phic31 plasmid  (Addgene inc)

Journal: bioRxiv

Article Title: Library transgenesis in zebrafish through delayed site-specific mosaic integration for in vivo pooled screening of transgenes

doi: 10.64898/2026.01.30.702415

Figure Lengend Snippet: (A) A single-copy genomic AttP landing site (orange) in the pIGLET (‘phiC31 Integrase Genomic Loci Engineered for Transgenesis’) line , with an exogenously introduced plasmid containing an AttB site (blue) and a transgene cassette (green). Once the PhiC31 integrase enzyme (red) is introduced, it catalyzes recombination between the AttP and AttB, leading to single-copy genomic integration of the plasmid. (B) Schematic of the overall procedure of delayed site-specific library transgenesis. (i) The 1-cell embryo is injected with a mixture of plasmids (the transgene library, drawn as circles with blue, magenta and green rectangles) and mRNA encoding for the PhiC31 integrase (red). (ii) During early development, the library passively spreads in the embryo as episomal plasmids together with the PhiC31 mRNA/protein as the cells divide. (iii) After an initial stage of development, the PhiC31 becomes active and integrates a single randomly-selected plasmid from the library in each cell. (iv) This produces a mosaic animal in which different cells express different library members, and only one library member in each cell.

Article Snippet: The PhiC31 plasmid (Addgene #68310) was used to produce purified PhiC31 mRNA using the mMESSAGE mMACHINETM T7 Transcription Kit (Thermo Fisher, AM1344) with lithium chloride purification.

Techniques: Plasmid Preparation, Injection

Journal: bioRxiv

Article Title: Library transgenesis in zebrafish through delayed site-specific mosaic integration for in vivo pooled screening of transgenes

doi: 10.64898/2026.01.30.702415

Figure Lengend Snippet: pIGLET heterozygous larvae display ∼99% mutually exclusive mosaic expression of a single library member per neuron. ( A ) Illustration of the experiment: pIGLET heterozygous embryos containing a single AttP site in chromosome 14 or 24 were injected with PhiC31 mRNA and a 50:50 mixture of plasmids containing an AttB site (blue) and constructs for neuronal expression of mScarlet (magenta) or GFP (green), fused to a CAAX tag for membrane targeting. 3 or 5 days later, the larvae were imaged. ( B-E ) Representative images of a mosaic 5 dpf pIGLET24b heterozygous animal (pIGLET24b;HuC::Gal4;nacre;RH1::DsRed) following library transgenesis, showing the forebrain and midbrain (B), midbrain and hindbrain (C), posterior hindbrain and spinal cord (D) and spinal cord (E). Max-projection images are shown with skin autofluorescence removed to aid visualization. ( F ) One plane of the fluorescent channels overlaid on a brightfield image of a mosaic 5 dpf pIGLET14a heterozygous larva (pIGLET14a;HuC::Gal4;nacre;RH1::DsRed, with prominent expression of the red eye marker). ( G ) Zoomed-in image of the section marked with a cyan box in the hindbrain in (C), showing a neuron co-expressing GFP and mScarlet. ( H ) Quantification of the ratio of neurons expressing both GFP and mScarlet (double-positives), out of all transduced neurons, in 8 mosaic larvae. The animals for which the whole hindbrain was quantified are marked in orange. The 3 dpf larva is marked in blue. The rest (marked in gray) are 5 dpf larvae for which 1-4 random FOVs were quantified. All the raw numbers are available in . ( I-L ) As in B-E, but for a 3 dpf larva. Scale bar: 50 μm.

Article Snippet: The PhiC31 plasmid (Addgene #68310) was used to produce purified PhiC31 mRNA using the mMESSAGE mMACHINETM T7 Transcription Kit (Thermo Fisher, AM1344) with lithium chloride purification.

Techniques: Expressing, Injection, Construct, Membrane, Marker

Journal: bioRxiv

Article Title: Library transgenesis in zebrafish through delayed site-specific mosaic integration for in vivo pooled screening of transgenes

doi: 10.64898/2026.01.30.702415

Figure Lengend Snippet: ( A ) Construct design for the barcoded GFP-CAAX library plasmids. Each plasmid includes an AttB sequence (light blue), HS4 insulator element (medium gray) embedded with a unique 15-nt random sequence barcode (15xN, purple), a 4xnrUAS minimal promoter for tissue-specific Gal4 transcription activation (light gray), GFP-CAAX (green arrow) and SV40 polyA (dark gray). ( B ) Scheme illustrating the experiment-a high-complexity library of barcoded GFP-CAAX plasmids, each containing a different 15xN barcode (dark blue, magenta and yellow rectangles on the plasmids), was injected into 1-cell embryos of heterozygous pIGLET24 zebrafish containing a genomic AttP site on chromosome 24. The library was co-injected together with mRNA encoding for the PhiC31 integrase (red). 5 days later, the larvae were imaged to confirm GFP expression in neurons, and then selected for extraction of genomic DNA from their entire bodies (n=12 larvae). ( C ) the genomic extracts were used as templates for 10-cycle PCR amplification of the barcodes from all genomically integrated plasmids, using primers that specifically target the integration junction (shown in red arrows). The resulting 650-bp amplicon library is then re-amplified with different, internal primers (shown in blue arrows), to attach overhangs for Illumina next generation sequencing (blue) and add a 5-nt sample-specific multiplexing barcode (pink) for pooled sequencing. ( D ) Number of unique high-confidence barcodes identified in each fish, after barcode collapsing and filtering. ( E ) Histogram of barcode abundance for the injected source library and for the barcodes recovered from the fish-integrated plasmids. The injected library displays a narrow distribution, indicating high complexity (many rare barcodes appearing at similar low frequency) while the fish-recovered barcodes display a broader long-tailed distribution (some barcodes appearing much more than others), consistent with intra-fish clonal expansion of the integrated transgenes. The per-fish barcode abundance histograms are available in . RPM=reads per millions (read counts normalized to the total number of reads sequenced for each sample). ( F ) Nucleotide composition for each position in the injected library and in the integrated barcodes shows high sequence diversity and no sequence bias for integration. Per-fish barcode sequence compositions are available in .

Article Snippet: The PhiC31 plasmid (Addgene #68310) was used to produce purified PhiC31 mRNA using the mMESSAGE mMACHINETM T7 Transcription Kit (Thermo Fisher, AM1344) with lithium chloride purification.

Techniques: Construct, Plasmid Preparation, Sequencing, Activation Assay, Injection, Expressing, Extraction, Amplification, Next-Generation Sequencing, Multiplexing

Journal: ACS synthetic biology

Article Title: A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR 21.

doi: 10.1021/acssynbio.5c00085

Figure Lengend Snippet: Figure 1. Engineering and rapid prototyping of the integrase eraser approach. (A) Cloning strategy based on (Guiziou et al.20) for the target integrase target with BsaI adapters highlighted for use in golden gate cloning strategies, see Plasmid Maps. (B) Design of the integrase target. The target is composed of two PhiC31 integrase sites (triangles) surrounding a constitutive promoter (pUBQ10), the rescue coding sequence for MED21:6xHA and the fluorescent reporter (mScarlet). In the absence of integrase, MED21:6xHA is expressed. In the presence of integrase, the integrase mediates inversion of the DNA between the integrase sites, inverting the promoter and leading to mScarlet expression. The expression of the integrase is mediated by the selected promoter selected. (C) Rapid prototyping of the MED21 Eraser target in transient transfections of Nicotiana benthamiana at 2 days after injection. On the left side is a control target that switches from mTurquoise to mScarlet alone (top) and with a p35S:PhiC31 construct (bottom). On the right side shows the MED21 target alone (top) and MED21:HA target with a p35S:PhiC31 construct (bottom). The BFP channel for the MED21:HA is shown to demonstrate the level of background expected for the BFP channel in the negative control. Microscopy images were taken on a 20x objective to allow a wide view of switching efficiency, and the 50-μm scale bar in the RFP channels applies to all paired BFP images.

Article Snippet: The Arabidopsis MED21:HA sequence was amplified by PCR with appropriate Golden Gate restriction sites and the construction of integrase targets was performed by Golden Gate reaction in the modified pGreenIIHygr vector containing compatible Golden Gate sites defined in Guiziou et al.20 Plasmids used for construction of the novel targets are available at Addgene: 5 prime side mScarlet cassette - L0-T4 tRBSC_mScarlet (Addgene #195887), Integrase site flanked pUBQ10 - L0-T1 Target PhiC31−(Addgene https://doi.org/10.1021/acssynbio.5c00085 ACS Synth.

