Journal: EMBO Reports

Article Title: Kin17 promotes rDNA transcription, ribosomal biogenesis, and cortical lamination

doi: 10.1038/s44319-025-00524-3

Figure Lengend Snippet: ( A ) Neurospheres were subjected to ChIP assays using an anti-Kin17 antibody, followed by qPCR-based detection of rDNA (Kin17, P = 0.000053; UBF, P = 0.000017) ( n = 3). UBF was included as positive control. ( B ) The global distribution pattern of Kin17 and UBF along the rDNA locus was determined by ChIP-qPCR. Kin17- or UBF-bound rDNA was quantified relative to input rDNA ( n = 3). ( C ) rDNA promoter reporter plasmid was transfected into control or Kin17 KD 293T cells. Luciferase activity was determined by Dual-Luciferase reporter assay (Kin17 KD1, P = 0.0024; Kin17 KD2, P = 0.0035) ( n = 3 per group). ( D ) Schematic illustrating the experimental strategy for measuring CpG methylation at rDNA promoter regions. Mouse rDNA was digested with the HpaII enzyme, followed by PCR detection using the indicated primers. Digestion efficiency was assessed by PCR amplification of Pbluescript sequences using the corresponding primers. ( E ) Kin17-associated rDNA was obtained by chromatin IP using an anti-Kin17 antibody. The relative abundance of methylated rDNA was quantified relative to input. As a positive control, UBF associated rDNA was isolated via chromatin IP using an anti-UBF antibody and the corresponding methylation status was determined. The distributions of methylated (orange bars) and unmethylated (grey bars) rDNA copies were plotted accordingly (Kin17, P = 0.0004; UBF, P = 0.0006) ( n = 3). ( F ) The interaction of Kin17 and NCL in neurospheres, determined by co-IP with an anti-Kin17 antibody, followed by immunoblotting detection with an anti-NCL antibody, and reciprocally by co-IP with an anti-NCL antibody followed by immunoblotting detection with an anti-Kin17 antibody ( n = 3). ( G ) The interaction of exogenous HA-Kin17 and Flag-NCL in 293T cells co-transfected with HA-Kin17 and Flag-NCL, determined by co-IP with an anti-HA antibody and immunoblotting detection with an anti-Flag antibody ( n = 3). ( H ) Generation of Kin17 or NCL truncation fragments. ( I ) Full-length Flag-NCL and each of truncated GST-Kin17 plasmids were transfected into 293T cells for expression, followed by co-IP with an anti-Flag antibody and immunoblotting with an anti-GST antibody ( n = 3). ( J ) Full-length GST-Kin17 and each of truncated Flag-NCL plasmids were transfected into 293T cells for expression, followed by co-IP with an anti-Flag antibody and immunoblotting with an anti-GST antibody ( n = 3). ( K ) 45S pre-rRNA level in control N2a cells, N2a cells with NCL KD ( P < 0.0001), N2a cells with Kin17 KD ( P = 0.001), and N2a cells with both NCL and Kin17 KD ( P < 0.0001), by qPCR ( n = 3 per group). ( L ) Relative Polr1a enrichment at the promoter of 45S rDNA in control N2a cells, N2a cells with NCL KD ( P < 0.0001), N2a cells with Kin17 KD ( P < 0.0001), and N2a cells with both NCL and Kin17 KD ( P < 0.0001), by ChIP-qPCR ( n = 3). ( M ) Relative NCL enrichment on the promoter of 45S rDNA in control and Kin17 KD N2a cells, by ChIP-qPCR analysis ( P = 0.004262) ( n = 3). ( N ) Relative Kin17 enrichment on the promoter of 45S rDNA, in control and NCL KD N2a cells, by ChIP-qPCR analysis ( P = 0.801241) ( n = 3). For this and subsequent figures, KD represents knockdown. Statistical analysis was performed using one-way ANOVA ( C , K , L ) with Bonferroni correction or two-tailed Student’s t test ( A , E , M , N ). Error bars denote the SEM. ** P < 0.01, *** P < 0.001; **** P < 0.0001; ns not significant.

Article Snippet: Pbluescript (pBS) , Addgene , Cat #212205.

Techniques: Positive Control, ChIP-qPCR, Plasmid Preparation, Transfection, Control, Luciferase, Activity Assay, Reporter Assay, CpG Methylation Assay, Amplification, Chromatin Immunoprecipitation, Methylation, Isolation, Co-Immunoprecipitation Assay, Western Blot, Expressing, Knockdown, Two Tailed Test

Journal: Hearing research

Article Title: Mesenchymal ETV transcription factors regulate cochlear length.

doi: 10.1016/j.heares.2020.108039

Figure Lengend Snippet: Fig. 7. Mesenchymal Etv1 is dispensable for cochlear development. Whole mount immunostaining of P0 cochlea from control (Etv1fl/þ; Etv4/þ; Etv5fl/þ;Twist2Cre/þ), Etv4/5 double mutant (Etv1fl/þ;Etv4/;Etv5fl/fl;Twist2Cre/þ) and Etv1/4/5 triple mutant (Etv1fl/fl;Etv4/;Etv5fl/fl;Twist2Cre/þ) showing whole cochlea stained with Myosin 6 antibody (green) (A), and representative regions from each cochlear turn stained with F-actin (green) (B), and Prox1 staining (green) (C) as a marker for supporting cells. Scale bar ¼ 100 mm. White arrowheads mark the beginning and the end of the cochlear length measurement. . (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Article Snippet: In situ hybridization antisense riboprobes were prepared from the following mouse cDNA plasmids: Etv1 (pBluescript SKEtv1, Addgene 16,282), Etv4 (pGEM-Etv4, gift of G. Martin), Etv5 (pBluescriptSK-Etv5, gift of G. Martin), Ebf1 (pCR4-TOPO-Ebf1, Transomic BC13936), and Tgfbi (pCR-BluntII-TOPO-Tgfbi, Transomic BC129900).

Techniques: Immunostaining, Control, Mutagenesis, Staining, Marker

Journal: Hearing research

Article Title: Mesenchymal ETV transcription factors regulate cochlear length.

doi: 10.1016/j.heares.2020.108039

Figure Lengend Snippet: Fig. 8. Quantification of cochlear length, hair cell and supporting cell density in Etv1/4/ 5 compound mutants. (A) Quantification of cochlear duct length at P0 from control (Etv1fl/þ;Etv4/þ;Etv5fl/

Article Snippet: In situ hybridization antisense riboprobes were prepared from the following mouse cDNA plasmids: Etv1 (pBluescript SKEtv1, Addgene 16,282), Etv4 (pGEM-Etv4, gift of G. Martin), Etv5 (pBluescriptSK-Etv5, gift of G. Martin), Ebf1 (pCR4-TOPO-Ebf1, Transomic BC13936), and Tgfbi (pCR-BluntII-TOPO-Tgfbi, Transomic BC129900).

Techniques: Control

Journal: Chemistry & biology

Article Title: A zebrafish chemical suppressor screening identifies small molecule inhibitors of the Wnt/β-catenin pathway.

doi: 10.1016/j.chembiol.2014.02.015

Figure Lengend Snippet: Figure 4. GGTase Is Required for Wnt/b-catenin Signaling (A) Knockdown of the b subunit of PGGT1B reduced Wnt3A-induced transcriptional activation of the b-catenin/TCF complex. MDA-MB-231 cells were trans- fected with a mixture of four siRNAs for PGGT1B and the reporter plasmids. The cells were treated with 50 ng/ml Wnt3A for 18 hr. Cont., control. (B) Reconstitution of PGGT1B with Flag-tagged PGGT1B reversed PGGT1B knockdown-mediated reduction in transcriptional activation of b-catenin/TCF. MDA- MB-231 cells were transfected with a siRNA targeting the 30 untranslated region (30 UTR) of pggt1b gene, an expression vector for Flag-tagged PGGT1B deleted the 30 UTR, and the reporter plasmids. The cells were treated with 50 ng/ml Wnt3A for 18 hr. Fold activation to the absence of Wnt3A is shown. Values are ± SEM (n = at least 3). PGGT1B expression levels were analyzed by Western blotting with antibodies against PGGT1B and actin. (C) Knockdown of PGGT1B inhibited BIO-induced goosecoid expression in zebrafish embryos. Embryos were injected with antisense MOs that target translation (ATG MO) or splicing (SP MO) of the zebrafish pggt1b gene at the one-cell stage and treated with 30 mM BIO or DMSO for 8 min at 32- to 64-cell stage. At 50% epiboly, embryos were fixed and subjected to in situ hybridization with an antisense goosecoid probe. Embryos are animal pole view, dorsal up if it can be distinguished. Arrowheads indicate tips of the goosecoid expression area. The central angles of goosecoid expression area were measured and scored into four classes: 0 to 90, 90 to 180, 180 to 270, and 270 to 360 (n = at least 56).

Article Snippet: Digoxigenin-labeled RNA probes were transcribed using RNA digoxigenin labeling mix, T7 RNA polymerase, and pBluescript goosecoid (Addgene) as a template plasmid.

Techniques: Knockdown, Activation Assay, Control, Transfection, Expressing, Plasmid Preparation, Western Blot, Injection, In Situ Hybridization