Limits...
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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Structural partitioning controls enhancer-target gene allocation and modulates enhancers' effective activity on target genes.Genes and enhancers are shown as rectangles and ovals, respectively. Active promoters and enhancers are marked with arrows and plain colors. The TZ organizes the locus into two distinct, partially overlapping spatial conformations (represented by light blue and green circles), where genes and enhancers can interact. In the heart (A) and forebrain (B), this situation prevents action of one enhancer on a gene in the other domain. In the lateral forebrain, enhancers adjacent to FB1 may contribute to Tfap2c expression. In the medial forebrain (C), the active Bmp7 promoter may compete, non productively, for the forebrain enhancer, and interferes (marked by a yellow oval) with its action on Tfap2c. The TZ may control the strength and therefore the consequences of this interference on Tfap2c expression.
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pgen-1004897-g007: Structural partitioning controls enhancer-target gene allocation and modulates enhancers' effective activity on target genes.Genes and enhancers are shown as rectangles and ovals, respectively. Active promoters and enhancers are marked with arrows and plain colors. The TZ organizes the locus into two distinct, partially overlapping spatial conformations (represented by light blue and green circles), where genes and enhancers can interact. In the heart (A) and forebrain (B), this situation prevents action of one enhancer on a gene in the other domain. In the lateral forebrain, enhancers adjacent to FB1 may contribute to Tfap2c expression. In the medial forebrain (C), the active Bmp7 promoter may compete, non productively, for the forebrain enhancer, and interferes (marked by a yellow oval) with its action on Tfap2c. The TZ may control the strength and therefore the consequences of this interference on Tfap2c expression.

Mentions: With regard to the allocation of the heart enhancer, the TZ behave similarly to a classical insulator (Fig. 7). However, the analysis of INV-L1 and –L2 indicates that the TZ does not provide complete shielding from external influences, as the presence, beyond the TZ, of an active Bmp7 promoter can interfere with the expression of Tfap2c in the medial forebrain. Although contacts between Bmp7 and Tfap2c and its associated forebrain enhancer(s) are limited and even insufficient to lead to productive interactions (i.e. activation of Bmp7), they are nonetheless present at higher than background level. Our data suggests that they may be frequent and/or strong enough to perturb the regulation of Tfap2c by its forebrain enhancer(s), most probably through promoter competition. Several studies have reported that promoters have a tendency to come into close proximity [40], [72], [73], particularly when they are co-active and linked. Our analysis indicates that the TZ appears to counteract this generic promoter clustering by limiting admixing of the two domains, but it does not however totally prevent the diffusion of regulatory influences between them. The functional impact of these influences underscores the difficulties of defining functional thresholds for the interaction data obtained with 4C or Hi-C. It also emphasizes that topological domains should not be considered as strict autarchic units: topological separation does not exclude neighborly relationships and semipermeable borders. Transformation of the intrinsically broad forebrain activity of FB1 into the graded expression pattern shown by Tfap2c may involve additional neighboring enhancer elements, as hinted to by the INV-M data. However, our observations suggest that the permeability of the TZ to active Bmp7 may also contribute to this fine-tuning (Fig. 7C). In operational terms, the TZ should be considered as a rheostatic controller rather than as a strict insulator.


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)

Structural partitioning controls enhancer-target gene allocation and modulates enhancers' effective activity on target genes.Genes and enhancers are shown as rectangles and ovals, respectively. Active promoters and enhancers are marked with arrows and plain colors. The TZ organizes the locus into two distinct, partially overlapping spatial conformations (represented by light blue and green circles), where genes and enhancers can interact. In the heart (A) and forebrain (B), this situation prevents action of one enhancer on a gene in the other domain. In the lateral forebrain, enhancers adjacent to FB1 may contribute to Tfap2c expression. In the medial forebrain (C), the active Bmp7 promoter may compete, non productively, for the forebrain enhancer, and interferes (marked by a yellow oval) with its action on Tfap2c. The TZ may control the strength and therefore the consequences of this interference on Tfap2c expression.
© Copyright Policy
Related In: Results  -  Collection

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

pgen-1004897-g007: Structural partitioning controls enhancer-target gene allocation and modulates enhancers' effective activity on target genes.Genes and enhancers are shown as rectangles and ovals, respectively. Active promoters and enhancers are marked with arrows and plain colors. The TZ organizes the locus into two distinct, partially overlapping spatial conformations (represented by light blue and green circles), where genes and enhancers can interact. In the heart (A) and forebrain (B), this situation prevents action of one enhancer on a gene in the other domain. In the lateral forebrain, enhancers adjacent to FB1 may contribute to Tfap2c expression. In the medial forebrain (C), the active Bmp7 promoter may compete, non productively, for the forebrain enhancer, and interferes (marked by a yellow oval) with its action on Tfap2c. The TZ may control the strength and therefore the consequences of this interference on Tfap2c expression.
Mentions: With regard to the allocation of the heart enhancer, the TZ behave similarly to a classical insulator (Fig. 7). However, the analysis of INV-L1 and –L2 indicates that the TZ does not provide complete shielding from external influences, as the presence, beyond the TZ, of an active Bmp7 promoter can interfere with the expression of Tfap2c in the medial forebrain. Although contacts between Bmp7 and Tfap2c and its associated forebrain enhancer(s) are limited and even insufficient to lead to productive interactions (i.e. activation of Bmp7), they are nonetheless present at higher than background level. Our data suggests that they may be frequent and/or strong enough to perturb the regulation of Tfap2c by its forebrain enhancer(s), most probably through promoter competition. Several studies have reported that promoters have a tendency to come into close proximity [40], [72], [73], particularly when they are co-active and linked. Our analysis indicates that the TZ appears to counteract this generic promoter clustering by limiting admixing of the two domains, but it does not however totally prevent the diffusion of regulatory influences between them. The functional impact of these influences underscores the difficulties of defining functional thresholds for the interaction data obtained with 4C or Hi-C. It also emphasizes that topological domains should not be considered as strict autarchic units: topological separation does not exclude neighborly relationships and semipermeable borders. Transformation of the intrinsically broad forebrain activity of FB1 into the graded expression pattern shown by Tfap2c may involve additional neighboring enhancer elements, as hinted to by the INV-M data. However, our observations suggest that the permeability of the TZ to active Bmp7 may also contribute to this fine-tuning (Fig. 7C). In operational terms, the TZ should be considered as a rheostatic controller rather than as a strict insulator.

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