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A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes.

Tsujimura T, Klein FA, Langenfeld K, Glaser J, Huber W, Spitz F - PLoS Genet. (2015)

Bottom Line: The impact of engineered chromosomal rearrangements on the topology of the locus and the resultant gene expression changes indicate that this transition zone functionally organizes the structural partition of the locus, thereby defining enhancer-target gene allocation.This partition is, however, not absolute: we show that it allows competing interactions across it that may be non-productive for the competing gene, but modulate expression of the competed one.Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression.

View Article: PubMed Central - PubMed

Affiliation: Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

ABSTRACT
Despite the well-documented role of remote enhancers in controlling developmental gene expression, the mechanisms that allocate enhancers to genes are poorly characterized. Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains. Chromosome conformation capture experiments reveal a corresponding partition of the locus in two distinct structural entities, demarcated by a discrete transition zone. The impact of engineered chromosomal rearrangements on the topology of the locus and the resultant gene expression changes indicate that this transition zone functionally organizes the structural partition of the locus, thereby defining enhancer-target gene allocation. This partition is, however, not absolute: we show that it allows competing interactions across it that may be non-productive for the competing gene, but modulate expression of the competed one. Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression.

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4C profiles describing the conformational structure of the Tfap2c-Bmp7 locus.(A) Hi-C heat-map of the Tfap2c-Bmp7 locus in mouse ES cells (top) and corresponding TADs identified in ES cells and adult cortex (bottom; shown by whiskered red bars) (data from Dixon et al. 2012; aligned with the other panels). (B–E) 4C-contact profiles for the different viewpoints (indicated by black triangles): promoter of Tfap2c (B) and Bmp7 (C), adjacent to the TZ (D) and within the TZ (E). Five different tissues (whole embryos, heart, lateral forebrain, medial forebrain at stage E11.5, limb buds at E12.5) were examined with the two promoter viewpoints (B, C). Only whole embryos and heart samples were used for the additional viewpoints (D, E). The estimated primary interaction domains are indicated by a bar below the corresponding 4C plots. The region of overlap of the different primary interaction domains (TZ) is outlined with a dashed red box. Stars (*) indicate two regions with low mappability [84] accounting for the absence of signal over these positions. For comparison, a schematic representation of the region including H3K27ac peaks detected in forebrain and heart chromatin (S3 Fig.) is shown below panels B and C. Surrounding gene bodies are represented with grey boxes. The FB1 and mm75 enhancers are shown as blue and pink ovals, respectively. Associated rectangles indicate the extended enhancer regions encompassing the additional H3K27ac regions detected within the del1 segment.
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pgen-1004897-g003: 4C profiles describing the conformational structure of the Tfap2c-Bmp7 locus.(A) Hi-C heat-map of the Tfap2c-Bmp7 locus in mouse ES cells (top) and corresponding TADs identified in ES cells and adult cortex (bottom; shown by whiskered red bars) (data from Dixon et al. 2012; aligned with the other panels). (B–E) 4C-contact profiles for the different viewpoints (indicated by black triangles): promoter of Tfap2c (B) and Bmp7 (C), adjacent to the TZ (D) and within the TZ (E). Five different tissues (whole embryos, heart, lateral forebrain, medial forebrain at stage E11.5, limb buds at E12.5) were examined with the two promoter viewpoints (B, C). Only whole embryos and heart samples were used for the additional viewpoints (D, E). The estimated primary interaction domains are indicated by a bar below the corresponding 4C plots. The region of overlap of the different primary interaction domains (TZ) is outlined with a dashed red box. Stars (*) indicate two regions with low mappability [84] accounting for the absence of signal over these positions. For comparison, a schematic representation of the region including H3K27ac peaks detected in forebrain and heart chromatin (S3 Fig.) is shown below panels B and C. Surrounding gene bodies are represented with grey boxes. The FB1 and mm75 enhancers are shown as blue and pink ovals, respectively. Associated rectangles indicate the extended enhancer regions encompassing the additional H3K27ac regions detected within the del1 segment.

Mentions: We next investigated how the regulatory subdivision of the locus corresponded to its topological organization. Hi-C data available for mouse ES cells and cortex [34] suggests that the locus has a relatively loose topological structure, confined between two prominent topologically associating domains (Fig. 3A, S4 Fig.). To determine the pattern of physical contacts involving Tfap2c and Bmp7, we carried out circular chromatin conformation capture experiments followed by high-throughput sequencing (4C-Seq) using the promoters of these two genes as viewpoints (Fig. 3). We performed these 4C-Seq analyses on dissected samples where one and/or the other gene were expressed (E11.5 heart, medial and lateral forebrain) and whole body of E11.5 embryos (where most cells are non-expressing either of the two genes). We also included samples from E12.5 limbs, which comprised a majority of non-expressing cells.


A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes.