Techniques: Cloning, Plasmid Preparation, Sequencing, Expressing, Transfection, Injection, Control, Construct, Negative Control, Microscopy

Journal: ACS synthetic biology

Article Title: A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR 21.

doi: 10.1021/acssynbio.5c00085

Figure Lengend Snippet: Figure 2. Cell-type-specific integrase eraser implemented in lateral root primordium results in MED21 loss of function and increases in lateral root initiation. (A) Schematic of the predicted behavior for the MED21 eraser approach. Lateral root primordium cells (red) will lose expression of the rescue construct, rendering them an effective knockout for MED21. (B−J) Confocal microscopy analysis of the wild-type control switch (from Figure 1C) and MED21 eraser lateral root initiation. All scale bars are 50 μm. (J) Still image from Supplemental Movie 1 of the root growth phenotype of MED21 eraser lines compared to the wild type at day 11. (K) Whole seedling epifluorescent image of MED21 eraser lines at day 14.

Article Snippet: The Arabidopsis MED21:HA sequence was amplified by PCR with appropriate Golden Gate restriction sites and the construction of integrase targets was performed by Golden Gate reaction in the modified pGreenIIHygr vector containing compatible Golden Gate sites defined in Guiziou et al.20 Plasmids used for construction of the novel targets are available at Addgene: 5 prime side mScarlet cassette - L0-T4 tRBSC_mScarlet (Addgene #195887), Integrase site flanked pUBQ10 - L0-T1 Target PhiC31−(Addgene https://doi.org/10.1021/acssynbio.5c00085 ACS Synth.

Techniques: Expressing, Construct, Knock-Out, Confocal Microscopy, Control

Journal: ACS synthetic biology

Article Title: A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR 21.

doi: 10.1021/acssynbio.5c00085

Figure Lengend Snippet: Figure 3. A chemically inducible MED21 eraser. (A) Schematic of the predicted behavior for the MED21 iEraser. The estradiol inducible integrase construct is composed of p35S:XVE (transcriptional activator composed of a DNA-binding domain of LexA, the transcription activation domain of VP16, and the regulatory region of the human estrogen receptor) and pLexA-minimal 35S driving expression of PhiC31. (B,C) Characterization of the iEraser by fluorescence microscopy shows induction as early as 48 h after treatment. The scale bar represents 50 μm (C). (D) Growth phenotypes were visible in estradiol-induced switched plants grown on 1 μM β-estradiol induction plates for 6 days. Seedlings were first grown for 6 days on LS media lacking β-estradiol before being transplanted to induction media (12 days total growth). (E) Protein expression analysis by Western blot for 12 independent iEraser lines. (F) Protein expression analysis by Western blot for roots and shoots isolated from plants grown with or without β-estradiol. Seedlings were grown on LS media for 6 days, and then transplanted to either control or induction media for another 6 days of growth. The experiment was performed in triplicate for each genotype. (G,H) Lengths of lateral (G) and primary (H) roots were quantified at 6 days from the indicated Integrase Eraser type. Seedlings were grown as in (F). Letters indicate significant difference (ANOVA and Tukey HSD multiple comparison test; p < 0.001).

Article Snippet: The Arabidopsis MED21:HA sequence was amplified by PCR with appropriate Golden Gate restriction sites and the construction of integrase targets was performed by Golden Gate reaction in the modified pGreenIIHygr vector containing compatible Golden Gate sites defined in Guiziou et al.20 Plasmids used for construction of the novel targets are available at Addgene: 5 prime side mScarlet cassette - L0-T4 tRBSC_mScarlet (Addgene #195887), Integrase site flanked pUBQ10 - L0-T1 Target PhiC31−(Addgene https://doi.org/10.1021/acssynbio.5c00085 ACS Synth.

