Journal: bioRxiv

Article Title: Functional impact of pathogenic Runt domain mutations in Runx2 in vivo : Insights into the skeletal and dental anomalies of cleidocranial dysplasia

doi: 10.1101/2025.06.18.660258

Figure Lengend Snippet: Generation of Runx2 mutant mice using Platinum TALENs. a Schematic representation of the mouse Runx2 gene with eight exons (labeled E1-E8 below), distal (P1) and proximal (P2) promoters for Type II (MASNSL) and Type I (MRIVD) isoforms, and target sites of Platinum TALENs ( mRunx2-TALEN-L and -R ). A 10 kb scale bar is shown. The SmaI site (red box) includes G695 (underlined). The ssODN contains target sites (green), a T>G silent mutation at 690 creating an ApaI site (blue box), and a G>A mutation at 695 disrupting the SmaI site. b Domain structure of the mRunx2 Type II protein (528 aa) and its corresponding exons. The protein comprises a QA repeat domain, RHD, NLS, PST-rich domain, NMTS, and a C-terminal VWRPY motif. Amino acid positions are indicated above, and the corresponding exons (E1-E8) are shown below. c Nucleotide sequences are shown for the wild-type ( Wt , 670-725), missense mutant ( m , c.695G>A; p.R232Q, 670-725), and two-base deletion ( Δ2 , c.697_698delGA; p.E233TfsTer9, 670-723) alleles. Wt is on top, m in the middle, and Δ2 at the bottom. d Representative electropherograms of the targeted Runx2 region in Runx2 +/+ , Runx2 m/+ , and Runx2 Δ2/+ mice. A black arrow marks T at 690 in Runx2 +/+ and Runx2 m/+ mice. A blue arrow indicates overlapping T and A peaks at 690 in Runx2 m/+ mice, and a red arrow shows overlapping A and G peaks at position 695 in Runx2 m/+ mice.

Article Snippet: TALEN plasmids targeting mouse Runx2 were constructed using the Platinum Gate TALEN Kit (Addgene, Watertown, MA) as previously described .

Techniques: Mutagenesis, TALENs, Labeling

Journal: STAR Protocols

Article Title: An optimized FusX assembly-based technique to introduce mitochondrial TC-to-TT variations in human cell lines

doi: 10.1016/j.xpro.2022.101288

Figure Lengend Snippet: Schematic diagram of FusXTBE pairs used in this protocol and their assembly (A) Golden Gate cloning of FusX library enables the rapid synthesis of FusXTBE clones. (B) Each FusXTBE arm consists of a DNA binding domain with either 15 or 16-RVDs targeting 15 or 16-nucleotides DNA binding sequence, which is preceded by a 5′ T nucleotide. Attached to this module is a split half of the DddA tox protein and an UGI molecule. The 14–18 bp protospacer region in between two arms are amenable for deaminase activity. Both the figures were created by using Biorender.com .

Article Snippet: The Ekker Lab’s FusX assembly kit can be ordered through Addgene (Kit No. 1000000063).

Techniques: Cloning, Clone Assay, Binding Assay, Sequencing, Activity Assay

Journal: STAR Protocols

Article Title: An optimized FusX assembly-based technique to introduce mitochondrial TC-to-TT variations in human cell lines

doi: 10.1016/j.xpro.2022.101288

Figure Lengend Snippet:

Article Snippet: The Ekker Lab’s FusX assembly kit can be ordered through Addgene (Kit No. 1000000063).

Techniques: Recombinant, Plasmid Preparation, Gel Extraction, Purification, Sequencing, Amplification, Software, Membrane, Pore Size, Spectrophotometry, Microscopy

Journal: Molecular Cell

Article Title: Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation

doi: 10.1016/j.molcel.2019.07.038

Figure Lengend Snippet:

Article Snippet: Musunuru/Cowan Lab TALEN Kit , Addgene , 1000000034.

Techniques: Virus, Modification, Recombinant, Protease Inhibitor, Transfection, SYBR Green Assay, Staining, Reverse Transcription, Whole Genome Amplification, Purification, Sequencing, Derivative Assay, Multiplex Assay, Software, Imaging, Microarray, Transformation Assay, RNA Sequencing