rabbit anti taf1 antibody  (Bethyl)

Journal: bioRxiv

Article Title: Activator–promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID

doi: 10.64898/2025.12.28.696747

Figure Lengend Snippet: Mapping the AD of Hcfc1. GFP intensity was measured by flow cytometry in reporter cell lines stably expressing the indicated constructs fused to TetR. Statistical significance was assessed using a one-sided Wilcoxon test. Box plots indicate the median (central line), 25 th -75 th percentiles (box), and 1.5x interquartile range (whiskers). b , Volcano plot comparing the TurboID profiles of Hcfc1 ΔAD versus wild-type Hcfc1. Data are from three biological replicates. Significantly depleted proteins in the Hcfc1 ΔAD sample (log2FC > 1, FDR < 0.05) are coloured. c , Heatmap showing the relative depletion of top 7 TFIID subunits from the TurboID comparison in ( b ). d , AF2 in silico screen to identify direct interactors of the Hcfc1-AD. Predictions with an average PEAK score > 0.75 are highlighted. e , AF2 model of the Hcfc1-AD (orange) interacting with Taf4b (blue) and Taf6 (violet). f , g , Close-up views of the interaction interfaces between the Hcfc1-AD and Taf6 ( f ) and Taf4b ( g ). Interacting residues are labelled, hydrogen bonds are shown as dashed lines, and residues mutated in this study are underlined. h , Co-affinity purification (co-AP) assay testing the interaction between wild-type (wt) or mutant (VV2RR) Hcfc1-AD core peptides and a wt or mutant (LI2RR) Taf4b-Taf6 fusion protein. Results are shown by Coomassie-stained SDS-PAGE. Equal bait loading was confirmed by fluorescein intensity. Asterisk (*), streptavidin. i , ChIP-qPCR analysis of TFIID, Mediator, and Pol II enrichment at a CGI4 reporter promoter. Enrichments are normalized to a negative control locus. Bar graphs display the mean of three biological replicates, error bars representing the standard deviation. Statistical significance was determined using two-sided Student’s t-test. j , GFP intensity measured by flow cytometry in reporter cell lines stably expressing the indicated constructs fused to TetR. Statistical analysis and box plots are as described in ( a ). k , Boxplot of PRO-seq log2FC in transcription after 3 h of Taf1 depletion for CGI and non-CGI genes, and for Hcfc1-dependent and -independent genes. Box plots are as described in ( a ). Data are from two biological replicates. l , Heatmap showing GFP induction (relative to TetR-DsRed) in reporter cell lines stably expressing the indicated TFIID subunits fused to TetR. GFP intensity was measured by flow cytometry. m , Summary model for Hcfc1-mediated activation of CGI-promoters. Hcfc1 is recruited to CGI promoters via HBM-containing TFs, and the Hcfc1-AD directly recruits TFIID to drive transcription.

Article Snippet: Antibodies used for ChIP-qPCR: mouse IgG (Invitrogen, 31903; 3 μg), rabbit anti-Taf1 antibody (Bethyl Laboratories, A303-505A; 3 μg), mouse anti-Taf6 antibody (Invitrogen, MA3-077; 0.5 μg), rabbit anti-Med17 antibody (Abcam, ab155593; 3 μg), rabbit anti-Rpb2 antibody (Sigma Aldrich, HPA037506; 0.6 μg).

Techniques: Flow Cytometry, Stable Transfection, Expressing, Construct, Comparison, In Silico, Affinity Purification, Mutagenesis, Staining, SDS Page, ChIP-qPCR, Negative Control, Standard Deviation, Activation Assay

Journal: bioRxiv

Article Title: Activator–promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID

doi: 10.64898/2025.12.28.696747

Figure Lengend Snippet: a , ChIP-qPCR measuring the enrichment of FLAG-tagged TetR fusion proteins at the CGI4 reporter promoter (schematic, left). Bar graphs (right) show mean enrichment from three biological replicates, normalized to a negative control locus. Error bars represent standard deviation. Statistical significance was determined by a two-sided Student’s t-test. b , Schematic of the rapid Taf1 depletion using the AID system (top). The western blot (bottom) is representative of two independent experiments and shows Taf1 loss after 1 h of IAA treatment. c , Time-course analysis of cell viability, comparing cells with Taf1 present (-IAA, grey) to those where Taf1 is depleted (+IAA, red). Data are from two biological replicates. d , Dendrogram of PCC comparing spike-in normalized PRO-seq counts between biological replicates for the Taf1-depleted line and the parental control line. e , MA plots of PRO-seq transcriptional changes after 3 h of IAA treatment for the parental cell line (left) and AID-tagged Taf1 cell line (right). Significantly up-(blue) and down-regulated (red) genes are highlighted (FDR < 0.05, log2FC > log2(1.5)). f , Enrichment of Taf1 in all ORFtag screens, displayed as a bar plot of the log2 Odds Ratio (sorted vs. input). The FDR for each screen is shown above the corresponding bar.

Article Snippet: Antibodies used for ChIP-qPCR: mouse IgG (Invitrogen, 31903; 3 μg), rabbit anti-Taf1 antibody (Bethyl Laboratories, A303-505A; 3 μg), mouse anti-Taf6 antibody (Invitrogen, MA3-077; 0.5 μg), rabbit anti-Med17 antibody (Abcam, ab155593; 3 μg), rabbit anti-Rpb2 antibody (Sigma Aldrich, HPA037506; 0.6 μg).

Techniques: ChIP-qPCR, Negative Control, Standard Deviation, Western Blot, Control

Journal: bioRxiv

Article Title: Activator–promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID

doi: 10.64898/2025.12.28.696747

Figure Lengend Snippet: Mapping the AD of Hcfc1. GFP intensity was measured by flow cytometry in reporter cell lines stably expressing the indicated constructs fused to TetR. Statistical significance was assessed using a one-sided Wilcoxon test. Box plots indicate the median (central line), 25 th -75 th percentiles (box), and 1.5x interquartile range (whiskers). b , Volcano plot comparing the TurboID profiles of Hcfc1 ΔAD versus wild-type Hcfc1. Data are from three biological replicates. Significantly depleted proteins in the Hcfc1 ΔAD sample (log2FC > 1, FDR < 0.05) are coloured. c , Heatmap showing the relative depletion of top 7 TFIID subunits from the TurboID comparison in ( b ). d , AF2 in silico screen to identify direct interactors of the Hcfc1-AD. Predictions with an average PEAK score > 0.75 are highlighted. e , AF2 model of the Hcfc1-AD (orange) interacting with Taf4b (blue) and Taf6 (violet). f , g , Close-up views of the interaction interfaces between the Hcfc1-AD and Taf6 ( f ) and Taf4b ( g ). Interacting residues are labelled, hydrogen bonds are shown as dashed lines, and residues mutated in this study are underlined. h , Co-affinity purification (co-AP) assay testing the interaction between wild-type (wt) or mutant (VV2RR) Hcfc1-AD core peptides and a wt or mutant (LI2RR) Taf4b-Taf6 fusion protein. Results are shown by Coomassie-stained SDS-PAGE. Equal bait loading was confirmed by fluorescein intensity. Asterisk (*), streptavidin. i , ChIP-qPCR analysis of TFIID, Mediator, and Pol II enrichment at a CGI4 reporter promoter. Enrichments are normalized to a negative control locus. Bar graphs display the mean of three biological replicates, error bars representing the standard deviation. Statistical significance was determined using two-sided Student’s t-test. j , GFP intensity measured by flow cytometry in reporter cell lines stably expressing the indicated constructs fused to TetR. Statistical analysis and box plots are as described in ( a ). k , Boxplot of PRO-seq log2FC in transcription after 3 h of Taf1 depletion for CGI and non-CGI genes, and for Hcfc1-dependent and -independent genes. Box plots are as described in ( a ). Data are from two biological replicates. l , Heatmap showing GFP induction (relative to TetR-DsRed) in reporter cell lines stably expressing the indicated TFIID subunits fused to TetR. GFP intensity was measured by flow cytometry. m , Summary model for Hcfc1-mediated activation of CGI-promoters. Hcfc1 is recruited to CGI promoters via HBM-containing TFs, and the Hcfc1-AD directly recruits TFIID to drive transcription.

Article Snippet: For the immunoprecipitation reactions, 150 μg chromatin in 500 μl 1x IP buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS) was incubated with the respective antibodies (3 μg mouse IgG [Invitrogen, 31903]; 3 μg anti-Taf1 antibody [Bethyl Laboratories, A303-505A]; 0.5 μg anti-Taf6 antibody [Invitrogen, MA3-077]; 3 μg anti-Med17 antibody [Abcam, ab155593]; 0.6 μg anti-Rpb2 antibody [Sigma Aldrich, HPA037506]) overnight at 4 °C with overhead shaking.

Techniques: Flow Cytometry, Stable Transfection, Expressing, Construct, Comparison, In Silico, Affinity Purification, Mutagenesis, Staining, SDS Page, ChIP-qPCR, Negative Control, Standard Deviation, Activation Assay

Journal: bioRxiv

Article Title: Activator–promoter compatibility in mammals: a CpG-Island-specific co-activator directly bridges transcription factors to TFIID

doi: 10.64898/2025.12.28.696747

Figure Lengend Snippet: a , ChIP-qPCR measuring the enrichment of FLAG-tagged TetR fusion proteins at the CGI4 reporter promoter (schematic, left). Bar graphs (right) show mean enrichment from three biological replicates, normalized to a negative control locus. Error bars represent standard deviation. Statistical significance was determined by a two-sided Student’s t-test. b , Schematic of the rapid Taf1 depletion using the AID system (top). The western blot (bottom) is representative of two independent experiments and shows Taf1 loss after 1 h of IAA treatment. c , Time-course analysis of cell viability, comparing cells with Taf1 present (-IAA, grey) to those where Taf1 is depleted (+IAA, red). Data are from two biological replicates. d , Dendrogram of PCC comparing spike-in normalized PRO-seq counts between biological replicates for the Taf1-depleted line and the parental control line. e , MA plots of PRO-seq transcriptional changes after 3 h of IAA treatment for the parental cell line (left) and AID-tagged Taf1 cell line (right). Significantly up-(blue) and down-regulated (red) genes are highlighted (FDR < 0.05, log2FC > log2(1.5)). f , Enrichment of Taf1 in all ORFtag screens, displayed as a bar plot of the log2 Odds Ratio (sorted vs. input). The FDR for each screen is shown above the corresponding bar.

Article Snippet: For the immunoprecipitation reactions, 150 μg chromatin in 500 μl 1x IP buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% DOC, 0.1% SDS) was incubated with the respective antibodies (3 μg mouse IgG [Invitrogen, 31903]; 3 μg anti-Taf1 antibody [Bethyl Laboratories, A303-505A]; 0.5 μg anti-Taf6 antibody [Invitrogen, MA3-077]; 3 μg anti-Med17 antibody [Abcam, ab155593]; 0.6 μg anti-Rpb2 antibody [Sigma Aldrich, HPA037506]) overnight at 4 °C with overhead shaking.

Techniques: ChIP-qPCR, Negative Control, Standard Deviation, Western Blot, Control

Journal: Science Advances

Article Title: MeCP2 interacts with the super elongation complex to regulate transcription

doi: 10.1126/sciadv.adt5937

Figure Lengend Snippet: ( A ) Endogenous MeCP2 interacts with endogenous SEC subunits (AFF4, AF9, ENL, and ELL2) and RNA pol II in HEK293T cells. Normal mouse immunoglobulin G was used as a negative control. ( B ) Endogenous MeCP2 interacts with SEC subunits (AFF4 and ELL2) and RNA pol II in the cortex of WT mouse at 7 weeks of age. ( C ) Reverse IP of endogenous AFF4 from WT cortical lysate and immunoblotting against MeCP2. Different brightness settings were used for the top and bottom blots because of the relatively weaker MeCP2 co-IP band intensity compared to the AFF4 IP band intensity. Immunoblotting against AFF4 for (A) and (B) was performed with the Bethyl Laboratories antibody (A302-538A), whereas IP and immunoblotting for AFF4 for (C) was performed with the Proteintech antibody (14662-1-AP).

Article Snippet: Membranes were blocked for 30 min using the INTERCEPT (TBS) blocking buffer (Li-Cor, 927-60010) and then incubated with the following primary antibodies overnight at 4°C: AFF4 (Bethyl Laboratories, A302-538A at 1:1000; Proteintech, 14662-1-AP at 1:5000; and Boster Bio, A03824 at 1:1000), AF9 (Genetex, GTX 102835 at 1:1000), ENL (Cell Signaling Technology; 14893 at 1:1000), ELL2 (Bethyl; A302-505A at 1:1000), total RNA pol II (Cell Signaling Technology; 14958S at 1:1000), pSer 2 RNA pol II (Millipore, 04-1571 at 1:1000), MeCP2 (Cell Signaling Technology; 3456S at 1:1000), GFP (Abcam; ab13970 at 1:10,000), β-actin (Cell Signaling Technology; 8457S at 1:10,000), vinculin (Sigma-Aldrich; V9131-.2ML at 1:20,000), FLAG (Sigma-Aldrich; F3165-1MG at 1:4000), and HA (Cell Signaling Technology; 3724S at 1:4000).

Techniques: Negative Control, Western Blot, Co-Immunoprecipitation Assay

Journal: Science Advances

Article Title: MeCP2 interacts with the super elongation complex to regulate transcription

doi: 10.1126/sciadv.adt5937

Figure Lengend Snippet: ( A ) Short hairpin–mediated knockdown of AFF4 in HEK293T cells abolishes the interaction between MeCP2 and the remaining subunits of the SEC (ENL and ELL2). While knockdown of ENL mildly dissociates MeCP2’s interaction with ELL2, it does not affect its interaction with AFF4. Knockdown of ELL2 does not affect the interaction between MeCP2 and the remaining subunits of the SEC. NT sh is a nontargeting short-hairpin negative control. ( B ) In vitro binding assay between recombinant FLAG-tagged MeCP2 and HA-tagged SEC subunits. ( C ) In vitro binding assay between FLAG-tagged MeCP2 fragments and HA-tagged AFF4. The fragments that show a decrease in interaction with HA-AFF4 are highlighted in bold. Diagram on the right shows a map of the MeCP2 fragments tested. NTD, N-terminal domain; MBD, methyl-CpG–binding domain; ID, intervening domain; TRD, transcriptional repression domain; CTD, C-terminal domain. ( D ) In vitro binding assay between AFF4 and MeCP2 with deletions in the NTD, ID, TRD, ID and TRD, and CTD. The domains critical for interaction are highlighted in bold.

Article Snippet: Membranes were blocked for 30 min using the INTERCEPT (TBS) blocking buffer (Li-Cor, 927-60010) and then incubated with the following primary antibodies overnight at 4°C: AFF4 (Bethyl Laboratories, A302-538A at 1:1000; Proteintech, 14662-1-AP at 1:5000; and Boster Bio, A03824 at 1:1000), AF9 (Genetex, GTX 102835 at 1:1000), ENL (Cell Signaling Technology; 14893 at 1:1000), ELL2 (Bethyl; A302-505A at 1:1000), total RNA pol II (Cell Signaling Technology; 14958S at 1:1000), pSer 2 RNA pol II (Millipore, 04-1571 at 1:1000), MeCP2 (Cell Signaling Technology; 3456S at 1:1000), GFP (Abcam; ab13970 at 1:10,000), β-actin (Cell Signaling Technology; 8457S at 1:10,000), vinculin (Sigma-Aldrich; V9131-.2ML at 1:20,000), FLAG (Sigma-Aldrich; F3165-1MG at 1:4000), and HA (Cell Signaling Technology; 3724S at 1:4000).

Techniques: Knockdown, Negative Control, In Vitro, Binding Assay, Recombinant

Journal: PLOS Pathogens

Article Title: Release of P-TEFb from the Super Elongation Complex promotes HIV-1 latency reversal

doi: 10.1371/journal.ppat.1012083

Figure Lengend Snippet: Primary antibody details.

Article Snippet: ELL2 , Bethyl , Rabbit , A302-505A , https://www.fortislife.com/products/primary-antibodies/rabbit-anti-ell2-antibody/BETHYL-A302-505.

Techniques: