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Dual functions of TAF7L in adipocyte differentiation.

Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, Eisen MB, Tjian R - Elife (2013)

Bottom Line: Depletion of TAF7L reduced adipocyte-specific gene expression, compromised adipocyte differentiation, and WAT development as well.Genome-wide mRNA-seq expression profiling and ChIP-seq binding studies confirmed that TAF7L is required for activating adipocyte-specific genes via a dual mechanism wherein it interacts with PPARγ at enhancers and TBP/Pol II at core promoters.In vitro binding studies confirmed that TAF7L forms complexes with both TBP and PPARγ.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology , Howard Hughes Medical Institute, University of California, Berkeley , Berkeley , United States ; Li Ka Shing Center For Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley , Berkeley , United States.

ABSTRACT
The diverse transcriptional mechanisms governing cellular differentiation and development of mammalian tissue remains poorly understood. Here we report that TAF7L, a paralogue of TFIID subunit TAF7, is enriched in adipocytes and white fat tissue (WAT) in mouse. Depletion of TAF7L reduced adipocyte-specific gene expression, compromised adipocyte differentiation, and WAT development as well. Ectopic expression of TAF7L in myoblasts reprograms these muscle precursors into adipocytes upon induction. Genome-wide mRNA-seq expression profiling and ChIP-seq binding studies confirmed that TAF7L is required for activating adipocyte-specific genes via a dual mechanism wherein it interacts with PPARγ at enhancers and TBP/Pol II at core promoters. In vitro binding studies confirmed that TAF7L forms complexes with both TBP and PPARγ. These findings suggest that TAF7L plays an integral role in adipocyte gene expression by targeting enhancers as a cofactor for PPARγ and promoters as a component of the core transcriptional machinery.DOI:http://dx.doi.org/10.7554/eLife.00170.001.

No MeSH data available.


Related in: MedlinePlus

TAF7L binds strongly on the majority of genes upregulated during adipogenesis.(A) Read accumulation for eight ChIP-seq datasets including TAF7L, PPARγ, TBP and Pol II before (_pre) and after (_post) adipocyte differentiation at the Rfc4 and Adipoq gene loci. (B) The same as in (A) at the Ccdc37 and Klf15 gene loci. Vertical axis is 0–500 reads for all factors, co-localized peaks were marked with boxes, black boxes indicate promoters and red boxes indicate enhancers, solid lines denote active genes and dashed lines denote inactive gene. (C) Frequency (vertical axis) of TAF7L occupancy on gene expression groups (horizontal axis) including unchanged (low, med, high) (three blue dots regions from left-bottom to right-top in Figure 3A), downregulated (blue dots in left-bottom region in Figure 3A), and upregulated (>5×, >50×, two orange dots regions from lower to higher in Figure 3A). (D) Average TAF7L binding signal strength (vertical axis) on the core promoters (500 bp from TSS) and proximal enhancers (500 bp to 5 kb from TSS) of three major gene expression groups as in (C). (Regular t-test for (C) and (D), NS is no significant, *p<0.05, ***p<0.001).DOI:http://dx.doi.org/10.7554/eLife.00170.012
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fig6: TAF7L binds strongly on the majority of genes upregulated during adipogenesis.(A) Read accumulation for eight ChIP-seq datasets including TAF7L, PPARγ, TBP and Pol II before (_pre) and after (_post) adipocyte differentiation at the Rfc4 and Adipoq gene loci. (B) The same as in (A) at the Ccdc37 and Klf15 gene loci. Vertical axis is 0–500 reads for all factors, co-localized peaks were marked with boxes, black boxes indicate promoters and red boxes indicate enhancers, solid lines denote active genes and dashed lines denote inactive gene. (C) Frequency (vertical axis) of TAF7L occupancy on gene expression groups (horizontal axis) including unchanged (low, med, high) (three blue dots regions from left-bottom to right-top in Figure 3A), downregulated (blue dots in left-bottom region in Figure 3A), and upregulated (>5×, >50×, two orange dots regions from lower to higher in Figure 3A). (D) Average TAF7L binding signal strength (vertical axis) on the core promoters (500 bp from TSS) and proximal enhancers (500 bp to 5 kb from TSS) of three major gene expression groups as in (C). (Regular t-test for (C) and (D), NS is no significant, *p<0.05, ***p<0.001).DOI:http://dx.doi.org/10.7554/eLife.00170.012

Mentions: To explore the potential mechanism by which TAF7L functions during adipogenesis, we took advantage of chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) to map TAF7L, TBP, and Pol II binding profiles genome-wide prior to and after adiopgenesis. Mapped ChIP tags were analyzed by intersecting MACS and Grizzly Peak algorithms (Zhang et al., 2008; Feng et al., 2011; Harrison et al., 2011) to identify binding regions for each factor. In agreement with the low concentration of TAF7L shown in Western blots prior to differentiation (Figure 1A), only one significant peak was identified in C3H10T1/2 cells compared to 18,672 significant TAF7L binding peaks detected after adipocyte formation. At the same time, we found comparably large numbers of peaks for TBP (12,883 and 14,587) and Pol II (14,502 and 11,424) in pre- and post-differentiation C3H10T1/2 cells. As an example of our TAF7L ChIP-seq data, the profiles of two typical adipocyte-specific genes Adipoq and Klf15, a general highly expressed gene Rfc4, and a nonactive gene Ccdc37 are shown in Figure 6A,B. The expression level of each gene before and after differentiation can be deduced from the enrichment levels of Pol II.10.7554/eLife.00170.012Figure 6.TAF7L binds strongly on the majority of genes upregulated during adipogenesis.


Dual functions of TAF7L in adipocyte differentiation.

