Limits...
BCL6 orchestrates Tfh cell differentiation via multiple distinct mechanisms.

Hatzi K, Nance JP, Kroenke MA, Bothwell M, Haddad EK, Melnick A, Crotty S - J. Exp. Med. (2015)

Bottom Line: BCL6 primarily acts as a repressor in Tfh cells, and BCL6 binding was associated with control of Tfh cell migration and repression of alternative cell fates.We show that BCL6 can directly bind AP1, and BCL6 depends on AP1 for recruitment to BCL6-binding sites with AP1 motifs, suggesting that BCL6 subverts AP1 activity.These findings reveal that BCL6 has broad and multifaceted effects on Tfh biology and provide insight into how this master regulator mediates distinct cell context-dependent phenotypes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Hematology and Medical Oncology, Weill Cornell Medical College, Cornell University, New York, NY 10065.

Show MeSH

Related in: MedlinePlus

BCL6-mediated repression of key Tfh target genes is linked to interaction with AP1 and recruitment to AP1 DNA–binding sites. (A) De novo motif analysis of BCL6 GC Tfh peaks using HOMER identified the AP1 and STAT DNA motifs among the most highly enriched in Tfh BCL6 peaks. P-values are indicated. (B) Human GC Tfh BCL6-binding sites identified in this study containing AP1 or STAT motifs that were homologous to sites in the mouse genome were queried for AP1 and STAT binding based on published Th17 ChIP-seq datasets. Bound versus unbound fractions are indicated. (C and D) GSEA analysis based on global gene expression changes after BCL6 lentiviral induction in CD4 T cells versus control lentivirus. Up and down indicate the relative gene up- or down-regulation after BCL6 expression. Data are from six independent replicates. The gene sets tested were as follows: (C) promoters with BCL6 peaks containing STAT motifs (left) and poised enhancers with BCL6 peaks containing STAT motifs (right); (D) promoters with BCL6 peaks containing AP1 motifs (left) and poised enhancers with BCL6 peaks containing AP1 motifs (right). FDR is based on 1,000 permutations. (E) Fraction of BCL6 peaks containing BCL6, AP1, or STAT motifs in peaks with lower, intermediate, or high BCL6 enrichment. (F) BCL6 and AP1 motif containing BCL6-bound peaks are primarily found in separate sets of gene.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4387288&req=5

fig8: BCL6-mediated repression of key Tfh target genes is linked to interaction with AP1 and recruitment to AP1 DNA–binding sites. (A) De novo motif analysis of BCL6 GC Tfh peaks using HOMER identified the AP1 and STAT DNA motifs among the most highly enriched in Tfh BCL6 peaks. P-values are indicated. (B) Human GC Tfh BCL6-binding sites identified in this study containing AP1 or STAT motifs that were homologous to sites in the mouse genome were queried for AP1 and STAT binding based on published Th17 ChIP-seq datasets. Bound versus unbound fractions are indicated. (C and D) GSEA analysis based on global gene expression changes after BCL6 lentiviral induction in CD4 T cells versus control lentivirus. Up and down indicate the relative gene up- or down-regulation after BCL6 expression. Data are from six independent replicates. The gene sets tested were as follows: (C) promoters with BCL6 peaks containing STAT motifs (left) and poised enhancers with BCL6 peaks containing STAT motifs (right); (D) promoters with BCL6 peaks containing AP1 motifs (left) and poised enhancers with BCL6 peaks containing AP1 motifs (right). FDR is based on 1,000 permutations. (E) Fraction of BCL6 peaks containing BCL6, AP1, or STAT motifs in peaks with lower, intermediate, or high BCL6 enrichment. (F) BCL6 and AP1 motif containing BCL6-bound peaks are primarily found in separate sets of gene.

Mentions: The canonical function of BCL6 involves repression of genes by directly binding to cis-regulatory elements containing a BCL6 DNA–binding motif (Figs. 3 E and 6 G). Strikingly, the vast majority of BCL6-bound loci in GC Tfh cells, 88%, lacked a BCL6 DNA–binding motif. We considered that BCL6 may be primarily recruited to DNA by other transcription factors in GC Tfh cells. To test this hypothesis, we first performed an unbiased DNA motif discovery analysis. The BCL6 DNA motif was the top motif observed (P = 10−221, observed in 1,043 peaks, 12%; motif shown in Fig. 1 C; TTCCTAGAAAGC), but in addition, AP1 (P = 10−112; Fig. 8 A) and STAT transcription factor motifs (P = 10−80; Fig. 8 A) were also highly ranked and highly enriched among BCL6-bound peaks in GC Tfh cells. To ascertain whether these BCL6-binding sites were bona fide STAT and AP1 targets in T cells, we cross-referenced the peaks to published ChIP-seq datasets from activated CD4 T cells. This analysis indicated that a majority of BCL6-binding peaks containing STAT- or AP1-binding motifs are indeed bound by STAT3 and AP1 family proteins (Fig. 8 B). Promoters or enhancers with consensus STAT motifs (TTC[N1-3]GAA) within BCL6 peaks were significantly associated with repression by BCL6 in BCL6-LV+ T cells (FDR = 0.003 and FDR < 0.001; Fig. 8 C). STAT proteins mold the enhancer landscape of helper T cells (Vahedi et al., 2012), and it is known that STAT consensus motif sequences can often be observed embedded in BCL6 DNA motifs. Accumulating evidence suggests that in B cells and macrophages BCL6 may antagonize STAT signaling (Dent et al., 1997; Harris et al., 1999; Huang et al., 2013). Therefore, a competition between certain STATs and BCL6 in Tfh cells may regulate promoter and enhancer activities, such as the IL17A/F enhancer, which is known to be regulated by competition between STAT3 and STAT5 (Yang et al., 2011).


BCL6 orchestrates Tfh cell differentiation via multiple distinct mechanisms.

Hatzi K, Nance JP, Kroenke MA, Bothwell M, Haddad EK, Melnick A, Crotty S - J. Exp. Med. (2015)

BCL6-mediated repression of key Tfh target genes is linked to interaction with AP1 and recruitment to AP1 DNA–binding sites. (A) De novo motif analysis of BCL6 GC Tfh peaks using HOMER identified the AP1 and STAT DNA motifs among the most highly enriched in Tfh BCL6 peaks. P-values are indicated. (B) Human GC Tfh BCL6-binding sites identified in this study containing AP1 or STAT motifs that were homologous to sites in the mouse genome were queried for AP1 and STAT binding based on published Th17 ChIP-seq datasets. Bound versus unbound fractions are indicated. (C and D) GSEA analysis based on global gene expression changes after BCL6 lentiviral induction in CD4 T cells versus control lentivirus. Up and down indicate the relative gene up- or down-regulation after BCL6 expression. Data are from six independent replicates. The gene sets tested were as follows: (C) promoters with BCL6 peaks containing STAT motifs (left) and poised enhancers with BCL6 peaks containing STAT motifs (right); (D) promoters with BCL6 peaks containing AP1 motifs (left) and poised enhancers with BCL6 peaks containing AP1 motifs (right). FDR is based on 1,000 permutations. (E) Fraction of BCL6 peaks containing BCL6, AP1, or STAT motifs in peaks with lower, intermediate, or high BCL6 enrichment. (F) BCL6 and AP1 motif containing BCL6-bound peaks are primarily found in separate sets of gene.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4387288&req=5

fig8: BCL6-mediated repression of key Tfh target genes is linked to interaction with AP1 and recruitment to AP1 DNA–binding sites. (A) De novo motif analysis of BCL6 GC Tfh peaks using HOMER identified the AP1 and STAT DNA motifs among the most highly enriched in Tfh BCL6 peaks. P-values are indicated. (B) Human GC Tfh BCL6-binding sites identified in this study containing AP1 or STAT motifs that were homologous to sites in the mouse genome were queried for AP1 and STAT binding based on published Th17 ChIP-seq datasets. Bound versus unbound fractions are indicated. (C and D) GSEA analysis based on global gene expression changes after BCL6 lentiviral induction in CD4 T cells versus control lentivirus. Up and down indicate the relative gene up- or down-regulation after BCL6 expression. Data are from six independent replicates. The gene sets tested were as follows: (C) promoters with BCL6 peaks containing STAT motifs (left) and poised enhancers with BCL6 peaks containing STAT motifs (right); (D) promoters with BCL6 peaks containing AP1 motifs (left) and poised enhancers with BCL6 peaks containing AP1 motifs (right). FDR is based on 1,000 permutations. (E) Fraction of BCL6 peaks containing BCL6, AP1, or STAT motifs in peaks with lower, intermediate, or high BCL6 enrichment. (F) BCL6 and AP1 motif containing BCL6-bound peaks are primarily found in separate sets of gene.
Mentions: The canonical function of BCL6 involves repression of genes by directly binding to cis-regulatory elements containing a BCL6 DNA–binding motif (Figs. 3 E and 6 G). Strikingly, the vast majority of BCL6-bound loci in GC Tfh cells, 88%, lacked a BCL6 DNA–binding motif. We considered that BCL6 may be primarily recruited to DNA by other transcription factors in GC Tfh cells. To test this hypothesis, we first performed an unbiased DNA motif discovery analysis. The BCL6 DNA motif was the top motif observed (P = 10−221, observed in 1,043 peaks, 12%; motif shown in Fig. 1 C; TTCCTAGAAAGC), but in addition, AP1 (P = 10−112; Fig. 8 A) and STAT transcription factor motifs (P = 10−80; Fig. 8 A) were also highly ranked and highly enriched among BCL6-bound peaks in GC Tfh cells. To ascertain whether these BCL6-binding sites were bona fide STAT and AP1 targets in T cells, we cross-referenced the peaks to published ChIP-seq datasets from activated CD4 T cells. This analysis indicated that a majority of BCL6-binding peaks containing STAT- or AP1-binding motifs are indeed bound by STAT3 and AP1 family proteins (Fig. 8 B). Promoters or enhancers with consensus STAT motifs (TTC[N1-3]GAA) within BCL6 peaks were significantly associated with repression by BCL6 in BCL6-LV+ T cells (FDR = 0.003 and FDR < 0.001; Fig. 8 C). STAT proteins mold the enhancer landscape of helper T cells (Vahedi et al., 2012), and it is known that STAT consensus motif sequences can often be observed embedded in BCL6 DNA motifs. Accumulating evidence suggests that in B cells and macrophages BCL6 may antagonize STAT signaling (Dent et al., 1997; Harris et al., 1999; Huang et al., 2013). Therefore, a competition between certain STATs and BCL6 in Tfh cells may regulate promoter and enhancer activities, such as the IL17A/F enhancer, which is known to be regulated by competition between STAT3 and STAT5 (Yang et al., 2011).

Bottom Line: BCL6 primarily acts as a repressor in Tfh cells, and BCL6 binding was associated with control of Tfh cell migration and repression of alternative cell fates.We show that BCL6 can directly bind AP1, and BCL6 depends on AP1 for recruitment to BCL6-binding sites with AP1 motifs, suggesting that BCL6 subverts AP1 activity.These findings reveal that BCL6 has broad and multifaceted effects on Tfh biology and provide insight into how this master regulator mediates distinct cell context-dependent phenotypes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Hematology and Medical Oncology, Weill Cornell Medical College, Cornell University, New York, NY 10065.

Show MeSH
Related in: MedlinePlus