UAG bulge motif with CCC. Right, a 7-nt oligonucleotide that mimics the SLII bulge loop sequence with adjacent nucleotides. ( D ) Calorimetric titrations of A-RRM1,2 into SLII CCC (left) and the 7-nt oligonucleotide (right). The A-RRM1,2-SLII CCC data were fit to a 1:1 stoichiometric binding model in Affinimeter . Reported values for K D and corresponding SD are from triplicate experiments. ( E ) Protein-biotinylated RNA pull-down experiments were performed to evaluate the influence of DMA-135 on the interaction between AUF1 and SLII resist . Biotinylated SLII and SLII resist RNAs were transfected into SF268 cells. Cells were cultured with increasing concentrations of DMA-135. Cell lysates were used for pull-down assays of SLII-associated proteins AUF1, hnRNP A1, Ago2, and HuR and detection by Western blotting.

Article Snippet: The primary antibodies used were as follows: anti-AUF1 rabbit polyclonal, 1:15,000 (Pocono Rabbit Farm & Lab, Canadensis, PA); anti-hnRNP A1 mouse monoclonal (Abcam), 1:200; anti-Ago2 rabbit polyclonal (Abcam), 1:200; and anti-HuR mouse monoclonal (Santa Cruz Biotechnology), 1:200.

Techniques: Titration, Labeling, Binding Assay, Construct, Sequencing, Transfection, Cell Culture, Western Blot