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Novus Biologicals pe2
Pe2, supplied by Novus Biologicals, used in various techniques. Bioz Stars score: 93/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/anti+ebna2/EBNA2+Antibody+(PE2)+-+BSA+Free/pmc10862363__BLOOD_BLD___2023___021346___mmc1-86-17-19
Average 93 stars, based on 5 article reviews

pe2 - by Bioz Stars, 2026-09

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Article Title: Epstein-Barr virus–encoded EBNA2 downregulates ICOSL by inducing miR-24 in B-cell lymphoma
Article Snippet: Antigen retrieval was performed in BOND Epitope Retrieval Solution 2 (ER2, Leica Biosystems) at pH 9 for 30 minutes at 95°C. .. The sections were stained with anti-EBNA2 (NBP2-50382, NOVUS), at 1:150 dilution, followed by incubation with the secondary antibody using the Bond Polymer Refine Red Detection (Leica Microsystems, Newcastle, United Kingdom), a polymeric AP-linker antibody conjugate system containing Fast Red solution as substrate chromogen. .. For ICOSL, after antigen retrieval with Cell conditioner 1 (CC1, Ventana) at pH 6, for 20 min at 95°C, FFPE sections were incubated with anti-ICOSL antibody (CD274) (PA5-96572, Invitrogen) at 1:120 dilution for 40 minutes followed by incubation with a cocktail of enzyme-labeled secondary antibodies (HQ Universal linker and Multimer, Ventana).

Article Title: Dasatinib exacerbates splenomegaly of mice inoculated with Epstein-Barr virus-infected lymphoblastoid cell lines
Article Snippet: .. In situ hybridization and immunohistochemistry staining were performed as previously reported , using Bond ready-to-use ISH EBER probe (Leica Microsystems), anti-LMP1 (CS-1, CS-2, CS-3, and CS-4, mouse mAbs, Leica biosystems), and anti-EBNA2 (PE2, mouse mAb, Novus Biologicals). .. The tissue slides were observed and were photographed using Olympus BX63 microscope and cellSence software.

Incubation:

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In Situ Hybridization:

Immunohistochemistry:

Image Search Results

A. CRISPR/Cas9 gene editing was used to insert a 10 bp deletion in the EBNA2 gene of the AG876 EBV strain. The nucleotide sequences deleted, and the resultant translated EBNA2 protein, are shown. B. Protein extracts of human cord blood B cells stably infected with the ΔEBNA2 EBV mutant and maintained on a CD40L/IL21 expressing feeder layer were examined by immunoblot to assess expression of the EBV latency proteins EBNA2, EBNA1, LMP1, and EBNA3A and the GFP protein as indicated. EBV positive and EBV negative Akata Burkitt lymphoma cell lines and an LCL infected with Akata EBV (containing the GFP gene inserted into the viral BXLF1 gene locus) serve as negative and positive controls for expression of various EBV proteins and GFP.

Journal: PLOS Pathogens

Article Title: Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice

doi: 10.1371/journal.ppat.1012132

Figure Lengend Snippet: A. CRISPR/Cas9 gene editing was used to insert a 10 bp deletion in the EBNA2 gene of the AG876 EBV strain. The nucleotide sequences deleted, and the resultant translated EBNA2 protein, are shown. B. Protein extracts of human cord blood B cells stably infected with the ΔEBNA2 EBV mutant and maintained on a CD40L/IL21 expressing feeder layer were examined by immunoblot to assess expression of the EBV latency proteins EBNA2, EBNA1, LMP1, and EBNA3A and the GFP protein as indicated. EBV positive and EBV negative Akata Burkitt lymphoma cell lines and an LCL infected with Akata EBV (containing the GFP gene inserted into the viral BXLF1 gene locus) serve as negative and positive controls for expression of various EBV proteins and GFP.

Article Snippet: The following antibodies were used for immunoblot analyses in this study: anti-R rabbit polyclonal antibody directed against the R peptide (peptide sequence EDPDEETSSQAVKALREMAD, anti-BACH2 (Cell Signaling #80775), anti-BCL6 (Cell Signaling #14895), anti-BHRF1 (Millipore #MAB8188), anti-BIM (Cell Signaling #2933), anti-BLIMP1 (Cell Signaling #9115), anti-BMRF1 (Millipore #MAB8186), anti-BZLF1 (Santa Cruz #sc-53904), anti-CD10 (Abcam #ab227659), anti-CD19 (Abcam #ab134114), anti-CD30 (Invitrogen #MA536219), anti-CD179b (Invitrogen #702901), anti-Cyclin D2 (Cell Signaling #3741), anti-Cyclin D3 (Cell Signaling #2936), anti-DNMT1 (Abcam #ab188453), anti-DNMT3B (Santa Cruz #sc-376043), anti-EBNA1 (Santa Cruz #sc-81581), anti-EBNA2 (Abcam #ab90543), anti-EBNA3A (Exalpha #F115P), anti-GCSAM (Cell Signaling #20289), anti-GFP (Santa Cruz #sc-9996), anti-IL7R (Santa Cruz #sc-514445), anti-IL10Rα (R&D #MAB2742), anti-IL21R (R&D #MAB991), anti-IRF4 (Santa Cruz #sc-56713), anti-JAK1 (Cell Signaling #3332), anti-JAK2 (Cell Signaling #3230), anti-LMP1 (Abcam #ab78113), anti-c-Myb (Cell Signaling #12319), anti-c-Myc (Abcam #ab32072), anti-p100/52 (Cell Signaling #3017), anti-RAG1 (Cell Signaling #3968), anti-SOCS1 (Cell Signaling #55313), anti-SRC (Cell Signaling #2109), anti-phospho-SRC (Tyr416) (Cell Signaling #2101), anti-STAT3 (Cell Signaling #4904), anti-phospho-STAT3 (Y705) (Cell Signaling #9145), anti-phospho-STAT5 (Y694) (Cell Signaling #9359), anti-TCF3 (E2A) (Cell Signaling #4865), anti-TCL1 (Cell Signaling #4042), anti-TDT (Invitrogen #14-9739-82), anti-UHRF1 (Cell Signaling #12387), anti-Tubulin (Sigma #T5168), and anti-Actin (Sigma #A5441).

Techniques: CRISPR, Stable Transfection, Infection, Mutagenesis, Expressing, Western Blot

A. Human cord blood B cells stably infected with the ΔEBNA2 EBV mutant were co-infected with or without a retrovirus expressing mouse wild-type Myc protein as indicated and maintained on a CD40L/IL21 expressing feeder layer without antibiotic selection. One month after retrovirus infection, protein extracts were harvested and immunoblot analysis was performed to assess expression levels of Myc, LMP1, and tubulin as indicated. EBV-negative and EBV-positive BL cells (Akata) serve as a positive control for elevated Myc expression. B and C . NSG mice were injected subcutaneously with 10 million cord blood B cells (suspended in Matrigel) infected with ΔEBNA2 EBV alone, or co-infected with ΔEBNA2 EBV and a Myc expressing vector. Donor 1 cells (used in B ) were co-infected with a wild-type mouse Myc expressing retrovirus, while Donor 2 cells (used in C ) were co-infected with a retrovirus expressing a mutant human Myc (T58A) protein. The number of animals sacrificed with tumors at various time points after injection of cells is shown. The p-values were calculated using the Kruskal-Wallis method and program M-Stat 7.0. D. Tumors were paraffin-fixed and H&E staining performed to examine tumor morphology and IHC staining performed to examine expression of the germinal center B cell marker, CD10.

Journal: PLOS Pathogens

Article Title: Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice

doi: 10.1371/journal.ppat.1012132

Figure Lengend Snippet: A. Human cord blood B cells stably infected with the ΔEBNA2 EBV mutant were co-infected with or without a retrovirus expressing mouse wild-type Myc protein as indicated and maintained on a CD40L/IL21 expressing feeder layer without antibiotic selection. One month after retrovirus infection, protein extracts were harvested and immunoblot analysis was performed to assess expression levels of Myc, LMP1, and tubulin as indicated. EBV-negative and EBV-positive BL cells (Akata) serve as a positive control for elevated Myc expression. B and C . NSG mice were injected subcutaneously with 10 million cord blood B cells (suspended in Matrigel) infected with ΔEBNA2 EBV alone, or co-infected with ΔEBNA2 EBV and a Myc expressing vector. Donor 1 cells (used in B ) were co-infected with a wild-type mouse Myc expressing retrovirus, while Donor 2 cells (used in C ) were co-infected with a retrovirus expressing a mutant human Myc (T58A) protein. The number of animals sacrificed with tumors at various time points after injection of cells is shown. The p-values were calculated using the Kruskal-Wallis method and program M-Stat 7.0. D. Tumors were paraffin-fixed and H&E staining performed to examine tumor morphology and IHC staining performed to examine expression of the germinal center B cell marker, CD10.

Techniques: Stable Transfection, Infection, Mutagenesis, Expressing, Selection, Western Blot, Positive Control, Injection, Plasmid Preparation, Staining, Immunohistochemistry, Marker

A. Protein extracts were harvested from tumors derived with Donor 1 cells infected with ΔEBNA2 EBV alone, or co-infected with ΔEBNA2 EBV and a Myc-expressing vector, and immunoblot analysis was performed to examine expression of various different EBV latency proteins, GFP and various cellular proteins as indicated. EBV-negative Akata BL cells serve as a positive control for Myc expression (and other cellular proteins such as CD10 expressed in BL tumors) and a negative control for EBV protein expression, while an AG876 wild-type EBV-infected LCL serves as a positive control for viral proteins expressed in type III latency. B . Lymphomas infected with ΔEBNA2 EBV and Myc or ΔEBNA2 EBV alone were examined for expression of the EBV EBNA3A latency protein by immunoblot. EBV-neg and EBV+ Akata BL cells serve as a negative control. C. Lymphomas infected with ΔEBNA2 EBV and Myc or ΔEBNA2 EBV alone were examined for expression of Myc, the EBV BHRF1 protein or the cellular BIM protein (the predominant isoform BIM EL or extra-large) by immunoblot. EBV-neg Akata BL cells serve as a negative control for BHRF1 expression and a BL5 strain EBV infected LCL serves as a positive control for BHRF1 expression. Tumors derived from Donor 1 versus Donor 2 are indicated. D. p53 immunoblot was performed to compare p53 expression in extracts isolated from stable cell lines derived from Donor 2 ΔEBNA2 + Myc tumors (N1, N3, N4, R3, R4), the Akata (p53-deleted) BL line, the Mutu I (p53 mutant) BL line, the P3HR1 (p53 mutant) BL line, or an EBV-transformed LCL (BL5) line as indicated.

Journal: PLOS Pathogens

Article Title: Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice

doi: 10.1371/journal.ppat.1012132

Figure Lengend Snippet: A. Protein extracts were harvested from tumors derived with Donor 1 cells infected with ΔEBNA2 EBV alone, or co-infected with ΔEBNA2 EBV and a Myc-expressing vector, and immunoblot analysis was performed to examine expression of various different EBV latency proteins, GFP and various cellular proteins as indicated. EBV-negative Akata BL cells serve as a positive control for Myc expression (and other cellular proteins such as CD10 expressed in BL tumors) and a negative control for EBV protein expression, while an AG876 wild-type EBV-infected LCL serves as a positive control for viral proteins expressed in type III latency. B . Lymphomas infected with ΔEBNA2 EBV and Myc or ΔEBNA2 EBV alone were examined for expression of the EBV EBNA3A latency protein by immunoblot. EBV-neg and EBV+ Akata BL cells serve as a negative control. C. Lymphomas infected with ΔEBNA2 EBV and Myc or ΔEBNA2 EBV alone were examined for expression of Myc, the EBV BHRF1 protein or the cellular BIM protein (the predominant isoform BIM EL or extra-large) by immunoblot. EBV-neg Akata BL cells serve as a negative control for BHRF1 expression and a BL5 strain EBV infected LCL serves as a positive control for BHRF1 expression. Tumors derived from Donor 1 versus Donor 2 are indicated. D. p53 immunoblot was performed to compare p53 expression in extracts isolated from stable cell lines derived from Donor 2 ΔEBNA2 + Myc tumors (N1, N3, N4, R3, R4), the Akata (p53-deleted) BL line, the Mutu I (p53 mutant) BL line, the P3HR1 (p53 mutant) BL line, or an EBV-transformed LCL (BL5) line as indicated.

Techniques: Derivative Assay, Infection, Expressing, Plasmid Preparation, Western Blot, Positive Control, Negative Control, Isolation, Stable Transfection, Mutagenesis, Transformation Assay

RNA was isolated from Donor 1 derived tumors infected with ΔEBNA2 EBV alone or both ΔEBNA2 EBV and Myc vector and RNA-seq analysis was performed. A. A heatmap comparing cellular gene expression in tumors with and without Myc vector co-infection is shown. B. GSEA analysis was performed to compare gene expression in tumors with and without Myc. Selected gene sets that have up-regulated expression in the Myc-expressing tumors are shown. C. Selected gene sets that have down-regulated expression in the Myc-expressing tumors are shown.

Journal: PLOS Pathogens

Article Title: Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice

doi: 10.1371/journal.ppat.1012132

Figure Lengend Snippet: RNA was isolated from Donor 1 derived tumors infected with ΔEBNA2 EBV alone or both ΔEBNA2 EBV and Myc vector and RNA-seq analysis was performed. A. A heatmap comparing cellular gene expression in tumors with and without Myc vector co-infection is shown. B. GSEA analysis was performed to compare gene expression in tumors with and without Myc. Selected gene sets that have up-regulated expression in the Myc-expressing tumors are shown. C. Selected gene sets that have down-regulated expression in the Myc-expressing tumors are shown.

Techniques: Isolation, Derivative Assay, Infection, Plasmid Preparation, RNA Sequencing Assay, Expressing

Protein extracts were harvested from tumors infected with ΔEBNA2 EBV alone, or co-infected with ΔEBNA2 EBV and Myc vector, and immunoblot analysis was performed to examine expression of various cellular proteins known to be highly expressed in GC B cells and/or BL tumors as indicated. A. Extracts from Donor 1 derived tumors with or without Myc expression were examined for expression of Myc, the EBV LMP1 protein, cyclin D3, cyclin D2, GCSAM or TCL1 as indicated. EBV negative Akata BL cells serve as a positive control for Myc and GC B cell expressed proteins. The same actin immunoblot will be seen in Figs 5D, and , while the LMP1 and Myc blots will be repeated in Figs 5D and . B. Extracts harvested from Myc expressing tumors derived from Donor 1 or Donor 2 as indicated or Donor 1 derived tumors without Myc were examined by immunoblot for expression of Myc, Myb and BACH2 as indicated. Control extracts include the EBV-negative Akata human BL cell line and a BL5 strain EBV infected LCL. C. Extracts harvested from Myc expressing tumors derived from Donor 1 or Donor 2 as indicated or Donor 1 derived tumors without Myc were examined by immunoblot for expression of TCF3 as indicated. Control extracts include the EBV-negative Akata human BL cell line and a BL5 strain EBV infected LCL. D. Extracts from Donor 1 derived tumors with or without Myc expression were examined for expression of Myc, the EBV LMP1 protein, DNMT3B protein, DNMT1 protein and UHRF1 protein as indicated. The same extracts used in Fig 5A were used for this blot and the Myc, LMP1, and actin blots from Fig 5A are reproduced here to show levels of expression in each condition.

Journal: PLOS Pathogens

Article Title: Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice

doi: 10.1371/journal.ppat.1012132

Figure Lengend Snippet: Protein extracts were harvested from tumors infected with ΔEBNA2 EBV alone, or co-infected with ΔEBNA2 EBV and Myc vector, and immunoblot analysis was performed to examine expression of various cellular proteins known to be highly expressed in GC B cells and/or BL tumors as indicated. A. Extracts from Donor 1 derived tumors with or without Myc expression were examined for expression of Myc, the EBV LMP1 protein, cyclin D3, cyclin D2, GCSAM or TCL1 as indicated. EBV negative Akata BL cells serve as a positive control for Myc and GC B cell expressed proteins. The same actin immunoblot will be seen in Figs 5D, and , while the LMP1 and Myc blots will be repeated in Figs 5D and . B. Extracts harvested from Myc expressing tumors derived from Donor 1 or Donor 2 as indicated or Donor 1 derived tumors without Myc were examined by immunoblot for expression of Myc, Myb and BACH2 as indicated. Control extracts include the EBV-negative Akata human BL cell line and a BL5 strain EBV infected LCL. C. Extracts harvested from Myc expressing tumors derived from Donor 1 or Donor 2 as indicated or Donor 1 derived tumors without Myc were examined by immunoblot for expression of TCF3 as indicated. Control extracts include the EBV-negative Akata human BL cell line and a BL5 strain EBV infected LCL. D. Extracts from Donor 1 derived tumors with or without Myc expression were examined for expression of Myc, the EBV LMP1 protein, DNMT3B protein, DNMT1 protein and UHRF1 protein as indicated. The same extracts used in Fig 5A were used for this blot and the Myc, LMP1, and actin blots from Fig 5A are reproduced here to show levels of expression in each condition.

Techniques: Infection, Plasmid Preparation, Western Blot, Expressing, Derivative Assay, Positive Control

Journal: PLOS Pathogens

Article Title: Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice

doi: 10.1371/journal.ppat.1012132

Figure Lengend Snippet: A . Protein extracts were harvested from tumors derived with Donor 1 cells infected with ΔEBNA2 EBV alone, or co-infected with ΔEBNA2 EBV and a Myc expressing vector, and immunoblot analysis was performed to examine expression of Myc, LMP1, and p100 or its cleaved (activated) product, p52. The same extracts used in were used for this blot and the Myc, LMP1 and actin blots from are reproduced here to show levels of expression in each condition. B. Immunoblot analysis was performed on extracts isolated from Donor 1 tumors with or without Myc and expression of total STAT3, activated STAT3 (phosphorylated on tyrosine 705) or total Src was examined by immunoblot as indicated.

Techniques: Derivative Assay, Infection, Expressing, Plasmid Preparation, Western Blot, Isolation

Journal: PLOS Pathogens

Article Title: Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice

doi: 10.1371/journal.ppat.1012132

Figure Lengend Snippet: A. Protein extracts were harvested from tumors derived with Donor 1 cells infected with ΔEBNA2 EBV alone, or co-infected with ΔEBNA2 EBV and a Myc expressing vector, and immunoblot analysis was performed to examine expression of cellular proteins highly expressed in pro-B cells and/or pre-B cells, including CD179B (IGLL1), DNTT (TDT) and RAG1 as indicated. The extracts used are the same as those in with the same actin blot. B. Protein extracts harvested from Donor 1 derived tumors with or without Myc expression, or from an EBV-negative Akata BL cell line or an EBV strain BL5-infected LCL line, were examined by immunoblot analysis for expression of IL7R. C. Stable cell lines derived from Donor 2 ΔEBNA2 EBV plus Myc tumors (right panel), or the EBV-positive Akata Burkitt cell line (left panel) were treated with or without IL7 for 30 minutes and the level of Y694-phosphorylated STAT5 was examined by immunoblot.

Techniques: Derivative Assay, Infection, Expressing, Plasmid Preparation, Western Blot, Stable Transfection

A . Protein extracts were isolated from stable cell lines derived from Donor 2 ΔEBNA2 EBV plus Myc tumors (grown off the feeder layer) and immunoblot analysis was performed to examine expression of Myc, LMP1, total STAT3, phosphorylated STAT3, and total Src. The EBV negative Akata BL line and a BL5 EBV infected LCL serve as controls. B. Mutu I BL cells were transfected with a vector control, a STAT3 expression vector alone, a Src (constitutively active) expression vector alone, or both STAT3 and Src expression vectors. Two days later protein extracts were harvested and immunoblot analysis performed to examine expression of total STAT3, phosphorylated STAT3, Src, and LMP1 as indicated. C. Mutu I BL cells were infected with lentiviral vectors expressing a non-targeting control shRNA (NT) or STAT3 targeting shRNAs (left panel) or NF-κB2 (p100/52) targeted shRNAs (right panel). Three days later cells were treated with puromycin for 2 days, and then grown on or off an IL40/IL21 expressing feeder cell layer for another 2 days before harvesting protein extracts for immunoblot analysis. The levels of STAT3, LMP1, EBNA2, and p100/52 expression are shown for each condition as indicated. The numbers below each immunoblot in the left panel quantify the results using Image Studio Lite software to normalize the levels of STAT3 and LMP1 expression to actin expression. Results are presented as the ratio of STAT3 and LMP1 expression in STAT3 knockdown conditions relative to control (NT) shRNA, after being normalized to actin. Values of control conditions are set as 1. D. EBV+ Akata BL cells were infected with a lentivirus vector expressing LMP1 or a control lentivirus and two days later cells were treated with puromycin for 3 days. Protein extracts were harvested from puromycin resistant cells and immunoblot analysis performed to examine the levels of LMP1, total STAT3, phosphorylated STAT3, Src, and Myc as indicated. E. Cell lines derived from ΔEBNA2 EBV plus Myc lymphomas or Mutu I BL cells were treated with or without 5’azacitidine for 3 days and then protein extracts harvested for immunoblot to examine expression of LMP1, BZLF1, EBNA2, total STAT3, phosphorylated STAT3 or Src as indicated. F. Extracts isolated from Akata BL cells or Mutu I cells treated with non-targeting shRNA or Myb targeting shRNA (the same extracts used in ) were examined by immunoblot analysis for expression of Myb, LMP1, EBNA2 and BZLF1 as indicated. EBV-neg Akata BL cells and a BL5 EBV-infected LCL serve as controls.

Journal: PLOS Pathogens

Article Title: Latent Epstein-Barr virus infection collaborates with Myc over-expression in normal human B cells to induce Burkitt-like Lymphomas in mice

doi: 10.1371/journal.ppat.1012132

Figure Lengend Snippet: A . Protein extracts were isolated from stable cell lines derived from Donor 2 ΔEBNA2 EBV plus Myc tumors (grown off the feeder layer) and immunoblot analysis was performed to examine expression of Myc, LMP1, total STAT3, phosphorylated STAT3, and total Src. The EBV negative Akata BL line and a BL5 EBV infected LCL serve as controls. B. Mutu I BL cells were transfected with a vector control, a STAT3 expression vector alone, a Src (constitutively active) expression vector alone, or both STAT3 and Src expression vectors. Two days later protein extracts were harvested and immunoblot analysis performed to examine expression of total STAT3, phosphorylated STAT3, Src, and LMP1 as indicated. C. Mutu I BL cells were infected with lentiviral vectors expressing a non-targeting control shRNA (NT) or STAT3 targeting shRNAs (left panel) or NF-κB2 (p100/52) targeted shRNAs (right panel). Three days later cells were treated with puromycin for 2 days, and then grown on or off an IL40/IL21 expressing feeder cell layer for another 2 days before harvesting protein extracts for immunoblot analysis. The levels of STAT3, LMP1, EBNA2, and p100/52 expression are shown for each condition as indicated. The numbers below each immunoblot in the left panel quantify the results using Image Studio Lite software to normalize the levels of STAT3 and LMP1 expression to actin expression. Results are presented as the ratio of STAT3 and LMP1 expression in STAT3 knockdown conditions relative to control (NT) shRNA, after being normalized to actin. Values of control conditions are set as 1. D. EBV+ Akata BL cells were infected with a lentivirus vector expressing LMP1 or a control lentivirus and two days later cells were treated with puromycin for 3 days. Protein extracts were harvested from puromycin resistant cells and immunoblot analysis performed to examine the levels of LMP1, total STAT3, phosphorylated STAT3, Src, and Myc as indicated. E. Cell lines derived from ΔEBNA2 EBV plus Myc lymphomas or Mutu I BL cells were treated with or without 5’azacitidine for 3 days and then protein extracts harvested for immunoblot to examine expression of LMP1, BZLF1, EBNA2, total STAT3, phosphorylated STAT3 or Src as indicated. F. Extracts isolated from Akata BL cells or Mutu I cells treated with non-targeting shRNA or Myb targeting shRNA (the same extracts used in ) were examined by immunoblot analysis for expression of Myb, LMP1, EBNA2 and BZLF1 as indicated. EBV-neg Akata BL cells and a BL5 EBV-infected LCL serve as controls.

Techniques: Isolation, Stable Transfection, Derivative Assay, Western Blot, Expressing, Infection, Transfection, Plasmid Preparation, shRNA, Software

Schematic overview: study design for identification of type-specific EBNA2 binding events and binding partners. Starting with two human B cell lines with type 1 EBV infection and two human B cell lines with type 2 EBV infection, we performed EBNA2 chromatin immunoprecipitation (ChIP-seq). Using these data, we identified shared and type-specific EBNA2 ChIP-seq peaks in the human genome. Differential EBNA2 interactions with human cofactors were predicted computationally and validated experimentally

Journal: BMC Genomics

Article Title: Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

doi: 10.1186/s12864-024-10183-8

Figure Lengend Snippet: Schematic overview: study design for identification of type-specific EBNA2 binding events and binding partners. Starting with two human B cell lines with type 1 EBV infection and two human B cell lines with type 2 EBV infection, we performed EBNA2 chromatin immunoprecipitation (ChIP-seq). Using these data, we identified shared and type-specific EBNA2 ChIP-seq peaks in the human genome. Differential EBNA2 interactions with human cofactors were predicted computationally and validated experimentally

Article Snippet: The primary antibody was diluted (BATF, CST 8638, 1:1000; EBF1, Santa Cruz sc-137065, 1:500; EBNA2, [PE2] Abcam ab90543, 1:1000; JUNB, Active Motif 39,549, 1:1000; RBPJ, CST 5313, 1:1000; and SPI1, CST 2266, 1:1000) in Intercept Blocking Buffer (with Tween 20 diluted at 1:1000) and the membranes incubated in primary antibody overnight at 4 °C with rocking.

Techniques: Binding Assay, Infection, Chromatin Immunoprecipitation, ChIP-sequencing

EBNA2 types 1 and 2 interact with the human genome in a type-specific manner. A Schematic for identification of type 1 and type 2 specific EBNA2 peaks. B Shared and type-specific EBNA2 peak counts. C ChIP-seq signal strength (normalized read depth) for type 1 (GM12878, Mutu-III) and type 2 (AG876, Jiyoye) EBNA2 at shared and type-specific regions. As expected, shared peaks (top) have equivalent signal strength between the four cell lines. EBNA2 type 1 specific peaks have greater signal strength in EBV-1 cell lines (middle left) compared to EBV-2 cell lines (middle right). Likewise for type 2 (bottom). See for EBNA2 ChIP-seq analysis details. D Identification of EBNA2 type-specific enrichment of Gene Ontology Biological Processes. GO enrichment analysis of Biological Processes was performed within EBNA2 type 1 specific and type 2 specific ChIP-seq peaks. Each dot represents the normalized significance of one GO term. Type 1 specific (x-axis) and type 2 specific (y-axis) normalized significance are compared. The solid black line indicates equivalent significance between the compared peak sets. Dashed lines indicate the cut off for type specific enrichment (difference of 20% or more)

Journal: BMC Genomics

Article Title: Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

doi: 10.1186/s12864-024-10183-8

Figure Lengend Snippet: EBNA2 types 1 and 2 interact with the human genome in a type-specific manner. A Schematic for identification of type 1 and type 2 specific EBNA2 peaks. B Shared and type-specific EBNA2 peak counts. C ChIP-seq signal strength (normalized read depth) for type 1 (GM12878, Mutu-III) and type 2 (AG876, Jiyoye) EBNA2 at shared and type-specific regions. As expected, shared peaks (top) have equivalent signal strength between the four cell lines. EBNA2 type 1 specific peaks have greater signal strength in EBV-1 cell lines (middle left) compared to EBV-2 cell lines (middle right). Likewise for type 2 (bottom). See for EBNA2 ChIP-seq analysis details. D Identification of EBNA2 type-specific enrichment of Gene Ontology Biological Processes. GO enrichment analysis of Biological Processes was performed within EBNA2 type 1 specific and type 2 specific ChIP-seq peaks. Each dot represents the normalized significance of one GO term. Type 1 specific (x-axis) and type 2 specific (y-axis) normalized significance are compared. The solid black line indicates equivalent significance between the compared peak sets. Dashed lines indicate the cut off for type specific enrichment (difference of 20% or more)

Techniques: ChIP-sequencing

Identification of shared and type-dependent EBNA2 human cofactors. A Unbiased computational prediction of EBNA2 human cofactors. Human transcription factor (hTF) motif enrichment analysis was performed within EBNA2 type 1 specific, type 2 specific, and shared peaks. Each dot represents the normalized significance of one hTF motif. Type 1 specific (y-axis, left) or type 2 specific (y-axis, right) normalized motif significance is compared to shared peaks (x-axis in both panels). Black diamonds indicate exemplar hTF motifs for the four hTF classes that are depicted in ( B ). The black line indicates equivalent significance between the compared peak sets. Motifs are colored by class. B Frequency of occurrence of exemplary motifs in EBNA2 shared and type-specific peak sets. For the four exemplary motifs, the percent of peaks containing predicted binding sites for the motif is shown. Each bar represents percent foreground (i.e., the percent of actual peak DNA sequences containing a match to the motif). The horizontal black line within each bar depicts percent background (i.e., the percent of randomly selected genome sequences, matching GC content). Asterisks indicate significant motif enrichment ( P < 0.05), as calculated by HOMER. C Experimental validation of predicted EBNA2 co-occupancy with hTFs. Co-occupancy was assessed by hTF and EBNA2 ChIP-seq peak overlap. The hTFs BATF and JUNB were chosen as representative AP-1 family members (see ). For each of the five hTFs, a union peak set was created by combining peaks across all cell lines. For each bar, the percent of each hTF union peak set overlapping each EBNA2 ChIP-seq peak category is shown. Datasets with significant overlap between EBNA2 peak sets and the union peak set of hTFs (as calculated by RELI) are indicated with asterisks ( P < 0.05). Note the consistency between the motif-based predictions ( B ) and ChIP-seq experimental validation results ( C )

Journal: BMC Genomics

Article Title: Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

doi: 10.1186/s12864-024-10183-8

Figure Lengend Snippet: Identification of shared and type-dependent EBNA2 human cofactors. A Unbiased computational prediction of EBNA2 human cofactors. Human transcription factor (hTF) motif enrichment analysis was performed within EBNA2 type 1 specific, type 2 specific, and shared peaks. Each dot represents the normalized significance of one hTF motif. Type 1 specific (y-axis, left) or type 2 specific (y-axis, right) normalized motif significance is compared to shared peaks (x-axis in both panels). Black diamonds indicate exemplar hTF motifs for the four hTF classes that are depicted in ( B ). The black line indicates equivalent significance between the compared peak sets. Motifs are colored by class. B Frequency of occurrence of exemplary motifs in EBNA2 shared and type-specific peak sets. For the four exemplary motifs, the percent of peaks containing predicted binding sites for the motif is shown. Each bar represents percent foreground (i.e., the percent of actual peak DNA sequences containing a match to the motif). The horizontal black line within each bar depicts percent background (i.e., the percent of randomly selected genome sequences, matching GC content). Asterisks indicate significant motif enrichment ( P < 0.05), as calculated by HOMER. C Experimental validation of predicted EBNA2 co-occupancy with hTFs. Co-occupancy was assessed by hTF and EBNA2 ChIP-seq peak overlap. The hTFs BATF and JUNB were chosen as representative AP-1 family members (see ). For each of the five hTFs, a union peak set was created by combining peaks across all cell lines. For each bar, the percent of each hTF union peak set overlapping each EBNA2 ChIP-seq peak category is shown. Datasets with significant overlap between EBNA2 peak sets and the union peak set of hTFs (as calculated by RELI) are indicated with asterisks ( P < 0.05). Note the consistency between the motif-based predictions ( B ) and ChIP-seq experimental validation results ( C )

Techniques: Binding Assay, ChIP-sequencing

Expression levels (normalized RNA-seq read counts) for genes of interest. Values are the mean of biological triplicates. N/A Not applicable

Journal: BMC Genomics

Article Title: Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

doi: 10.1186/s12864-024-10183-8

Figure Lengend Snippet: Expression levels (normalized RNA-seq read counts) for genes of interest. Values are the mean of biological triplicates. N/A Not applicable

Techniques: Expressing

Average Western blot densitometry signal for proteins of interest in this study. Values are the mean of biological triplicates

Journal: BMC Genomics

Article Title: Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

doi: 10.1186/s12864-024-10183-8

Figure Lengend Snippet: Average Western blot densitometry signal for proteins of interest in this study. Values are the mean of biological triplicates

Techniques: Western Blot

EBF1 motif enrichment across datasets. Results are ordered from most to least enriched

Journal: BMC Genomics

Article Title: Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

doi: 10.1186/s12864-024-10183-8

Figure Lengend Snippet: EBF1 motif enrichment across datasets. Results are ordered from most to least enriched

Techniques:

Type-specific expression of human genes that corresponds with type-specific EBNA2 and hTF partner genomic occupancy. One example is shown for each of the following: shared EBNA2 binding ( A : MYC , chr8:128,168,540–128,775,448), type 1 specific EBNA2 binding ( B : CXCR7 , chr2:237,441,986–237,513,677), and type 2 specific EBNA2 binding ( C : CD21 , chr1:207,601,245–207,633,439). For each locus, the normalized counts (DESeq2) of the human gene are shown above a UCSC Genome Browser screenshot depicting (top to bottom): the gene, chromatin accessibility, EBNA2 binding (ChIP-seq), and hTF binding (ChIP-seq) in each cell line. Type-specific and shared EBNA2 peaks are indicated above the EBNA2 ChIP-seq tracks. In panel A, previously identified type 1 EBNA2 super enhancers at the MYC locus (; MYC ESE2, chr8:128,312,176–128,320,865; MYC ESE1: chr8:128,215,588–128,228,144) are boxed and labeled. Data from biological replicates are shown throughout. A = AG876; J = Jiyoye; M = Mutu-III; G = GM12878; L = LCL. Data ranges: MYC Overview [ATAC-seq (0 to 5; Mutu-III 0 to 0.7); EBNA2 ChIP-seq (0 to 14); EBF1 ChIP-seq (0 to 5); SPI1 ChIP-seq (0 to 5); RBPJ ChIP-seq (0 to 5)]; MYC 525 ESE [ATAC-seq (0 to 3; Mutu-III 0 to 0.4); EBNA2 ChIP-seq (0 to 13); EBF1 ChIP-seq (0 to 5); SPI1 ChIP-seq (0 to 1); RBPJ ChIP-seq (0 to 2)]; MYC 428 ESE [ATAC-seq (0 to 4; Mutu-III 0 to 0.7); EBNA2 ChIP-seq (0 to 8); EBF1 ChIP-seq (0 to 4); SPI1 ChIP-seq (0 to 5); RBPJ ChIP-seq (0 to 5)]; CXCR7 [ATAC-seq (0 to 3; Mutu-III 0 to 0.4); EBNA2 ChIP-seq (0 to 10); EBF1 ChIP-seq (0 to 4)]; CD21 [ATAC-seq (0 to 8; Mutu-III 0 to 0.4); EBNA2 ChIP-seq (0 to 6); SPI1 ChIP-seq (0 to 3); RBPJ ChIP-seq (0 to 3)]

Journal: BMC Genomics

Article Title: Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

doi: 10.1186/s12864-024-10183-8

Figure Lengend Snippet: Type-specific expression of human genes that corresponds with type-specific EBNA2 and hTF partner genomic occupancy. One example is shown for each of the following: shared EBNA2 binding ( A : MYC , chr8:128,168,540–128,775,448), type 1 specific EBNA2 binding ( B : CXCR7 , chr2:237,441,986–237,513,677), and type 2 specific EBNA2 binding ( C : CD21 , chr1:207,601,245–207,633,439). For each locus, the normalized counts (DESeq2) of the human gene are shown above a UCSC Genome Browser screenshot depicting (top to bottom): the gene, chromatin accessibility, EBNA2 binding (ChIP-seq), and hTF binding (ChIP-seq) in each cell line. Type-specific and shared EBNA2 peaks are indicated above the EBNA2 ChIP-seq tracks. In panel A, previously identified type 1 EBNA2 super enhancers at the MYC locus (; MYC ESE2, chr8:128,312,176–128,320,865; MYC ESE1: chr8:128,215,588–128,228,144) are boxed and labeled. Data from biological replicates are shown throughout. A = AG876; J = Jiyoye; M = Mutu-III; G = GM12878; L = LCL. Data ranges: MYC Overview [ATAC-seq (0 to 5; Mutu-III 0 to 0.7); EBNA2 ChIP-seq (0 to 14); EBF1 ChIP-seq (0 to 5); SPI1 ChIP-seq (0 to 5); RBPJ ChIP-seq (0 to 5)]; MYC 525 ESE [ATAC-seq (0 to 3; Mutu-III 0 to 0.4); EBNA2 ChIP-seq (0 to 13); EBF1 ChIP-seq (0 to 5); SPI1 ChIP-seq (0 to 1); RBPJ ChIP-seq (0 to 2)]; MYC 428 ESE [ATAC-seq (0 to 4; Mutu-III 0 to 0.7); EBNA2 ChIP-seq (0 to 8); EBF1 ChIP-seq (0 to 4); SPI1 ChIP-seq (0 to 5); RBPJ ChIP-seq (0 to 5)]; CXCR7 [ATAC-seq (0 to 3; Mutu-III 0 to 0.4); EBNA2 ChIP-seq (0 to 10); EBF1 ChIP-seq (0 to 4)]; CD21 [ATAC-seq (0 to 8; Mutu-III 0 to 0.4); EBNA2 ChIP-seq (0 to 6); SPI1 ChIP-seq (0 to 3); RBPJ ChIP-seq (0 to 3)]

Techniques: Expressing, Binding Assay, ChIP-sequencing, Labeling

EBNA2 type 1 and 2 occupancy at human disease risk loci. Statistical enrichment of the overlap between type 1 and type 2 EBNA2 ChIP-seq peaks with human disease risk genetic variants. A Top: Enrichment of full EBNA2 ChIP-seq peak sets at disease risk loci for diseases previously established for type 1 EBNA2 (multiple sclerosis (MS) and systemic lupus erythematosus (SLE)). Bottom: Enrichment of type-specific and shared EBNA2 peak sets. Datasets with significant overlap (as calculated by RELI) are marked with asterisks ( P < 0.05). B Enrichment of type-specific EBNA2 ChIP-seq peak sets at all disease risk loci. Each dot represents RELI results (normalized -log corrected p -value) for EBNA2 enrichment for a given disease. Results were normalized to the max negative log p -value for each EBNA2 dataset to facilitate comparisons. The black line indicates equivalently significant enrichment for type 1 and type 2 EBNA2. Previously established “EBNA2 disorders” (dark blue dots) and other diseases discussed in the text are labeled. Disease abbreviations: CD Celiac Disease, IBD Inflammatory Bowel Disease, JIA Juvenile Idiopathic Arthritis, MS Multiple Sclerosis, PBC Primary Biliary Cholangitis, RA Rheumatoid Arthritis, SLE Systemic Lupus Erythematosus, T1D Type 1 Diabetes, UC Ulcerative Colitis

Journal: BMC Genomics

Article Title: Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome

doi: 10.1186/s12864-024-10183-8

Figure Lengend Snippet: EBNA2 type 1 and 2 occupancy at human disease risk loci. Statistical enrichment of the overlap between type 1 and type 2 EBNA2 ChIP-seq peaks with human disease risk genetic variants. A Top: Enrichment of full EBNA2 ChIP-seq peak sets at disease risk loci for diseases previously established for type 1 EBNA2 (multiple sclerosis (MS) and systemic lupus erythematosus (SLE)). Bottom: Enrichment of type-specific and shared EBNA2 peak sets. Datasets with significant overlap (as calculated by RELI) are marked with asterisks ( P < 0.05). B Enrichment of type-specific EBNA2 ChIP-seq peak sets at all disease risk loci. Each dot represents RELI results (normalized -log corrected p -value) for EBNA2 enrichment for a given disease. Results were normalized to the max negative log p -value for each EBNA2 dataset to facilitate comparisons. The black line indicates equivalently significant enrichment for type 1 and type 2 EBNA2. Previously established “EBNA2 disorders” (dark blue dots) and other diseases discussed in the text are labeled. Disease abbreviations: CD Celiac Disease, IBD Inflammatory Bowel Disease, JIA Juvenile Idiopathic Arthritis, MS Multiple Sclerosis, PBC Primary Biliary Cholangitis, RA Rheumatoid Arthritis, SLE Systemic Lupus Erythematosus, T1D Type 1 Diabetes, UC Ulcerative Colitis

Techniques: ChIP-sequencing, Labeling

Journal: Virology Journal

Article Title: Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray

doi: 10.1186/1743-422X-3-43

Figure Lengend Snippet: Probes for Epstein-Barr Virus genes

Article Snippet: For immunoblotting, the following antibodies and dilutions were used: anti-EBV Z Replication Activator (ZEBRA, Zta), clone AZ-69 (1:100 dilution, Argene Biosoft, Varilhes, France), the monoclonal rat-anti LMP2A, (clone TP 14B7, 1:100 dilution, Ascenion, Germany), the mouse anti EBNA2 (DakoCytomation, Baar, Switzerland), and the PCNA (BD Bioscience, Basel, Switzerland).

Techniques:

Selection of microarray probes . The specificity of EBV gene probes was tested in the reference cell line B95.8 as positive control (A) and in the EBV-negative cell line BJAB (B). The P3HR1 strain of EBV is characterized by a large deletion in the region coding for EBNA2 and was used to validate the specificity of EBNA2 probes (C). Black bars represent probes considered specific and selected for the final version of the chip. Mean ± SEM values (with background subtracted) were normalized to the set of eight housekeeping genes. Robust signals were measured for most latent and lytic EBV genes in the reference cell line B95.8. White bars indicate probes that were not selected.

Journal: Virology Journal

Article Title: Quantitative profiling of housekeeping and Epstein-Barr virus gene transcription in Burkitt lymphoma cell lines using an oligonucleotide microarray

doi: 10.1186/1743-422X-3-43

Figure Lengend Snippet: Selection of microarray probes . The specificity of EBV gene probes was tested in the reference cell line B95.8 as positive control (A) and in the EBV-negative cell line BJAB (B). The P3HR1 strain of EBV is characterized by a large deletion in the region coding for EBNA2 and was used to validate the specificity of EBNA2 probes (C). Black bars represent probes considered specific and selected for the final version of the chip. Mean ± SEM values (with background subtracted) were normalized to the set of eight housekeeping genes. Robust signals were measured for most latent and lytic EBV genes in the reference cell line B95.8. White bars indicate probes that were not selected.

Techniques: Selection, Microarray, Positive Control

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pe2 (Novus Biologicals)

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