Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: Overall coverage frequencies of ChIP-Seq data. Overall alignment (bp) and genomic coverage percentage of H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H4K20me1 histone modifications and their combinations over the whole M. incognita genome and the Transposable Element annotations (TE), for Egg and J2 samples. M. incognita genome has been fragmented in silico into 500 bp bins on which histone modification enrichment was predicted with a posterior probability >0.5. If a histone modification was predicted, the corresponding 500 bp bin was counted. Coverage frequencies were calculated based on 184 Mb total M. incognita genome size. Three biological replicates of M. incognita eggs and J2s have been treated jointly to identify common histone modification enrichment using ChromstaR.

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: In Silico, Modification

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: Genome wide distribution of histone modifications in relation to annotations for the M. incognita genome. The distribution of histone modifications was analyzed with ChromstaR, which calculated the spatial enrichment in histone modifications for different available genomic annotations in (A) Eggs or (B) J2s. Enrichment is represented as the log (observed/expected) value and ranges from 2.5 (highly enriched, red) to −2.5 (depletion, blue). This enrichment heatmap is a 5 × 10 matrix representing five histone modifications (H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H4K20me1) and 10 genomic annotated elements (CDS, exon, five prime UTR, gene, mRNA, ncRNA, rRNA, TE, three prime UTR and tRNA). Three biological replicates of M. incognita eggs have been treated jointly to identify common histone modification enrichment.

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: Genome Wide, Modification

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: H3K4me3, H3K9me3, H3K27ac, H27me3 and H4K20me1 histone modifications on the M. incognita genome. The general tracks of histone modifications are illustrated on the longest scaffold (Minc3s00001) of the M. incognita genome. Sequence reads for H3K4me3 (blue), H3K9me3 (red), H3K27ac (pink), H3K27me3 (green) and H4K20me1 (black) samples were visualized in IGV software. Values shown on the y axis represent the relative enrichment of ChIP-Seq signals obtained with PeakRanger (peaks correspond to read counts after background/input subtraction). The tracks were overlaid with the M. incognita ’s annotations (dark blue) of Genes and Transposable Elements (TE), as well as RNA-seq reads (grey). Each track contains information from one biological replicate of eggs.

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: Sequencing, Software, ChIP-sequencing, RNA Sequencing Assay

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: Distribution of histone modifications in relation to transposable element (TE) orders. The distribution of histone modifications was analyzed with ChromstaR, which calculated the spatial enrichment in histone modifications for annotated subfamilies of TE in M. incognita (A) Eggs or (B) J2s. Enrichment is represented as the log (observed/expected) value and ranges from +4 (highly enriched, red) to −4 (depletion, blue). This enrichment heatmap is a 5 × 11 matrix representing five histone modifications (H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H4K20me1) and 11 TE orders (4 DNA-transposons (Helitron, Maverick, TIR, MITE), and five RNA transposons (LINE, LTR, SINE, LARD and TRIM)). Three biological replicates of M. incognita eggs have been treated jointly to identify common histone modification enrichment.

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: Modification

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: Distribution of histone modifications in relation to protein-coding genes. Numbers of M. incognita ’s annotated protein-coding genes associated with H3K4me3, H3K9me3, H3K27ac, H3K27me3 and H4K20me1 histone modifications and their combinations, for Egg and J2 samples. Protein-coding genes were considered to be associated with a histone modification if at least 1 bp of the protein-coding gene annotation overlapped with the identified histone modification.

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: Modification

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: RNA-seq regulation of the protein-coding genes associated with histone modifications. Analysis of transcript levels of the genes associated with H3K27ac (blue), H3K27me3 (yellow), H3K4me3 (sky blue), H3K9me3 (dark pink) and H4K20me1 (green) in (A) Eggs and (B) J2s. Genes were considered to be associated with a histone modification if at least 1 bp of the annotation overlapped with an identified histone modification. Three biological replicates of M. incognita eggs and J2s have been treated jointly to identify common histone modification enrichment using ChromstaR. Normalized expression Log (median FPKM+1) of genes, calculated triplicates is shown. A Kruskal-Wallis test was performed, followed by a pairwise Dunn test, to assess the significance of differences in gene expression level between the five histone modifications. ns p > 0.05, * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, **** p ≤ 0.0001.

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: RNA Sequencing Assay, Modification, Expressing

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: Average H3K4me3 enrichment profiles correlate with TSS regions of 10% most expressed genes. Average enrichment profiles of five histone modifications along a 4 kb region framing expressed protein-coding genes after ChIP-Seq of (A, B) eggs and (B, D) J2s. Average enrichment profiles were generated by ChromstaR, [log (observed/expected) value ranging from 1 (highly enriched) to -2 (depletion)], for five histone modifications: H3K27ac (blue), H3K27me3 (yellow), H3K4me3 (sky blue), H3K9me3 (dark pink) and H4K20me1 (green). Three biological replicates of M. incognita eggs and J2s have been treated jointly to identify common histone modification enrichment. Enrichment was analyzed for the (A, C) top and (B, D) bottom 10% of associated protein-coding genes ranked on the basis of RNA-seq normalized expression data Log (median FPKM+1). x -axis: % in gene bodies and distance in bp upstream of TSS or downstream of TES. y -axis: Density of mapped reads log (observed/expected).

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: ChIP-sequencing, Generated, Modification, RNA Sequencing Assay, Expressing

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: Functional annotation of protein-coding genes associated with H3K4me3. Histogram showing the “Biological processes”/Gene ontology (GO) term enrichment of protein-coding genes associated with H3K4me3. Protein-coding genes were considered to be associated with H3K4me3 if at least 1 bp of the protein-coding gene annotation overlapped with this histone modification. Three biological replicates of M. incognita eggs and J2s have been treated jointly to identify common histone modification enrichment. Overrepresented GO terms, in eggs (blue; 6,014 genes) and J2s (orange, 10,564 genes), were identified with GoFuncR with a FWER <0.05 cutoff. X-axis is the −log10 (pvalue) calculated to represent GO term enrichment on the bar chart.

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: Functional Assay, Modification

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: Stage-specific enrichment in Gene Ontology (GO) terms for protein-coding genes associated with H3K4me3. Histogram showing the “Biological processes”/GO term enrichment of protein-coding genes showing both 1) differential gene expression during eggs-to-J2s transition; and 2) H3K4me3 association. Differential gene expression was calculated using DESeq2 on triplicates, with a p value <0.05 as a threshold for overexpression. Protein-coding genes were considered to be associated with H3K4me3 if at least 1 bp of the protein-coding gene annotation overlapped with this histone modification. Three biological replicates of M. incognita eggs and J2s have been treated jointly to identify common histone modification enrichment. Overrepresented GO terms, in eggs (blue; 89 genes) and J2s (orange, 117 genes), were identified with GoFuncR. with a FWER <0.05 cutoff. X-axis is the −log10 (pvalue) calculated to represent GO term enrichment on the bar chart.

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: Expressing, Over Expression, Modification

Journal: Frontiers in Cell and Developmental Biology

Article Title: Chromatin Landscape Dynamics in the Early Development of the Plant Parasitic Nematode Meloidogyne incognita

doi: 10.3389/fcell.2021.765690

Figure Lengend Snippet: Transcriptional regulation of known subventral glands (SvG) effector genes. According to the literature ( Da Rocha et al., 2021 ), 48 non-redundant M. incognita effectors have been identified in SvG (i.e., columns: effector-gene number, gene name and accession number on M. incognita genome). For this study, SvG effector genes were classified according to both their expression level and flanking histone modifications during eggs-to-J2s transition. Differential gene expression is shown as RNA-seq fold expression changes, Log2 (Fold Change), calculated using DESeq2 on triplicates, with a p value <0.05 as a threshold for overexpression. Effector genes were considered to be associated with a histone modification if at least 1 bp of the annotation overlapped with an identified histone modification. Three biological replicates of M. incognita eggs and J2s have been treated jointly to identify common histone modification enrichment using ChromstaR. [] indicates no histone modification has been identified. Full table of known subventral glands (SvG) effector genes can be found as Supplementary Table S5 .

Article Snippet: C01011000), with specific antibodies validated for M. incognita , targeting the histone modifications H3K4me3 (Merck Millipore ref 04-745, batch 2452485), H3K9me3 (Abcam ref ab8898, batch GR306402-2), H3K27ac (Abcam ref ab4729, batch GR150367-2), H3K27me3 (Epigentek ref A-4039, batch 503019) and H4K20me1 (Abcam ref ab9051, batch GR158874-1).

Techniques: Expressing, Over Expression, Modification

Journal: Molecular Therapy. Nucleic Acids

Article Title: lncRNA NEAT1 Binds to MiR-339-5p to Increase HOXA1 and Alleviate Ischemic Brain Damage in Neonatal Mice

doi: 10.1016/j.omtn.2020.01.009

Figure Lengend Snippet: Elevation of lncRNA NEAT1 Downregulates miR-339-5p to Increase the Expression of HOXA1 and Neuronal Cell Apoptosis during Hypoxia-Ischemia (A) The binding site between lncRNA NEAT1 and miR-339-5p predicted by starBase database. (B) The mRNA expression of HOXA1 in neuronal cells measured by qRT-PCR. (C) The binding between miR-339-5p and lncRNA NEAT1 by dual-luciferase reporter gene assay. (D) The expression of miR-339-5p and HOXA1 in neuronal cells measured by qRT-PCR. (E) The protein expression of HOXA1 in neuronal cells normalized to β-actin determined by western blot analysis. (F) The expression of lncRNA NEAT1 in OGD-treated neuronal cells in response to lncRNA NEAT1 knockdown. (G) The apoptosis of OGD-treated neuronal cells detected by TUNEL staining (original magnification ×200). (H) The expression of neuronal cell apoptosis-related proteins normalized to β-actin as determined by western blot analysis. *p < 0.05 versus untreated neuronal cells or neuronal cells treated with sh-NEAT1. The measurement data were expressed as mean ± standard deviation. Data between two groups were analyzed using unpaired t test, and data among multiple groups were tested using one-way ANOVA, followed by Tukey’s post hoc test. The experiment was repeated three times independently.

Article Snippet: Next, short hairpin RNA targeting lncRNA NEAT1 (shRNA-NEAT1), negative control shRNA sequence (shRNA-NC), or miR-339-5p-antagomir (Guangzhou RiboBio, Guangzhou, Guangdong, China) was continuously administered into the lateral ventricle of the HIBD mice for 7 days using an osmotic pump (n = 18 in each group).

Techniques: Expressing, Binding Assay, Quantitative RT-PCR, Luciferase, Reporter Gene Assay, Western Blot, Knockdown, TUNEL Assay, Staining, Standard Deviation

Journal: Molecular Therapy. Nucleic Acids

Article Title: lncRNA NEAT1 Binds to MiR-339-5p to Increase HOXA1 and Alleviate Ischemic Brain Damage in Neonatal Mice

doi: 10.1016/j.omtn.2020.01.009

Figure Lengend Snippet: Effects of lncRNA NEAT1 and miR-339-5p Inhibition on HOXA1 Expression and Neonatal HIBD Mice (A) The escape latency in the navigation test of Morris water maze. (B) The time spent in platform quadrant in the spatial probe test of Morris water maze. (C) The representative micrographs showing morphological changes in hippocampal tissues after H&E staining (original magnification ×200). (D) The neuronal cell apoptosis determined by TUNEL staining (original magnification ×400). (E) The mRNA expression of HOXA1 in hippocampal tissues detected by qRT-PCR. (F) HOXA1 protein expression in hippocampal tissues determined by immunohistochemistry (original magnification ×400). *p < 0.05 versus sham-operated mice or neonatal HIBD mice treated with sh-NEAT1. The measurement data were expressed as mean ± standard deviation. Data among multiple groups were compared using one-way ANOVA, followed by Tukey’s post hoc test. Data in Morris water maze task were analyzed using repeated-measures ANOVA, followed by Bonferroni’s post hoc test.

Article Snippet: Next, short hairpin RNA targeting lncRNA NEAT1 (shRNA-NEAT1), negative control shRNA sequence (shRNA-NC), or miR-339-5p-antagomir (Guangzhou RiboBio, Guangzhou, Guangdong, China) was continuously administered into the lateral ventricle of the HIBD mice for 7 days using an osmotic pump (n = 18 in each group).

Techniques: Inhibition, Expressing, Staining, TUNEL Assay, Quantitative RT-PCR, Immunohistochemistry, Standard Deviation

Journal: Molecular Therapy. Nucleic Acids

Article Title: lncRNA NEAT1 Binds to MiR-339-5p to Increase HOXA1 and Alleviate Ischemic Brain Damage in Neonatal Mice

doi: 10.1016/j.omtn.2020.01.009

Figure Lengend Snippet: Schematic Diagram Showing Potential Mechanism in which the lncRNA NEAT1/miR-339-5/HOXA1 Axis Is Involved in HIBD lncRNA NEAT1 sponges miR-339-5p, reduces inhibition to HOXA1, and inhibits neuronal cell apoptosis during hypoxia-ischemia in neonatal HIBD mice.

Article Snippet: Next, short hairpin RNA targeting lncRNA NEAT1 (shRNA-NEAT1), negative control shRNA sequence (shRNA-NC), or miR-339-5p-antagomir (Guangzhou RiboBio, Guangzhou, Guangdong, China) was continuously administered into the lateral ventricle of the HIBD mice for 7 days using an osmotic pump (n = 18 in each group).

Techniques: Inhibition

Journal: Molecular Therapy. Nucleic Acids

Article Title: lncRNA NEAT1 Binds to MiR-339-5p to Increase HOXA1 and Alleviate Ischemic Brain Damage in Neonatal Mice

doi: 10.1016/j.omtn.2020.01.009

Figure Lengend Snippet: Primer Sequence of qRT-PCR

Article Snippet: Next, short hairpin RNA targeting lncRNA NEAT1 (shRNA-NEAT1), negative control shRNA sequence (shRNA-NC), or miR-339-5p-antagomir (Guangzhou RiboBio, Guangzhou, Guangdong, China) was continuously administered into the lateral ventricle of the HIBD mice for 7 days using an osmotic pump (n = 18 in each group).

Techniques: Sequencing

Journal: Bioengineered

Article Title: Silencing of long chain noncoding RNA paternally expressed gene (PEG10) inhibits the progression of neuroblastoma by regulating microRNA-449a (miR-449a)/ribosomal protein S2 (RPS2) axis

doi: 10.1080/21655979.2022.2042999

Figure Lengend Snippet: LncRNA PEG10 expression was up-regulated in NB tissues and cells. (a) PEG10 expression in NB and normal tissues was detected by RT-QPCR. (b) PEG10 expression was measured in HUVEC and NB cells [SK-N-SH, SH-SY5Y, SK-N-AS, SK-N-BE (2)] by RT-qPCR. (c) Subcellular fractionation for PEG10 in SK-N-BE (2) and SH-SY5Y cells. Compared with normal tissues or HUVEC cells:*P < 0.05; **P < 0.01.

Article Snippet: The small interfering RNA (siRNA) targeting LncRNA PEG10 (si-PEG10-1 and si-PEG10-2) and ribosomal protein S2 (RPS2; si-RPS2-1 and si-RPS2-2), LncRNA PEG10 or RPS2 overexpression plasmid (PEG10, RPS2), miR-449a mimic, miR-449a inhibitor, and their corresponding controls (si-NC, vector, mimic NC and inhibitor NC, respectively) were provided by Ribobio (Guangzhou, China) and transfected using Lipofectamine 3000 (Invitrogen, Carlsbad, CA), according to the manufacturer’s description.

Techniques: Expressing, Quantitative RT-PCR, Fractionation

Journal: Bioengineered

Article Title: Silencing of long chain noncoding RNA paternally expressed gene (PEG10) inhibits the progression of neuroblastoma by regulating microRNA-449a (miR-449a)/ribosomal protein S2 (RPS2) axis

doi: 10.1080/21655979.2022.2042999

Figure Lengend Snippet: Relationship between PEG10 expression and clinicopathologic characteristics of neuroblastoma patients

Article Snippet: The small interfering RNA (siRNA) targeting LncRNA PEG10 (si-PEG10-1 and si-PEG10-2) and ribosomal protein S2 (RPS2; si-RPS2-1 and si-RPS2-2), LncRNA PEG10 or RPS2 overexpression plasmid (PEG10, RPS2), miR-449a mimic, miR-449a inhibitor, and their corresponding controls (si-NC, vector, mimic NC and inhibitor NC, respectively) were provided by Ribobio (Guangzhou, China) and transfected using Lipofectamine 3000 (Invitrogen, Carlsbad, CA), according to the manufacturer’s description.

Techniques: Expressing

Journal: Bioengineered

Article Title: Silencing of long chain noncoding RNA paternally expressed gene (PEG10) inhibits the progression of neuroblastoma by regulating microRNA-449a (miR-449a)/ribosomal protein S2 (RPS2) axis

doi: 10.1080/21655979.2022.2042999

Figure Lengend Snippet: LncRNA PEG10 silencing inhibited NB cell proliferation, migration and invasion. (a) PEG10 expression in SK-N-BE (2) and SH-SY5Y cells was tested by qRT-PCR. (b) The activity of SK-N-BE (2) and SH-SY5Y cells was measured by CCK-8 assay. (c) The proliferation of SK-N-BE (2) and SH-SY5Y cells was detected via colony formation assay. (d) Transwell assay was used to detect the migration of SK-N-BE (2) and SH-SY5Y cells. (e) Transwell assay was used to detect the invasion of SK-N-BE (2) and SH-SY5Y cells. (f) The protein levels of MMP-2, MMP-9 and MMP-14 in SK-N-BE (2) and SH-SY5Y cells were detected by Western blotting. **P < 0.01, compared with si-NC or vector group.

Article Snippet: The small interfering RNA (siRNA) targeting LncRNA PEG10 (si-PEG10-1 and si-PEG10-2) and ribosomal protein S2 (RPS2; si-RPS2-1 and si-RPS2-2), LncRNA PEG10 or RPS2 overexpression plasmid (PEG10, RPS2), miR-449a mimic, miR-449a inhibitor, and their corresponding controls (si-NC, vector, mimic NC and inhibitor NC, respectively) were provided by Ribobio (Guangzhou, China) and transfected using Lipofectamine 3000 (Invitrogen, Carlsbad, CA), according to the manufacturer’s description.

Techniques: Migration, Expressing, Quantitative RT-PCR, Activity Assay, CCK-8 Assay, Colony Assay, Transwell Assay, Western Blot, Plasmid Preparation

Journal: Bioengineered

Article Title: Silencing of long chain noncoding RNA paternally expressed gene (PEG10) inhibits the progression of neuroblastoma by regulating microRNA-449a (miR-449a)/ribosomal protein S2 (RPS2) axis

doi: 10.1080/21655979.2022.2042999

Figure Lengend Snippet: LncRNA PEG10 negatively regulated the expression of miR-449a. (a) Binding sites of PEG10 to miR-449a. (b) Luciferase activity was detected by Dual-luciferase reporter to verify the binding of PEG10 to miR-449a. (c) RIP assay was used to verify the binding of PEG10 to miR-449a. (d) MiR-449a expression in generalized carcinoma was analyzed by the Cancer Genome Atlas (TCGA) database. (e) QRT-PCR was used to test miR-449a expression in NB and normal tissues. (f) MiR-449a expression was measured in HUVEC and NB cells [SK-N-SH, SH-SY5Y, SK-N-AS, SK-N-BE (2)] by RT-qPCR. (g)The miR-449a expression in SK-N-BE (2) and SH-SY5Y cells was detected by qRT-PCR. **P < 0.01, compared with IgG, mimic NC, Normal, si-NC, or vector group.

Article Snippet: The small interfering RNA (siRNA) targeting LncRNA PEG10 (si-PEG10-1 and si-PEG10-2) and ribosomal protein S2 (RPS2; si-RPS2-1 and si-RPS2-2), LncRNA PEG10 or RPS2 overexpression plasmid (PEG10, RPS2), miR-449a mimic, miR-449a inhibitor, and their corresponding controls (si-NC, vector, mimic NC and inhibitor NC, respectively) were provided by Ribobio (Guangzhou, China) and transfected using Lipofectamine 3000 (Invitrogen, Carlsbad, CA), according to the manufacturer’s description.

Techniques: Expressing, Binding Assay, Luciferase, Activity Assay, Quantitative RT-PCR, Plasmid Preparation

Journal: Bioengineered

Article Title: Silencing of long chain noncoding RNA paternally expressed gene (PEG10) inhibits the progression of neuroblastoma by regulating microRNA-449a (miR-449a)/ribosomal protein S2 (RPS2) axis

doi: 10.1080/21655979.2022.2042999

Figure Lengend Snippet: LncRNA PEG10 silencing inhibited the proliferation, migration, and invasion of NB cells via modulating the miR-449a/RPS2 axis. (a) RPS2 expression in SK-N-BE (2) and SH-SY5Y cells was tested using Western blotting. (b) The proliferation of SK-N-BE (2) and SH-SY5Y cells was tested via clone formation assay. (c) The invasion of SK-N-BE (2) and SH-SY5Y cells was detected by Transwell assay. (d) The protein expression of MMP-2, MMP-9, and MMP-14 in SK-N-BE (2) and SH-SY5Y cells were detected via Western blotting. **P < 0.01, compared with control group; ##P < 0.01, compared with si-PEG10-2 or PEG10 group; &&P < 0.01, compared with mimic or inhibitor group.

Article Snippet: The small interfering RNA (siRNA) targeting LncRNA PEG10 (si-PEG10-1 and si-PEG10-2) and ribosomal protein S2 (RPS2; si-RPS2-1 and si-RPS2-2), LncRNA PEG10 or RPS2 overexpression plasmid (PEG10, RPS2), miR-449a mimic, miR-449a inhibitor, and their corresponding controls (si-NC, vector, mimic NC and inhibitor NC, respectively) were provided by Ribobio (Guangzhou, China) and transfected using Lipofectamine 3000 (Invitrogen, Carlsbad, CA), according to the manufacturer’s description.

Techniques: Migration, Expressing, Western Blot, Tube Formation Assay, Transwell Assay