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(A) Allelic ratio (AR) of Pvt1 in F 1 -23 hybrid NPC clonal lines compared to other genes. Each point represents a clonal line ( n = 120). NPC clonal lines used for other experiments are highlighted with different shapes. (B) Summary of F 1 hybrid clonal lines used in this paper and their respective Pvt1 allelic expression status based on an AR cutoff of 0.2. (C) Allele-specific H2K27ac ChIP-seq with 3 different F 1 -23 clonal lines. Top row shows SNP differences between the 129 allele and the CAST allele in relation to the H3K27ac ChIP-seq signals across three samples. <t>Tfap2a</t> SNP is highlighted in the black box, the second of the two SNPs. (D) Allele-specific ATAC-seq and ChIP-seq from mE6 NPCs, clonal line with Pvt1 CAST monoallelic expression (mE6 NPC, blue). (E) Allele-specific ATAC-seq and ChIP-seq from Ch8 NPCs, clonal line with Pvt1 129 monoallelic expression (Ch8 NPC, pink). (F) ChIP input tracks (black) with allele-specific ChIP-seq tracks from mE6 NPCs. (G) ChIP input track (black) with allele-specific ChIP-seq tracks from Ch8 NPCs.
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Image Search Results


(A) Allelic ratio (AR) of Pvt1 in F 1 -23 hybrid NPC clonal lines compared to other genes. Each point represents a clonal line ( n = 120). NPC clonal lines used for other experiments are highlighted with different shapes. (B) Summary of F 1 hybrid clonal lines used in this paper and their respective Pvt1 allelic expression status based on an AR cutoff of 0.2. (C) Allele-specific H2K27ac ChIP-seq with 3 different F 1 -23 clonal lines. Top row shows SNP differences between the 129 allele and the CAST allele in relation to the H3K27ac ChIP-seq signals across three samples. Tfap2a SNP is highlighted in the black box, the second of the two SNPs. (D) Allele-specific ATAC-seq and ChIP-seq from mE6 NPCs, clonal line with Pvt1 CAST monoallelic expression (mE6 NPC, blue). (E) Allele-specific ATAC-seq and ChIP-seq from Ch8 NPCs, clonal line with Pvt1 129 monoallelic expression (Ch8 NPC, pink). (F) ChIP input tracks (black) with allele-specific ChIP-seq tracks from mE6 NPCs. (G) ChIP input track (black) with allele-specific ChIP-seq tracks from Ch8 NPCs.

Journal: Cell reports

Article Title: Genetic and chromatin regulation of Pvt1 monoallelic expression

doi: 10.1016/j.celrep.2025.116554

Figure Lengend Snippet: (A) Allelic ratio (AR) of Pvt1 in F 1 -23 hybrid NPC clonal lines compared to other genes. Each point represents a clonal line ( n = 120). NPC clonal lines used for other experiments are highlighted with different shapes. (B) Summary of F 1 hybrid clonal lines used in this paper and their respective Pvt1 allelic expression status based on an AR cutoff of 0.2. (C) Allele-specific H2K27ac ChIP-seq with 3 different F 1 -23 clonal lines. Top row shows SNP differences between the 129 allele and the CAST allele in relation to the H3K27ac ChIP-seq signals across three samples. Tfap2a SNP is highlighted in the black box, the second of the two SNPs. (D) Allele-specific ATAC-seq and ChIP-seq from mE6 NPCs, clonal line with Pvt1 CAST monoallelic expression (mE6 NPC, blue). (E) Allele-specific ATAC-seq and ChIP-seq from Ch8 NPCs, clonal line with Pvt1 129 monoallelic expression (Ch8 NPC, pink). (F) ChIP input tracks (black) with allele-specific ChIP-seq tracks from mE6 NPCs. (G) ChIP input track (black) with allele-specific ChIP-seq tracks from Ch8 NPCs.

Article Snippet: Antibodies used: H3K27ac (Abcam, 4729), H3K27ac (Active Motif, 39133), H3K4me2 (Abcam, ab7766), H3K4me3 (Active Motif, 39159), H3K9me3 (Abcam, ab8898), H2AK199ub (Cell signaling, D27C4), H3K27me3 (Cell Signaling, C36B11), RNA Pol II-RPB1 (Bio-legend, 664906), and TFAP2a (Novus, NB100-74359).

Techniques: Expressing, ChIP-sequencing

(A) Differential gene expression analysis (DESeq) between NPC clonal lines with Pvt1 CAST monoallelic expression ( n = 50) against NPC clonal lines with Pvt1 biallelic expression ( n = 58). Non-significant genes are in gray, and the significant genes based on log2 fold change and adjusted p value are in red, with the top 15 significant genes labeled. The adjusted p value cutoff is 0.01, and the log2 fold change cutoff is 0.5. (B) Tfap2a expression from F 1 -23 hybrid NPC clonal lines. Pvt1 allelic expression status is based on an AR cutoff of 0.2 ( n = 56, blue; n = 60, yellow; n = 4, red). Significance was calculated with a t test: NS p > 0.05 and ** p ≤ 0.01. (C) Summary of Tfap2a expression levels in transcript per million (TPM) between the different F 1 -23 clonal lines. The color of the clonal line is based on Pvt1 allelic status. (D) Tfap2a expression from RT-qPCR of R1-57 NPC clonal lines. Pvt1 allelic expression status is based on an AR cutoff of 0.2 ( n = 12 WT; n = 29, bi-allelic; n = 6, mutant). The relative fold change is compared to the NPC clonal line with the lowest Tfap2a expression. Significance was calculated with a t test: NS p > 0.05. (E) TFAP2a motif comparison between sequences from 129 allele (pink) and CAST allele (blue). (F) TFAP2a ChIP-seq tracks from four different samples: mE6 NPCs (blue), Ch8 NPCs (pink), Ch1 NPCs (yellow), and mESCs (green). The dotted line and black box around the SNPs demonstrate where the SNPs near the TFAP2a binding site can be found. (G) Violin plot of the AR from a non-clonal population of F 1 -23 NPCs ( n = 3) and a non-clonal population of F 1 -23 NPCs with Tfap2a overexpression ( n = 6, purple). Additionally, there is the AR of mE6 NPCs ( n = 3) and mE6 NPCs with Tfap2a overexpression ( n = 3, blue). The AR was obtained with targeted RNA-seq of Pvt1 . p values were calculated with an unpaired t test: *** p ≤ 0.001. The experimental schematic is provided in .

Journal: Cell reports

Article Title: Genetic and chromatin regulation of Pvt1 monoallelic expression

doi: 10.1016/j.celrep.2025.116554

Figure Lengend Snippet: (A) Differential gene expression analysis (DESeq) between NPC clonal lines with Pvt1 CAST monoallelic expression ( n = 50) against NPC clonal lines with Pvt1 biallelic expression ( n = 58). Non-significant genes are in gray, and the significant genes based on log2 fold change and adjusted p value are in red, with the top 15 significant genes labeled. The adjusted p value cutoff is 0.01, and the log2 fold change cutoff is 0.5. (B) Tfap2a expression from F 1 -23 hybrid NPC clonal lines. Pvt1 allelic expression status is based on an AR cutoff of 0.2 ( n = 56, blue; n = 60, yellow; n = 4, red). Significance was calculated with a t test: NS p > 0.05 and ** p ≤ 0.01. (C) Summary of Tfap2a expression levels in transcript per million (TPM) between the different F 1 -23 clonal lines. The color of the clonal line is based on Pvt1 allelic status. (D) Tfap2a expression from RT-qPCR of R1-57 NPC clonal lines. Pvt1 allelic expression status is based on an AR cutoff of 0.2 ( n = 12 WT; n = 29, bi-allelic; n = 6, mutant). The relative fold change is compared to the NPC clonal line with the lowest Tfap2a expression. Significance was calculated with a t test: NS p > 0.05. (E) TFAP2a motif comparison between sequences from 129 allele (pink) and CAST allele (blue). (F) TFAP2a ChIP-seq tracks from four different samples: mE6 NPCs (blue), Ch8 NPCs (pink), Ch1 NPCs (yellow), and mESCs (green). The dotted line and black box around the SNPs demonstrate where the SNPs near the TFAP2a binding site can be found. (G) Violin plot of the AR from a non-clonal population of F 1 -23 NPCs ( n = 3) and a non-clonal population of F 1 -23 NPCs with Tfap2a overexpression ( n = 6, purple). Additionally, there is the AR of mE6 NPCs ( n = 3) and mE6 NPCs with Tfap2a overexpression ( n = 3, blue). The AR was obtained with targeted RNA-seq of Pvt1 . p values were calculated with an unpaired t test: *** p ≤ 0.001. The experimental schematic is provided in .

Article Snippet: Antibodies used: H3K27ac (Abcam, 4729), H3K27ac (Active Motif, 39133), H3K4me2 (Abcam, ab7766), H3K4me3 (Active Motif, 39159), H3K9me3 (Abcam, ab8898), H2AK199ub (Cell signaling, D27C4), H3K27me3 (Cell Signaling, C36B11), RNA Pol II-RPB1 (Bio-legend, 664906), and TFAP2a (Novus, NB100-74359).

Techniques: Gene Expression, Expressing, Labeling, Quantitative RT-PCR, Mutagenesis, Comparison, ChIP-sequencing, Binding Assay, Over Expression, RNA Sequencing