Techniques: Construct, Binding Assay, Activation Assay, Expressing, Fluorescence, Microscopy, Western Blot, Isolation, Control, Comparison

Journal: ACS synthetic biology

Article Title: A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR 21.

doi: 10.1021/acssynbio.5c00085

Figure Lengend Snippet: Figure 4. Engineering and rapid prototyping of the “hot-swap” isoform switch approach. (A) Schematic of the predicted behavior for the MED21 Swap. Lateral root primordia will switch the expression of the rescue construct from wild-type (blue) to mutant isoform (red). (B) Design of the integrase target. The target is composed of two integrase sites (triangles) surrounding a constitutive promoter (pUBQ10), and each MED21 isoform is fused to the P2A self-cleaving peptide sequence and a fluorescent reporter (mTurquoise or mScarlet). In the basal state, MED21 and mTurquoise are produced. Once the PhiC31 integrase is expressed, it mediates inversion of the DNA between the integrase sites, inverting the promoter and leading to production of mMED21 and mScarlet. (C) Alignment of the AtMED21 N-terminal mutants. (D−G) Epifluorescence microscopy analysis of wild-type and mMED21 swap lateral root initiation in Arabidopsis primary transformants. Microscopy images were taken on a 20x objective, and the scale bar represents 50 μm. (H) Lateral root density (LRD per mm) and (I) lengths of lateral roots (Lateral root length in mm) from primary transformant lines were quantified at 14 days post germination from the indicated Integrase Swap type. At least 15 independent primary transformant lines were tested for each swap type. Lines were transplanted to soil and PCR genotyped for the med21 genotype. In (H), the LRD data points from med21 homozygous plants are colored in blue, while heterozygotes are colored dark gray, and ungenotyped samples are colored light gray. Letters indicate significant difference (ANOVA and Tukey HSD multiple comparison test; p < 0.001). In (I), data are presented as violin plots with nested boxplots to demonstrate that medians and interquartile ranges are comparable across conditions.

Article Snippet: The Arabidopsis MED21:HA sequence was amplified by PCR with appropriate Golden Gate restriction sites and the construction of integrase targets was performed by Golden Gate reaction in the modified pGreenIIHygr vector containing compatible Golden Gate sites defined in Guiziou et al.20 Plasmids used for construction of the novel targets are available at Addgene: 5 prime side mScarlet cassette - L0-T4 tRBSC_mScarlet (Addgene #195887), Integrase site flanked pUBQ10 - L0-T1 Target PhiC31−(Addgene https://doi.org/10.1021/acssynbio.5c00085 ACS Synth.

Techniques: Expressing, Construct, Mutagenesis, Sequencing, Produced, Epifluorescence Microscopy, Microscopy, Comparison

Journal: ACS synthetic biology

Article Title: A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR 21.

doi: 10.1021/acssynbio.5c00085

Figure Lengend Snippet: Figure 1. Engineering and rapid prototyping of the integrase eraser approach. (A) Cloning strategy based on (Guiziou et al.20) for the target integrase target with BsaI adapters highlighted for use in golden gate cloning strategies, see Plasmid Maps. (B) Design of the integrase target. The target is composed of two PhiC31 integrase sites (triangles) surrounding a constitutive promoter (pUBQ10), the rescue coding sequence for MED21:6xHA and the fluorescent reporter (mScarlet). In the absence of integrase, MED21:6xHA is expressed. In the presence of integrase, the integrase mediates inversion of the DNA between the integrase sites, inverting the promoter and leading to mScarlet expression. The expression of the integrase is mediated by the selected promoter selected. (C) Rapid prototyping of the MED21 Eraser target in transient transfections of Nicotiana benthamiana at 2 days after injection. On the left side is a control target that switches from mTurquoise to mScarlet alone (top) and with a p35S:PhiC31 construct (bottom). On the right side shows the MED21 target alone (top) and MED21:HA target with a p35S:PhiC31 construct (bottom). The BFP channel for the MED21:HA is shown to demonstrate the level of background expected for the BFP channel in the negative control. Microscopy images were taken on a 20x objective to allow a wide view of switching efficiency, and the 50-μm scale bar in the RFP channels applies to all paired BFP images.

Article Snippet: Each target was constructed into the Plant MoClo backbone vector pICH86966 (Addgene #48075), see Plasmid Maps below. pGATA23 driven PhiC31�L1_GATA23_1�(Addgene #195913) and estradiol inducible promoter: p35S_XVE-PhiC31-tUBQ1−(Addgene # 195932) were made previously.

Techniques: Cloning, Plasmid Preparation, Sequencing, Expressing, Transfection, Injection, Control, Construct, Negative Control, Microscopy

Journal: ACS synthetic biology

Article Title: A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR 21.

doi: 10.1021/acssynbio.5c00085

Figure Lengend Snippet: Figure 3. A chemically inducible MED21 eraser. (A) Schematic of the predicted behavior for the MED21 iEraser. The estradiol inducible integrase construct is composed of p35S:XVE (transcriptional activator composed of a DNA-binding domain of LexA, the transcription activation domain of VP16, and the regulatory region of the human estrogen receptor) and pLexA-minimal 35S driving expression of PhiC31. (B,C) Characterization of the iEraser by fluorescence microscopy shows induction as early as 48 h after treatment. The scale bar represents 50 μm (C). (D) Growth phenotypes were visible in estradiol-induced switched plants grown on 1 μM β-estradiol induction plates for 6 days. Seedlings were first grown for 6 days on LS media lacking β-estradiol before being transplanted to induction media (12 days total growth). (E) Protein expression analysis by Western blot for 12 independent iEraser lines. (F) Protein expression analysis by Western blot for roots and shoots isolated from plants grown with or without β-estradiol. Seedlings were grown on LS media for 6 days, and then transplanted to either control or induction media for another 6 days of growth. The experiment was performed in triplicate for each genotype. (G,H) Lengths of lateral (G) and primary (H) roots were quantified at 6 days from the indicated Integrase Eraser type. Seedlings were grown as in (F). Letters indicate significant difference (ANOVA and Tukey HSD multiple comparison test; p < 0.001).

Article Snippet: Each target was constructed into the Plant MoClo backbone vector pICH86966 (Addgene #48075), see Plasmid Maps below. pGATA23 driven PhiC31�L1_GATA23_1�(Addgene #195913) and estradiol inducible promoter: p35S_XVE-PhiC31-tUBQ1−(Addgene # 195932) were made previously.

Techniques: Construct, Binding Assay, Activation Assay, Expressing, Fluorescence, Microscopy, Western Blot, Isolation, Control, Comparison

Journal: ACS synthetic biology

Article Title: A Hot-Swappable Genetic Switch: Building an Inducible and Trackable Functional Assay for the Essential Gene MEDIATOR 21.

doi: 10.1021/acssynbio.5c00085

Figure Lengend Snippet: Figure 4. Engineering and rapid prototyping of the “hot-swap” isoform switch approach. (A) Schematic of the predicted behavior for the MED21 Swap. Lateral root primordia will switch the expression of the rescue construct from wild-type (blue) to mutant isoform (red). (B) Design of the integrase target. The target is composed of two integrase sites (triangles) surrounding a constitutive promoter (pUBQ10), and each MED21 isoform is fused to the P2A self-cleaving peptide sequence and a fluorescent reporter (mTurquoise or mScarlet). In the basal state, MED21 and mTurquoise are produced. Once the PhiC31 integrase is expressed, it mediates inversion of the DNA between the integrase sites, inverting the promoter and leading to production of mMED21 and mScarlet. (C) Alignment of the AtMED21 N-terminal mutants. (D−G) Epifluorescence microscopy analysis of wild-type and mMED21 swap lateral root initiation in Arabidopsis primary transformants. Microscopy images were taken on a 20x objective, and the scale bar represents 50 μm. (H) Lateral root density (LRD per mm) and (I) lengths of lateral roots (Lateral root length in mm) from primary transformant lines were quantified at 14 days post germination from the indicated Integrase Swap type. At least 15 independent primary transformant lines were tested for each swap type. Lines were transplanted to soil and PCR genotyped for the med21 genotype. In (H), the LRD data points from med21 homozygous plants are colored in blue, while heterozygotes are colored dark gray, and ungenotyped samples are colored light gray. Letters indicate significant difference (ANOVA and Tukey HSD multiple comparison test; p < 0.001). In (I), data are presented as violin plots with nested boxplots to demonstrate that medians and interquartile ranges are comparable across conditions.

Article Snippet: Each target was constructed into the Plant MoClo backbone vector pICH86966 (Addgene #48075), see Plasmid Maps below. pGATA23 driven PhiC31�L1_GATA23_1�(Addgene #195913) and estradiol inducible promoter: p35S_XVE-PhiC31-tUBQ1−(Addgene # 195932) were made previously.

Techniques: Expressing, Construct, Mutagenesis, Sequencing, Produced, Epifluorescence Microscopy, Microscopy, Comparison