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CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex.

Holohan EE, Kwong C, Adryan B, Bartkuhn M, Herold M, Renkawitz R, Russell S, White R - PLoS Genet. (2007)

Bottom Line: CTCF binding sites identified in the BX-C map precisely to the known insulator elements Mcp, Fab-6, and Fab-8.Other CTCF binding sites correlate with boundaries of regulatory domains allowing us to locate three additional presumptive insulator elements; "Fab-2," "Fab-3," and "Fab-4." With the exception of Fab-7, our data indicate that CTCF is directly associated with all known or predicted insulators in the BX-C, suggesting that the functioning of these insulators involves a common CTCF-dependent mechanism.Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.

ABSTRACT
Insulator or enhancer-blocking elements are proposed to play an important role in the regulation of transcription by preventing inappropriate enhancer/promoter interaction. The zinc-finger protein CTCF is well studied in vertebrates as an enhancer blocking factor, but Drosophila CTCF has only been characterised recently. To date only one endogenous binding location for CTCF has been identified in the Drosophila genome, the Fab-8 insulator in the Abdominal-B locus in the Bithorax complex (BX-C). We carried out chromatin immunopurification coupled with genomic microarray analysis to identify CTCF binding sites within representative regions of the Drosophila genome, including the 3-Mb Adh region, the BX-C, and the Antennapedia complex. Location of in vivo CTCF binding within these regions enabled us to construct a robust CTCF binding-site consensus sequence. CTCF binding sites identified in the BX-C map precisely to the known insulator elements Mcp, Fab-6, and Fab-8. Other CTCF binding sites correlate with boundaries of regulatory domains allowing us to locate three additional presumptive insulator elements; "Fab-2," "Fab-3," and "Fab-4." With the exception of Fab-7, our data indicate that CTCF is directly associated with all known or predicted insulators in the BX-C, suggesting that the functioning of these insulators involves a common CTCF-dependent mechanism. Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation.

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Genomic Context of CTCF Sites in the BX-C(A) Shown is a comparison between the locations of CTCF binding sites, Polycomb target sites, and histone H3 lysine 27 (H3K27) methylation from the data of Schwartz et al. [42]. For the Polycomb targets the Psc track is shown but the Pc and E(Z) binding profiles identify the same targets sites in this region. CTCF sites are closely related to Polycomb targets sites as illustrated by the schematic with CTCF sites in green and Polycomb sites in red.(B) Detailed view of the Mcp region shows the relationship between the CTCF site, the mapped domains of the insulator, the PRE, and the PhastCons conservation track. The CTCF site sits within the mapped insulator and lies over a clear discrete conservation peak.
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pgen-0030112-g005: Genomic Context of CTCF Sites in the BX-C(A) Shown is a comparison between the locations of CTCF binding sites, Polycomb target sites, and histone H3 lysine 27 (H3K27) methylation from the data of Schwartz et al. [42]. For the Polycomb targets the Psc track is shown but the Pc and E(Z) binding profiles identify the same targets sites in this region. CTCF sites are closely related to Polycomb targets sites as illustrated by the schematic with CTCF sites in green and Polycomb sites in red.(B) Detailed view of the Mcp region shows the relationship between the CTCF site, the mapped domains of the insulator, the PRE, and the PhastCons conservation track. The CTCF site sits within the mapped insulator and lies over a clear discrete conservation peak.

Mentions: In Figure 5, we display the relationship between these Polycomb data [42] and our in vivo CTCF binding data in the region from “Fab-4” to the 5′ end of the Abd-B transcription unit. Strikingly, the four Polycomb target sites in this region that are occupied by Polycomb complexes in S2 cells are all located in close proximity to CTCF binding sites. Furthermore, the Polycomb target peak always lies to one side of the CTCF site suggesting the relative arrangements as indicated in the schematic in Figure 5A. However, although the CTCF sites are precisely located, the Polycomb target sites are represented by peaks that span several hundred base pairs leaving some uncertainty as to the precise location of the Polycomb target sequences. Nevertheless, for Mcp this ordering agrees with the functional mapping where the PRE and the boundary have been mapped to adjacent but separate regions as illustrated in Figure 5B [4,41]. Overall, this arrangement suggests that each of these Polycomb target site sits within a domain flanked by CTCF boundaries.


CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex.

Holohan EE, Kwong C, Adryan B, Bartkuhn M, Herold M, Renkawitz R, Russell S, White R - PLoS Genet. (2007)

Genomic Context of CTCF Sites in the BX-C(A) Shown is a comparison between the locations of CTCF binding sites, Polycomb target sites, and histone H3 lysine 27 (H3K27) methylation from the data of Schwartz et al. [42]. For the Polycomb targets the Psc track is shown but the Pc and E(Z) binding profiles identify the same targets sites in this region. CTCF sites are closely related to Polycomb targets sites as illustrated by the schematic with CTCF sites in green and Polycomb sites in red.(B) Detailed view of the Mcp region shows the relationship between the CTCF site, the mapped domains of the insulator, the PRE, and the PhastCons conservation track. The CTCF site sits within the mapped insulator and lies over a clear discrete conservation peak.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1904468&req=5

pgen-0030112-g005: Genomic Context of CTCF Sites in the BX-C(A) Shown is a comparison between the locations of CTCF binding sites, Polycomb target sites, and histone H3 lysine 27 (H3K27) methylation from the data of Schwartz et al. [42]. For the Polycomb targets the Psc track is shown but the Pc and E(Z) binding profiles identify the same targets sites in this region. CTCF sites are closely related to Polycomb targets sites as illustrated by the schematic with CTCF sites in green and Polycomb sites in red.(B) Detailed view of the Mcp region shows the relationship between the CTCF site, the mapped domains of the insulator, the PRE, and the PhastCons conservation track. The CTCF site sits within the mapped insulator and lies over a clear discrete conservation peak.
Mentions: In Figure 5, we display the relationship between these Polycomb data [42] and our in vivo CTCF binding data in the region from “Fab-4” to the 5′ end of the Abd-B transcription unit. Strikingly, the four Polycomb target sites in this region that are occupied by Polycomb complexes in S2 cells are all located in close proximity to CTCF binding sites. Furthermore, the Polycomb target peak always lies to one side of the CTCF site suggesting the relative arrangements as indicated in the schematic in Figure 5A. However, although the CTCF sites are precisely located, the Polycomb target sites are represented by peaks that span several hundred base pairs leaving some uncertainty as to the precise location of the Polycomb target sequences. Nevertheless, for Mcp this ordering agrees with the functional mapping where the PRE and the boundary have been mapped to adjacent but separate regions as illustrated in Figure 5B [4,41]. Overall, this arrangement suggests that each of these Polycomb target site sits within a domain flanked by CTCF boundaries.

Bottom Line: CTCF binding sites identified in the BX-C map precisely to the known insulator elements Mcp, Fab-6, and Fab-8.Other CTCF binding sites correlate with boundaries of regulatory domains allowing us to locate three additional presumptive insulator elements; "Fab-2," "Fab-3," and "Fab-4." With the exception of Fab-7, our data indicate that CTCF is directly associated with all known or predicted insulators in the BX-C, suggesting that the functioning of these insulators involves a common CTCF-dependent mechanism.Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation.

View Article: PubMed Central - PubMed

Affiliation: Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.

ABSTRACT
Insulator or enhancer-blocking elements are proposed to play an important role in the regulation of transcription by preventing inappropriate enhancer/promoter interaction. The zinc-finger protein CTCF is well studied in vertebrates as an enhancer blocking factor, but Drosophila CTCF has only been characterised recently. To date only one endogenous binding location for CTCF has been identified in the Drosophila genome, the Fab-8 insulator in the Abdominal-B locus in the Bithorax complex (BX-C). We carried out chromatin immunopurification coupled with genomic microarray analysis to identify CTCF binding sites within representative regions of the Drosophila genome, including the 3-Mb Adh region, the BX-C, and the Antennapedia complex. Location of in vivo CTCF binding within these regions enabled us to construct a robust CTCF binding-site consensus sequence. CTCF binding sites identified in the BX-C map precisely to the known insulator elements Mcp, Fab-6, and Fab-8. Other CTCF binding sites correlate with boundaries of regulatory domains allowing us to locate three additional presumptive insulator elements; "Fab-2," "Fab-3," and "Fab-4." With the exception of Fab-7, our data indicate that CTCF is directly associated with all known or predicted insulators in the BX-C, suggesting that the functioning of these insulators involves a common CTCF-dependent mechanism. Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation.

Show MeSH
Related in: MedlinePlus