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Genome-wide binding patterns of thyroid hormone receptor beta.

Ayers S, Switnicki MP, Angajala A, Lammel J, Arumanayagam AS, Webb P - PLoS ONE (2014)

Bottom Line: In contrast, no significant enrichment of TRβ is seen at negatively regulated genes or genes that respond to unliganded TRs in this system.There is also significant enrichment of binding sites for TR associated transcription factors, including AP-1 and CTCF, near TR peaks.We conclude that T3-dependent gene induction commonly involves proximal TRβ binding events but that far-distant binding events are needed for T3 induction of some genes and that distinct, indirect, mechanisms are often at play in negative regulation and unliganded TR actions.

View Article: PubMed Central - PubMed

Affiliation: The Methodist Hospital Research Institute, Genomic Medicine Program, Houston, Texas, United States of America.

ABSTRACT
Thyroid hormone (TH) receptors (TRs) play central roles in metabolism and are major targets for pharmaceutical intervention. Presently, however, there is limited information about genome wide localizations of TR binding sites. Thus, complexities of TR genomic distribution and links between TRβ binding events and gene regulation are not fully appreciated. Here, we employ a BioChIP approach to capture TR genome-wide binding events in a liver cell line (HepG2). Like other NRs, TRβ appears widely distributed throughout the genome. Nevertheless, there is striking enrichment of TRβ binding sites immediately 5' and 3' of transcribed genes and TRβ can be detected near 50% of T3 induced genes. In contrast, no significant enrichment of TRβ is seen at negatively regulated genes or genes that respond to unliganded TRs in this system. Canonical TRE half-sites are present in more than 90% of TRβ peaks and classical TREs are also greatly enriched, but individual TRE organization appears highly variable with diverse half-site orientation and spacing. There is also significant enrichment of binding sites for TR associated transcription factors, including AP-1 and CTCF, near TR peaks. We conclude that T3-dependent gene induction commonly involves proximal TRβ binding events but that far-distant binding events are needed for T3 induction of some genes and that distinct, indirect, mechanisms are often at play in negative regulation and unliganded TR actions. Better understanding of genomic context of TR binding sites will help us determine why TR regulates genes in different ways and determine possibilities for selective modulation of TR action.

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Patterns of TRβ binding and transcriptional regulation.Heatmap depicting log2-transformed expression levels (left) and TRβ binding events within 1 KB, 5 KB or 25 KB of TSS (right) of genes that met statistical significance and an arbitrary +/−2.55-fold cut-off of gene induction in TRβ-BioChIP cells +/−T3. Columns reflect the average of three experimental samples. Expression values in heatmap are as indicated by color scale (bottom, green indicating −5.7-fold repression, red indicating 13-fold induction), and location of binding events within the indicated ranges are depicted by the presence or absence of black bars in the three right-most columns.
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pone-0081186-g003: Patterns of TRβ binding and transcriptional regulation.Heatmap depicting log2-transformed expression levels (left) and TRβ binding events within 1 KB, 5 KB or 25 KB of TSS (right) of genes that met statistical significance and an arbitrary +/−2.55-fold cut-off of gene induction in TRβ-BioChIP cells +/−T3. Columns reflect the average of three experimental samples. Expression values in heatmap are as indicated by color scale (bottom, green indicating −5.7-fold repression, red indicating 13-fold induction), and location of binding events within the indicated ranges are depicted by the presence or absence of black bars in the three right-most columns.

Mentions: We performed a detailed survey of TRβ binding near genes regulated more than 2.5-fold by T3 in the microarray (Fig. 3 and supplementary data). As expected, large numbers of TRβ binding events occurred near highly induced targets; >50% of these genes exhibit TRβ binding within 25 KB and >10% within 1 KB. Genes in this TRβ bound, T3 induced, set were physiologically relevant and representative of TRß's known functions in liver (not shown). There was high correlation between identities of highly T3 responsive genes in B7B cells and observed T3 responses that were insensitive to cycloheximide (CHX) treatment in related HepG2 cells that express flag tagged TRβ (see data in reference [49] and not shown). Further, these genes displayed rapid onset of T3 response in Flag-TRβ cells at early time points (see [54]). This implies that this gene set is highly enriched for direct TR targets. By contrast, only one T3 repressed gene (PDE2A) displayed nearby binding events, within 1 Kb of the transcriptional start site, and no other repressed genes displayed detectable TRβ binding events.


Genome-wide binding patterns of thyroid hormone receptor beta.

Ayers S, Switnicki MP, Angajala A, Lammel J, Arumanayagam AS, Webb P - PLoS ONE (2014)

Patterns of TRβ binding and transcriptional regulation.Heatmap depicting log2-transformed expression levels (left) and TRβ binding events within 1 KB, 5 KB or 25 KB of TSS (right) of genes that met statistical significance and an arbitrary +/−2.55-fold cut-off of gene induction in TRβ-BioChIP cells +/−T3. Columns reflect the average of three experimental samples. Expression values in heatmap are as indicated by color scale (bottom, green indicating −5.7-fold repression, red indicating 13-fold induction), and location of binding events within the indicated ranges are depicted by the presence or absence of black bars in the three right-most columns.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3928038&req=5

pone-0081186-g003: Patterns of TRβ binding and transcriptional regulation.Heatmap depicting log2-transformed expression levels (left) and TRβ binding events within 1 KB, 5 KB or 25 KB of TSS (right) of genes that met statistical significance and an arbitrary +/−2.55-fold cut-off of gene induction in TRβ-BioChIP cells +/−T3. Columns reflect the average of three experimental samples. Expression values in heatmap are as indicated by color scale (bottom, green indicating −5.7-fold repression, red indicating 13-fold induction), and location of binding events within the indicated ranges are depicted by the presence or absence of black bars in the three right-most columns.
Mentions: We performed a detailed survey of TRβ binding near genes regulated more than 2.5-fold by T3 in the microarray (Fig. 3 and supplementary data). As expected, large numbers of TRβ binding events occurred near highly induced targets; >50% of these genes exhibit TRβ binding within 25 KB and >10% within 1 KB. Genes in this TRβ bound, T3 induced, set were physiologically relevant and representative of TRß's known functions in liver (not shown). There was high correlation between identities of highly T3 responsive genes in B7B cells and observed T3 responses that were insensitive to cycloheximide (CHX) treatment in related HepG2 cells that express flag tagged TRβ (see data in reference [49] and not shown). Further, these genes displayed rapid onset of T3 response in Flag-TRβ cells at early time points (see [54]). This implies that this gene set is highly enriched for direct TR targets. By contrast, only one T3 repressed gene (PDE2A) displayed nearby binding events, within 1 Kb of the transcriptional start site, and no other repressed genes displayed detectable TRβ binding events.

Bottom Line: In contrast, no significant enrichment of TRβ is seen at negatively regulated genes or genes that respond to unliganded TRs in this system.There is also significant enrichment of binding sites for TR associated transcription factors, including AP-1 and CTCF, near TR peaks.We conclude that T3-dependent gene induction commonly involves proximal TRβ binding events but that far-distant binding events are needed for T3 induction of some genes and that distinct, indirect, mechanisms are often at play in negative regulation and unliganded TR actions.

View Article: PubMed Central - PubMed

Affiliation: The Methodist Hospital Research Institute, Genomic Medicine Program, Houston, Texas, United States of America.

ABSTRACT
Thyroid hormone (TH) receptors (TRs) play central roles in metabolism and are major targets for pharmaceutical intervention. Presently, however, there is limited information about genome wide localizations of TR binding sites. Thus, complexities of TR genomic distribution and links between TRβ binding events and gene regulation are not fully appreciated. Here, we employ a BioChIP approach to capture TR genome-wide binding events in a liver cell line (HepG2). Like other NRs, TRβ appears widely distributed throughout the genome. Nevertheless, there is striking enrichment of TRβ binding sites immediately 5' and 3' of transcribed genes and TRβ can be detected near 50% of T3 induced genes. In contrast, no significant enrichment of TRβ is seen at negatively regulated genes or genes that respond to unliganded TRs in this system. Canonical TRE half-sites are present in more than 90% of TRβ peaks and classical TREs are also greatly enriched, but individual TRE organization appears highly variable with diverse half-site orientation and spacing. There is also significant enrichment of binding sites for TR associated transcription factors, including AP-1 and CTCF, near TR peaks. We conclude that T3-dependent gene induction commonly involves proximal TRβ binding events but that far-distant binding events are needed for T3 induction of some genes and that distinct, indirect, mechanisms are often at play in negative regulation and unliganded TR actions. Better understanding of genomic context of TR binding sites will help us determine why TR regulates genes in different ways and determine possibilities for selective modulation of TR action.

Show MeSH
Related in: MedlinePlus