Zhou H, Kaplan T, Li Y, Grubisic I, Zhang Z, Wang PJ, Eisen MB, Tjian R - Elife (2013)

TAF7L binds strongly on the majority of genes upregulated during adipogenesis.(A) Read accumulation for eight ChIP-seq datasets including TAF7L, PPARγ, TBP and Pol II before (_pre) and after (_post) adipocyte differentiation at the Rfc4 and Adipoq gene loci. (B) The same as in (A) at the Ccdc37 and Klf15 gene loci. Vertical axis is 0–500 reads for all factors, co-localized peaks were marked with boxes, black boxes indicate promoters and red boxes indicate enhancers, solid lines denote active genes and dashed lines denote inactive gene. (C) Frequency (vertical axis) of TAF7L occupancy on gene expression groups (horizontal axis) including unchanged (low, med, high) (three blue dots regions from left-bottom to right-top in Figure 3A), downregulated (blue dots in left-bottom region in Figure 3A), and upregulated (>5×, >50×, two orange dots regions from lower to higher in Figure 3A). (D) Average TAF7L binding signal strength (vertical axis) on the core promoters (500 bp from TSS) and proximal enhancers (500 bp to 5 kb from TSS) of three major gene expression groups as in (C). (Regular t-test for (C) and (D), NS is no significant, *p<0.05, ***p<0.001).DOI:http://dx.doi.org/10.7554/eLife.00170.012
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fig6: TAF7L binds strongly on the majority of genes upregulated during adipogenesis.(A) Read accumulation for eight ChIP-seq datasets including TAF7L, PPARγ, TBP and Pol II before (_pre) and after (_post) adipocyte differentiation at the Rfc4 and Adipoq gene loci. (B) The same as in (A) at the Ccdc37 and Klf15 gene loci. Vertical axis is 0–500 reads for all factors, co-localized peaks were marked with boxes, black boxes indicate promoters and red boxes indicate enhancers, solid lines denote active genes and dashed lines denote inactive gene. (C) Frequency (vertical axis) of TAF7L occupancy on gene expression groups (horizontal axis) including unchanged (low, med, high) (three blue dots regions from left-bottom to right-top in Figure 3A), downregulated (blue dots in left-bottom region in Figure 3A), and upregulated (>5×, >50×, two orange dots regions from lower to higher in Figure 3A). (D) Average TAF7L binding signal strength (vertical axis) on the core promoters (500 bp from TSS) and proximal enhancers (500 bp to 5 kb from TSS) of three major gene expression groups as in (C). (Regular t-test for (C) and (D), NS is no significant, *p<0.05, ***p<0.001).DOI:http://dx.doi.org/10.7554/eLife.00170.012
Mentions: To explore the potential mechanism by which TAF7L functions during adipogenesis, we took advantage of chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) to map TAF7L, TBP, and Pol II binding profiles genome-wide prior to and after adiopgenesis. Mapped ChIP tags were analyzed by intersecting MACS and Grizzly Peak algorithms (Zhang et al., 2008; Feng et al., 2011; Harrison et al., 2011) to identify binding regions for each factor. In agreement with the low concentration of TAF7L shown in Western blots prior to differentiation (Figure 1A), only one significant peak was identified in C3H10T1/2 cells compared to 18,672 significant TAF7L binding peaks detected after adipocyte formation. At the same time, we found comparably large numbers of peaks for TBP (12,883 and 14,587) and Pol II (14,502 and 11,424) in pre- and post-differentiation C3H10T1/2 cells. As an example of our TAF7L ChIP-seq data, the profiles of two typical adipocyte-specific genes Adipoq and Klf15, a general highly expressed gene Rfc4, and a nonactive gene Ccdc37 are shown in Figure 6A,B. The expression level of each gene before and after differentiation can be deduced from the enrichment levels of Pol II.10.7554/eLife.00170.012Figure 6.TAF7L binds strongly on the majority of genes upregulated during adipogenesis.

Bottom Line: Depletion of TAF7L reduced adipocyte-specific gene expression, compromised adipocyte differentiation, and WAT development as well.Genome-wide mRNA-seq expression profiling and ChIP-seq binding studies confirmed that TAF7L is required for activating adipocyte-specific genes via a dual mechanism wherein it interacts with PPARγ at enhancers and TBP/Pol II at core promoters.In vitro binding studies confirmed that TAF7L forms complexes with both TBP and PPARγ.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular and Cell Biology , Howard Hughes Medical Institute, University of California, Berkeley , Berkeley , United States ; Li Ka Shing Center For Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley , Berkeley , United States.

ABSTRACT
The diverse transcriptional mechanisms governing cellular differentiation and development of mammalian tissue remains poorly understood. Here we report that TAF7L, a paralogue of TFIID subunit TAF7, is enriched in adipocytes and white fat tissue (WAT) in mouse. Depletion of TAF7L reduced adipocyte-specific gene expression, compromised adipocyte differentiation, and WAT development as well. Ectopic expression of TAF7L in myoblasts reprograms these muscle precursors into adipocytes upon induction. Genome-wide mRNA-seq expression profiling and ChIP-seq binding studies confirmed that TAF7L is required for activating adipocyte-specific genes via a dual mechanism wherein it interacts with PPARγ at enhancers and TBP/Pol II at core promoters. In vitro binding studies confirmed that TAF7L forms complexes with both TBP and PPARγ. These findings suggest that TAF7L plays an integral role in adipocyte gene expression by targeting enhancers as a cofactor for PPARγ and promoters as a component of the core transcriptional machinery.DOI:http://dx.doi.org/10.7554/eLife.00170.001.

No MeSH data available.


Related in: MedlinePlus