Journal: bioRxiv

Article Title: NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

doi: 10.64898/2025.12.29.696819

Figure Lengend Snippet: (A) Relative mRNA levels of YAP target genes (Cyr61, CTGF, ANKRD1) following siRNA-mediated knockdown of MePCE (7SKsnRNP subunit) in HEK293Ts (N=4). (B) Expression of Cyr61, CTGF, and ANKRD1 after HEXIM1/2 knockdown in HEK293Ts (N=4). (C) Expression of Cyr61, CTGF, and ANKRD1 following NELFA (NELF complex subunit) knockdown in HEK293Ts (N=4). (D) Expression of YAP target genes after NELFA knockdown in MDA-MB-231 cells (N=3). mRNA levels were quantified by RT-qPCR and normalised to GAPDH. Statistical analysis was performed using one-way ANOVA with multiple comparisons; p-values are indicated, with P<0.05 considered significant compared to control.

Article Snippet: To optimize immunohistochemistry (IHC) conditions for NELFA (Santa Cruz, #sc-365004) and NELFB (Abcam, ab167401) antibodies, we tested epitope retrieval at pH levels of 6, 8, and 9 on high-tumor-content tissues using a 1:50 dilution of the antibody.

Techniques: Knockdown, Expressing, Quantitative RT-PCR, Control

Journal: bioRxiv

Article Title: NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

doi: 10.64898/2025.12.29.696819

Figure Lengend Snippet: (A) Gene Set Enrichment Analysis (GSEA) for MSigDB Oncogenic Signatures (C6) collection of significantly altered genes (p < 0.05) after NELFA knockdown compared to control knockdown. The Normalized Enrichment Score (NES) is plotted on the x-axis, with dot size corresponding to the number of genes overlapping with the ranked list, and color indicating statistical significance (−log₁₀ p -value), with red denoting higher significance. (B) GSEA Enrichment analysis for MSigDB HALLMARK Pathways. (C) Transcription Factor (TF) enrichment results from user-defined gene sets using a combination of perturbation and binding datasets. Y-axis lists the enrichment terms from Enrichr. Each term represents either a TF perturbation experiment (e.g., RNAi, overexpression) from public datasets (like GEO) or a TF binding profile from ENCODE ChIP-seq data (2015). Dot Size reflects the significance of enrichment with the z-score. Dot colour encodes the −log₁₀(p-value) from Fisher’s exact test, with red indicating higher significance. (D) Venn diagram showing the overlap of significantly differentially expressed genes (p < 0.05) across siNELFA, siYAP, and siNELFA-siYAP knockdowns compared to siControl. (E) Upset Plot showing the distribution of genes across four regulatory categories. Genes were classified based on log2FC≥ 1 thresholds from siNELFA, siYAP, and double knockdown comparisons. Each bar represents the number of genes exclusively assigned to one of the four categories. (F) Heatmap of genes grouped into four categories based on log2 fold change

Article Snippet: To optimize immunohistochemistry (IHC) conditions for NELFA (Santa Cruz, #sc-365004) and NELFB (Abcam, ab167401) antibodies, we tested epitope retrieval at pH levels of 6, 8, and 9 on high-tumor-content tissues using a 1:50 dilution of the antibody.

Techniques: Knockdown, Control, Binding Assay, Over Expression, ChIP-sequencing

Journal: bioRxiv

Article Title: NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

doi: 10.64898/2025.12.29.696819

Figure Lengend Snippet: NELFA expression and its association with patient survival outcomes. (A) Representative immunohistochemistry (IHC) images of invasive ductal carcinoma (IDC) tumours displaying high (#505) and low (#376) NELFA expression, with scale bars of 500 µm (overview) and 100 µm (zoomed region) included for reference. (B-I) Kaplan-Meier (KM) plots are based on the NELFA expression cohort. Statistical significances are computed using the log-rank test (Mantel-Cox) in GraphPad Prism 8.0.1 (244). For each KM Plot, the number of patients in each NELFA expression category is listed, along with the number of events in parentheses. (B) Overall Survival of the IDC cohort, (C) Disease-free survival of the IDC cohort, (D-F) Overall Survival of the molecular subtypes, and (G-I) Disease-free survival of the molecular subtypes.

Article Snippet: To optimize immunohistochemistry (IHC) conditions for NELFA (Santa Cruz, #sc-365004) and NELFB (Abcam, ab167401) antibodies, we tested epitope retrieval at pH levels of 6, 8, and 9 on high-tumor-content tissues using a 1:50 dilution of the antibody.

Techniques: Expressing, Immunohistochemistry

Journal: bioRxiv

Article Title: NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

doi: 10.64898/2025.12.29.696819

Figure Lengend Snippet:

Article Snippet: To optimize immunohistochemistry (IHC) conditions for NELFA (Santa Cruz, #sc-365004) and NELFB (Abcam, ab167401) antibodies, we tested epitope retrieval at pH levels of 6, 8, and 9 on high-tumor-content tissues using a 1:50 dilution of the antibody.

Techniques: Expressing

Journal: bioRxiv

Article Title: NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

doi: 10.64898/2025.12.29.696819

Figure Lengend Snippet: (A) Representative immunohistochemistry (IHC) images of invasive ductal carcinoma (IDC) tumours displaying high (#499) and low (#216) YAP expression, with scale bars of 500 µm (overview) and 100 µm (zoomed region) included for reference. (B-I) Kaplan-Meier (KM) plots are based on the YAP expression cohort. Statistical significances are computed using the log-rank test (Mantel-Cox) in GraphPad Prism 8.0.1 (244). For each KM Plot, the number of patients in each YAP expression category is listed, along with the number of events in parentheses. (B) Overall Survival of the IDC cohort, (C) Disease-free survival of the IDC cohort, (D-F) Overall Survival of the molecular subtypes, and (G-I) Disease-free survival of the molecular subtypes.

Article Snippet: To optimize immunohistochemistry (IHC) conditions for NELFA (Santa Cruz, #sc-365004) and NELFB (Abcam, ab167401) antibodies, we tested epitope retrieval at pH levels of 6, 8, and 9 on high-tumor-content tissues using a 1:50 dilution of the antibody.

Techniques: Immunohistochemistry, Expressing

Journal: bioRxiv

Article Title: NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

doi: 10.64898/2025.12.29.696819

Figure Lengend Snippet: (A) Representative immunohistochemistry (IHC) images of invasive ductal carcinoma (IDC) tumours displaying combination of high and low YAP expression with high and low NELFA. YAP-High, NELFA-High (#499); YAP-High, NELFA-Low (#503); YAP-Low, NELFA-High (#92); YAP-Low, NELFA-Low (#288), with scale bars of 250 µm (overview) included for reference. (B-I) Kaplan-Meier (KM) plots are based on the combination of YAP and NELFA expression cohort. Statistical significances are computed using the log-rank test (Mantel-Cox) in GraphPad Prism 8.0.1 (244). For each KM Plot, the number of patients in each YAP and NELFA expression category is listed, along with the number of events in parentheses. (B) Overall Survival of the IDC cohort, (C) Disease-free survival of the IDC cohort, (D-F) Overall Survival of the molecular subtypes, and (G-I) Disease-free survival of the molecular subtypes.

Article Snippet: To optimize immunohistochemistry (IHC) conditions for NELFA (Santa Cruz, #sc-365004) and NELFB (Abcam, ab167401) antibodies, we tested epitope retrieval at pH levels of 6, 8, and 9 on high-tumor-content tissues using a 1:50 dilution of the antibody.

Techniques: Immunohistochemistry, Expressing

Journal: bioRxiv

Article Title: NELFA-mediated promoter-proximal pausing restrains YAP-driven transcription and shapes context-dependent outcomes in breast cancer

doi: 10.64898/2025.12.29.696819

Figure Lengend Snippet: (A-C) KM plots of Breast cancer patients divided based expression of individual genes NELFA, YAP, and NELFA within High YAP expression of BC (Breast Cancer) IDC cohort. Statistical significances are computed using the log-rank test (Mantel-Cox) in GraphPad Prism 8.0.1 (244). (A) Overall and disease-free survival of NELFA expression for molecular subtypes of BC (B) Overall and disease-free survival of YAP expression for molecular subtypes of BC (C) Overall and disease-free survival of NELFA expression within high YAP for molecular subtypes of BC

Article Snippet: To optimize immunohistochemistry (IHC) conditions for NELFA (Santa Cruz, #sc-365004) and NELFB (Abcam, ab167401) antibodies, we tested epitope retrieval at pH levels of 6, 8, and 9 on high-tumor-content tissues using a 1:50 dilution of the antibody.

Techniques: Expressing