Tsujimura T, Klein FA, Langenfeld K, Glaser J, Huber W, Spitz F - PLoS Genet. (2015)

4C profiles describing the conformational structure of the Tfap2c-Bmp7 locus.(A) Hi-C heat-map of the Tfap2c-Bmp7 locus in mouse ES cells (top) and corresponding TADs identified in ES cells and adult cortex (bottom; shown by whiskered red bars) (data from Dixon et al. 2012; aligned with the other panels). (B–E) 4C-contact profiles for the different viewpoints (indicated by black triangles): promoter of Tfap2c (B) and Bmp7 (C), adjacent to the TZ (D) and within the TZ (E). Five different tissues (whole embryos, heart, lateral forebrain, medial forebrain at stage E11.5, limb buds at E12.5) were examined with the two promoter viewpoints (B, C). Only whole embryos and heart samples were used for the additional viewpoints (D, E). The estimated primary interaction domains are indicated by a bar below the corresponding 4C plots. The region of overlap of the different primary interaction domains (TZ) is outlined with a dashed red box. Stars (*) indicate two regions with low mappability [84] accounting for the absence of signal over these positions. For comparison, a schematic representation of the region including H3K27ac peaks detected in forebrain and heart chromatin (S3 Fig.) is shown below panels B and C. Surrounding gene bodies are represented with grey boxes. The FB1 and mm75 enhancers are shown as blue and pink ovals, respectively. Associated rectangles indicate the extended enhancer regions encompassing the additional H3K27ac regions detected within the del1 segment.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4288730&req=5

pgen-1004897-g003: 4C profiles describing the conformational structure of the Tfap2c-Bmp7 locus.(A) Hi-C heat-map of the Tfap2c-Bmp7 locus in mouse ES cells (top) and corresponding TADs identified in ES cells and adult cortex (bottom; shown by whiskered red bars) (data from Dixon et al. 2012; aligned with the other panels). (B–E) 4C-contact profiles for the different viewpoints (indicated by black triangles): promoter of Tfap2c (B) and Bmp7 (C), adjacent to the TZ (D) and within the TZ (E). Five different tissues (whole embryos, heart, lateral forebrain, medial forebrain at stage E11.5, limb buds at E12.5) were examined with the two promoter viewpoints (B, C). Only whole embryos and heart samples were used for the additional viewpoints (D, E). The estimated primary interaction domains are indicated by a bar below the corresponding 4C plots. The region of overlap of the different primary interaction domains (TZ) is outlined with a dashed red box. Stars (*) indicate two regions with low mappability [84] accounting for the absence of signal over these positions. For comparison, a schematic representation of the region including H3K27ac peaks detected in forebrain and heart chromatin (S3 Fig.) is shown below panels B and C. Surrounding gene bodies are represented with grey boxes. The FB1 and mm75 enhancers are shown as blue and pink ovals, respectively. Associated rectangles indicate the extended enhancer regions encompassing the additional H3K27ac regions detected within the del1 segment.
Mentions: We next investigated how the regulatory subdivision of the locus corresponded to its topological organization. Hi-C data available for mouse ES cells and cortex [34] suggests that the locus has a relatively loose topological structure, confined between two prominent topologically associating domains (Fig. 3A, S4 Fig.). To determine the pattern of physical contacts involving Tfap2c and Bmp7, we carried out circular chromatin conformation capture experiments followed by high-throughput sequencing (4C-Seq) using the promoters of these two genes as viewpoints (Fig. 3). We performed these 4C-Seq analyses on dissected samples where one and/or the other gene were expressed (E11.5 heart, medial and lateral forebrain) and whole body of E11.5 embryos (where most cells are non-expressing either of the two genes). We also included samples from E12.5 limbs, which comprised a majority of non-expressing cells.

Bottom Line: The impact of engineered chromosomal rearrangements on the topology of the locus and the resultant gene expression changes indicate that this transition zone functionally organizes the structural partition of the locus, thereby defining enhancer-target gene allocation.This partition is, however, not absolute: we show that it allows competing interactions across it that may be non-productive for the competing gene, but modulate expression of the competed one.Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression.

View Article: PubMed Central - PubMed

Affiliation: Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.

ABSTRACT
Despite the well-documented role of remote enhancers in controlling developmental gene expression, the mechanisms that allocate enhancers to genes are poorly characterized. Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains. Chromosome conformation capture experiments reveal a corresponding partition of the locus in two distinct structural entities, demarcated by a discrete transition zone. The impact of engineered chromosomal rearrangements on the topology of the locus and the resultant gene expression changes indicate that this transition zone functionally organizes the structural partition of the locus, thereby defining enhancer-target gene allocation. This partition is, however, not absolute: we show that it allows competing interactions across it that may be non-productive for the competing gene, but modulate expression of the competed one. Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression.

Show MeSH
Related in: MedlinePlus