Journal: Epigenetics & chromatin

Article Title: EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter.

doi: 10.1186/s13072-023-00516-4

Figure Lengend Snippet: Fig. 3 EphrinA5 stimulation leads to reduced association of DNMT1 to Ncam1 and diminished motility of CB cells. a, b The motility of CB cells is significantly reduced upon stimulation with ephrinA5-Fc, which can be rescued by a preceding knockdown of Ncam1. a Temporal color-coded migratory distance over 20 h of imaging. The starting point of migration for each cell is shown in dark blue and the end point in white. b Quantitative analysis of average migratory speed (n = 557 for ctrl siR + ctrl-Fc, n = 455 for ctrl siR + efnA5-Fc, n = 481 for Ncam1 siR + ctrl-Fc, n = 495 for Ncam1 siR + efnA5-Fc, N = 4 biological replicates). c-f Native ChIP revealed decreased enrichment of DNMT1 in the Ncam1 promoter region close to putative Snhg15-binding sites. c Genomic map depicting the promoter region of the murine Ncam1 gene. Regions targeted by the primer pairs P1, P2 and P3 are shown in turquoise, the promoter in dark blue, candidate cis-regulatory elements in red, CpG site with a significantly reduced methylation level in black, and putative Snhg15-binding sites in pink. d-f ChIP-qPCR analysis using anti-DNMT1 and anti-H3K27me3 antibodies normalized against the input material and IgG (N = 4 biological replicates). Significances were determined with one-way ANOVA (b) and two-tailed Student’s t-test (d-f). Significance levels: p value < 0.05 *; p value < 0.01 **; p value < 0.001 ***. Scale bar: 100 μm. ctrl: control. efnA5: ephrinA5. siR: siRNA

Article Snippet: 24 h after seeding, cells were transfected with siRNA oligos targeting Ncam1 (#sc-36017, SantaCruz Biotechnology) or EphA2 (#sc-35320, SantaCruz Biotechnology) at a final concentration of 9 nM by forward lipofection using Lipofectamine 2000© (#11,668,019, Invitrogen) according to the manufacturer’s protocol.

Techniques: Knockdown, Imaging, Migration, Binding Assay, Methylation, ChIP-qPCR, Two Tailed Test, Control

Journal: Epigenetics & chromatin

Article Title: EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter.

doi: 10.1186/s13072-023-00516-4

Figure Lengend Snippet: Fig. 4 In silico modeling of Snhg15 binding to Ncam1 and Adamts14 promoter regions. a Snapshot of Snhg15 triple helix formation with the extended Ncam1 sequence (Ncam1-ext) during MD simulations. b Total interaction energy (LJ + CB) between DNA and RNA with phosphate and sugar backbone included as a function of time. When comparing Ncam1 and Ncam1-ext, we only considered the sequence without the extension (clipped Ncam1-ext sequence, see Additional file 3: Table S2) to maintain comparable energies for both models. c Number of hydrogen bonds between RNA and DNA. Please note that the hydrogen bonds counts have been smoothed using a running average with a window size of 5, as the curves would otherwise overlap too much. Again, we only considered the sequence without the extension (clipped Ncam1-ext sequence) to compare Ncam1 and Ncam1-ext. d Occurrence of in-register hydrogen bonded pairs between the RNA and the DNA– purine strand in Adamts14-1 along the simulation trajectory. Labels starting with a “D” indicate the DNA residue of the pair. e Occurrence of in-register hydrogen bonded pairs between the RNA and the DNA–purine strand in Ncam1-ext (clipped) along the simulation trajectory. Note that predicted interactions get more stable over time as indicated by less noise in the lower lanes. Labels starting with a “D” indicate the DNA residue of the pair. LJ: Lennard–Jones. CB: Coulomb

Article Snippet: 24 h after seeding, cells were transfected with siRNA oligos targeting Ncam1 (#sc-36017, SantaCruz Biotechnology) or EphA2 (#sc-35320, SantaCruz Biotechnology) at a final concentration of 9 nM by forward lipofection using Lipofectamine 2000© (#11,668,019, Invitrogen) according to the manufacturer’s protocol.

Techniques: In Silico, Binding Assay, Sequencing, Residue

Journal: Journal of Molecular Neuroscience

Article Title: Expression of the CGRP Family of Neuropeptides and their Receptors in the Trigeminal Ganglion

doi: 10.1007/s12031-020-01493-z

Figure Lengend Snippet: Details of primary and secondary antibodies

Article Snippet: CGRP (guinea pig) PA1–36017 , 1:500 , Synthetic human CGRP , Thermo Scientific, IL, USA , Eftekhari S, Salvatore CA, Gaspar RC, Roberts R, O’Malley S, Zeng Z, Edvinsson L. 2013 Dec;12(6):937–49..

Techniques: