tcl1a protein  (Human Protein Atlas)

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Coimmunoprecipitation was used to determine whether TCL1A protein could interact with p65 in LCLs. Whole cell lysates from 1 × 107 LCLs were immunoprecipitated with (left panel) anti-TCL1A (1:50) antibodies or anti-IgG antibodies and protein samples were immunoblotted and probed with antibodies against TCL1A. Reversed IP was preformed to confirm that p65 and TCL1A interacted (right panel). (B) Heat-map plots showing the association between TCL1A binding and p65 binding in LCLs (Zhao et al., 2014). The signals for TCL1A ChIP-seq peaks and p65 ChIP-seq peaks are shown as heat-maps using red (the strongest signal) and white (the weakest signal) color schemes. Each row shows ±500 bp centered on the TCL1A ChIP-seq peak summits. (C) TCL1A occupancy versus p65 occupancy in LCLs. Scatter plots depicting the Pearson correlations (r) between TCL1A ChIP tag density (y axis) and p65 ChIP tag density (x axis) for the 357 TCL1A target genes are shown in Fig. 1C.

Article Snippet: Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Immunoprecipitation, Binding Assay, ChIP-sequencing

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Schematic diagram of three TCL1A SNPs: rs11849538, the “top hit” signal from the MA.27 musculoskeletal adverse event GWAS, rs7359033, and rs7160302. All three of these SNPs map near the 3′-terminus of TCL1A and are in tight linkage disequilibrium. Locations of estrogen response elements (EREs) are shown as boxes. (B) SNP- and estrogen-related variation of TCL1A mRNA expression in lymphoblastoid cell lines with known TCL1A SNP genotypes after exposure to E2 with or without 4OH-TAM. Student’s t test was performed to compare gene expression in LCLs with differing TCL1A SNP genotypes for each treatment condition, ***P < 0.001. (C) Heat map showing expression profiles for 357 genes regulated by TCL1A SNPs in an estrogen-dependent fashion, all of which could be reversed by 4OH-TAM treatment, as determined by RNA-seq using LCLs with either homozygous wild-type (W/W) (n = 2) or homozygous variant (V/V) (n = 3) genotypes for the TCL1A SNPs.

Article Snippet: Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Expressing, Gene Expression, RNA Sequencing, Variant Assay

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Genome-wide TCL1A occupancy profiles. Regions (Tss ± 2 kb) were clustered based on their profiles for TCL1A ChIP enrichment over input for all four samples using k-means clustering. Clustering was used to identify regions with distinct binding intensities. The gradient blue-to-red color indicates high-to-low counts in the corresponding genome region. (B) Percentage distributions of TCL1A ChIP-seq peaks for all four samples. (C) Identification of TCL1A consensus binding sequence motifs using HOMER and MEME.

Article Snippet: Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Genome Wide, Binding Assay, ChIP-sequencing, Sequencing

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) EMSA results showing that one TCL1A DNA binding motif sequence, CCATATAGG, is sufficient for DNA–TCL1A protein interaction. (B) Immunofluorescence staining showing TCL1A nuclear translocation in response to E2 (0.1 nM) treatment in LCLs. (C) Representative examples of TCL1A occupancy peaks depicted for the CCR6 and IL17RA loci in LCLs with known TCL1A SNP genotypes in the absence of E2 or in the presence of E2 (0.1 nM). Red boxes indicate that TCL1A binding in both CCR6 and IL17RA is significantly increased in response to E2 treatment, but that only occurs in cells with homozygous variant genotypes for TCL1A SNPs. (D) Changes in TCL1A occupancy are highly correlated with changes in mRNA expression levels for CCR6 and IL17RA. Student’s t test was performed to compare gene expression in LCLs with differing TCL1A SNPs (homozygous wild-type versus homozygous variant) for each treatment condition, ***P < 0.001.

Article Snippet: Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Binding Assay, Sequencing, Immunofluorescence, Staining, Translocation Assay, Variant Assay, Expressing, Gene Expression

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Venn diagram showing 357 gene that displayed TCL1A SNP- and estrogen-dependent gene expression patterns as determined by RNA-seq, and 57 of those 357 genes that displayed TCL1A SNP- and estrogen-dependent TCL1A occupancy. (B and C) TCL1A ChIP assays were performed to confirm results obtained from TCL1A ChIP-seq for all 57 genes, all of which showed greater TCL1A binding in the presence of E2, but only in cells homozygous variant for the TCL1A SNP genotypes. In contrast, in the presence of 4OH-TAM, this binding pattern was reversed for all 57 genes (n = 4 for each genotype group). (D and E) Changes in TCL1A binding were correlated with changes in mRNA expression for all 57 genes using the same cell lines from which the data shown in B and C were obtained. Specifically, in the presence of E2, all those genes showed significant induction only for the variant genotype. However, the expression pattern could be reversed by 4OH-TAM, thus confirming that changes in TCL1A occupancy were highly correlated with transcription.

Article Snippet: Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Gene Expression, RNA Sequencing, ChIP-sequencing, Binding Assay, Variant Assay, Expressing

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A and B) p65 ChIP-re-ChIP assays were performed to confirm the co-occupancy of TCL1A and p65 on 57 selected binding regions as shown in Fig. 4, B and C (n = 4 for each genotype group).

Article Snippet: Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Binding Assay

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Western blot analysis after TCL1A knockout or p65 knockdown in LCLs. (B) Knockdown of p65 resulted in the abolition of SNP- and estrogen-dependent TCL1A occupancy. (C) Knockdown of TCL1A abolished the TCL1A SNP- and estrogen-dependent p65 binding. (D and E) TCL1A SNP- and estrogen-dependent gene expression was lost after the knockdown of p65 or the knockout of TCL1A.

Article Snippet: Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Western Blot, Knock-Out, Knockdown, Binding Assay, Gene Expression

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: Coimmunoprecipitation was used to determine whether TCL1A protein could interact with NF-kB subunits in LCLs.

Article Snippet: Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques:

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Coimmunoprecipitation was used to determine whether TCL1A protein could interact with p65 in LCLs. Whole cell lysates from 1 × 107 LCLs were immunoprecipitated with (left panel) anti-TCL1A (1:50) antibodies or anti-IgG antibodies and protein samples were immunoblotted and probed with antibodies against TCL1A. Reversed IP was preformed to confirm that p65 and TCL1A interacted (right panel). (B) Heat-map plots showing the association between TCL1A binding and p65 binding in LCLs (Zhao et al., 2014). The signals for TCL1A ChIP-seq peaks and p65 ChIP-seq peaks are shown as heat-maps using red (the strongest signal) and white (the weakest signal) color schemes. Each row shows ±500 bp centered on the TCL1A ChIP-seq peak summits. (C) TCL1A occupancy versus p65 occupancy in LCLs. Scatter plots depicting the Pearson correlations (r) between TCL1A ChIP tag density (y axis) and p65 ChIP tag density (x axis) for the 357 TCL1A target genes are shown in Fig. 1C.

Article Snippet: Electrophoretic Mobility Shift Assay Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Immunoprecipitation, Binding Assay, ChIP-sequencing

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Schematic diagram of three TCL1A SNPs: rs11849538, the “top hit” signal from the MA.27 musculoskeletal adverse event GWAS, rs7359033, and rs7160302. All three of these SNPs map near the 3′-terminus of TCL1A and are in tight linkage disequilibrium. Locations of estrogen response elements (EREs) are shown as boxes. (B) SNP- and estrogen-related variation of TCL1A mRNA expression in lymphoblastoid cell lines with known TCL1A SNP genotypes after exposure to E2 with or without 4OH-TAM. Student’s t test was performed to compare gene expression in LCLs with differing TCL1A SNP genotypes for each treatment condition, ***P < 0.001. (C) Heat map showing expression profiles for 357 genes regulated by TCL1A SNPs in an estrogen-dependent fashion, all of which could be reversed by 4OH-TAM treatment, as determined by RNA-seq using LCLs with either homozygous wild-type (W/W) (n = 2) or homozygous variant (V/V) (n = 3) genotypes for the TCL1A SNPs.

Article Snippet: Electrophoretic Mobility Shift Assay Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Expressing, Gene Expression, RNA Sequencing, Variant Assay

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Genome-wide TCL1A occupancy profiles. Regions (Tss ± 2 kb) were clustered based on their profiles for TCL1A ChIP enrichment over input for all four samples using k-means clustering. Clustering was used to identify regions with distinct binding intensities. The gradient blue-to-red color indicates high-to-low counts in the corresponding genome region. (B) Percentage distributions of TCL1A ChIP-seq peaks for all four samples. (C) Identification of TCL1A consensus binding sequence motifs using HOMER and MEME.

Article Snippet: Electrophoretic Mobility Shift Assay Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Genome Wide, Binding Assay, ChIP-sequencing, Sequencing

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) EMSA results showing that one TCL1A DNA binding motif sequence, CCATATAGG, is sufficient for DNA–TCL1A protein interaction. (B) Immunofluorescence staining showing TCL1A nuclear translocation in response to E2 (0.1 nM) treatment in LCLs. (C) Representative examples of TCL1A occupancy peaks depicted for the CCR6 and IL17RA loci in LCLs with known TCL1A SNP genotypes in the absence of E2 or in the presence of E2 (0.1 nM). Red boxes indicate that TCL1A binding in both CCR6 and IL17RA is significantly increased in response to E2 treatment, but that only occurs in cells with homozygous variant genotypes for TCL1A SNPs. (D) Changes in TCL1A occupancy are highly correlated with changes in mRNA expression levels for CCR6 and IL17RA. Student’s t test was performed to compare gene expression in LCLs with differing TCL1A SNPs (homozygous wild-type versus homozygous variant) for each treatment condition, ***P < 0.001.

Article Snippet: Electrophoretic Mobility Shift Assay Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Binding Assay, Sequencing, Immunofluorescence, Staining, Translocation Assay, Variant Assay, Expressing, Gene Expression

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Venn diagram showing 357 gene that displayed TCL1A SNP- and estrogen-dependent gene expression patterns as determined by RNA-seq, and 57 of those 357 genes that displayed TCL1A SNP- and estrogen-dependent TCL1A occupancy. (B and C) TCL1A ChIP assays were performed to confirm results obtained from TCL1A ChIP-seq for all 57 genes, all of which showed greater TCL1A binding in the presence of E2, but only in cells homozygous variant for the TCL1A SNP genotypes. In contrast, in the presence of 4OH-TAM, this binding pattern was reversed for all 57 genes (n = 4 for each genotype group). (D and E) Changes in TCL1A binding were correlated with changes in mRNA expression for all 57 genes using the same cell lines from which the data shown in B and C were obtained. Specifically, in the presence of E2, all those genes showed significant induction only for the variant genotype. However, the expression pattern could be reversed by 4OH-TAM, thus confirming that changes in TCL1A occupancy were highly correlated with transcription.

Article Snippet: Electrophoretic Mobility Shift Assay Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Gene Expression, RNA Sequencing, ChIP-sequencing, Binding Assay, Variant Assay, Expressing

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A and B) p65 ChIP-re-ChIP assays were performed to confirm the co-occupancy of TCL1A and p65 on 57 selected binding regions as shown in Fig. 4, B and C (n = 4 for each genotype group).

Article Snippet: Electrophoretic Mobility Shift Assay Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Binding Assay

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: (A) Western blot analysis after TCL1A knockout or p65 knockdown in LCLs. (B) Knockdown of p65 resulted in the abolition of SNP- and estrogen-dependent TCL1A occupancy. (C) Knockdown of TCL1A abolished the TCL1A SNP- and estrogen-dependent p65 binding. (D and E) TCL1A SNP- and estrogen-dependent gene expression was lost after the knockdown of p65 or the knockout of TCL1A.

Article Snippet: Electrophoretic Mobility Shift Assay Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: Western Blot, Knock-Out, Knockdown, Binding Assay, Gene Expression

Journal: The Journal of Pharmacology and Experimental Therapeutics

Article Title: TCL1A , a Novel Transcription Factor and a Coregulator of Nuclear Factor κ B p65: Single Nucleotide Polymorphism and Estrogen Dependence

doi: 10.1124/jpet.118.247718

Figure Lengend Snippet: Coimmunoprecipitation was used to determine whether TCL1A protein could interact with NF-kB subunits in LCLs.

Article Snippet: Electrophoretic Mobility Shift Assay Recombinant Human TCL1A Protein (NBP1-30239) was purchased from Novus Biologicals (Littleton, CO).

Techniques: