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: 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: 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 : 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: Neuro-Signals

Article Title: Hypoxic preconditioning improves spatial cognitive ability in mice.

doi: 10.1159/000121368

Figure Lengend Snippet: Fig. 1. a Electrophoresis of NCAM and GAPDH RT-PCR prod- ucts in agarose gel. b Western blotting of NCAM proteins in mouse hippocampus.

Article Snippet: Acute and Repeated Exposure of Mice to Hypoxia on NCAM Protein Expression in the Hippocampus By using a rabbit polyclonal antibody (Santa Cruz Bio- technology), NCAM protein was detected by Western blot in the 3 groups ( fig. 1 b).

Techniques: Electrophoresis, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Western Blot