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Using a modified RNA FISH method called RNA-TRAP, the authors show that a distal enhancer is held in close physical proximity to an active β-globin gene in vivo. The intervening silent embryonic genes are not found positioned close to the enhancer. This provides direct evidence for regulation by long-range enhancer communication.
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Carter D., Chakalova L., Osbourne C.S., Dai Y-F., Fraser P. Long-range chromatin regulatory interactions in vivo. Nat Genet. 32:2002;623-626 Using a modified RNA FISH method called RNA-TRAP, the authors show that a distal enhancer is held in close physical proximity to an active β-globin gene in vivo. The intervening silent embryonic genes are not found positioned close to the enhancer. This provides direct evidence for regulation by long-range enhancer communication.
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The authors use the 3C technique to demonstrate that distal regulatory elements and active genes of the murine β-globin locus interact in vivo while the intervening DNA loops out. The interaction and looping are not observed in non-expressing tissue. They propose that the interaction between regulatory elements and the looping out of the chromatin domain is crucial to establishing an open chromatin domain and activating transcription.
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Tolhuis B., Palstra R.J., Splinter E., Grosveld F., de Laat W. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol Cell. 10:2002;1453-1465 The authors use the 3C technique to demonstrate that distal regulatory elements and active genes of the murine β-globin locus interact in vivo while the intervening DNA loops out. The interaction and looping are not observed in non-expressing tissue. They propose that the interaction between regulatory elements and the looping out of the chromatin domain is crucial to establishing an open chromatin domain and activating transcription.
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This paper reports the spatial organisation of the β-globin cluster at different stages of development in erythroid cells. The authors demonstrate that the interaction between regulatory elements is conserved between primitive and definitive erythroid cells. However, there is a developmental switch in the β-globin genes that interact with the regulatory elements that correlates with the switch in their expression. Furthermore, in erythroid progenitor cells that do not yet express the globin genes, the looped conformation of the cluster is already detected. This is evidence that loop formation is necessary to establish a structure permissive for β-globin expression.
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Palstra R.J., Tolhuis B., Splinter E., Nijmeijer R., Grosveld F., de Laat W. The β-globin nuclear compartment in development and erythroid differentiation. Nat Genet. 35:2003;190-194 This paper reports the spatial organisation of the β-globin cluster at different stages of development in erythroid cells. The authors demonstrate that the interaction between regulatory elements is conserved between primitive and definitive erythroid cells. However, there is a developmental switch in the β-globin genes that interact with the regulatory elements that correlates with the switch in their expression. Furthermore, in erythroid progenitor cells that do not yet express the globin genes, the looped conformation of the cluster is already detected. This is evidence that loop formation is necessary to establish a structure permissive for β-globin expression.
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Palstra, R.J.1
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GAGA can mediate enhancer function in trans by linking two separate DNA molecules
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The authors show that GAGA could form a protein link between separate DNA elements. This GAGA-dependent bridge involves oligomerization via its POZ domain. GAGA also acts as an anchor that facilitates gene activation by linking an enhancer to a promoter, even when the enhancer and the promoter are located on separate DNA molecules. The authors propose that GAGA facilitates long-range activation by providing a protein bridge that mediates enhancer-promoter communication.
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Mahmoudi T., Katsani K.R., Verrijzer C.P. GAGA can mediate enhancer function in trans by linking two separate DNA molecules. EMBO J. 21:2002;1775-1781 The authors show that GAGA could form a protein link between separate DNA elements. This GAGA-dependent bridge involves oligomerization via its POZ domain. GAGA also acts as an anchor that facilitates gene activation by linking an enhancer to a promoter, even when the enhancer and the promoter are located on separate DNA molecules. The authors propose that GAGA facilitates long-range activation by providing a protein bridge that mediates enhancer-promoter communication.
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Bulger M., Schubeler D., Bender M.A., Hamilton J., Farrell C.M., Hardison R.C., Groudine M. A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse β-globin locus. Mol Cell Biol. 23:2003;5234-5244
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This paper shows that the scs and scs′ insulators interact with each other in vivo. This interaction is mediated by the Zw5 and BEAF32 proteins associated with each element. Loop formation is confirmed by 3C and illustrates how insulators could subdivide the chromosome into autonomous functional units (loops).
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Blanton J., Gaszner M., Schedl P. Protein:protein interactions and the pairing of boundary elements in vivo. Genes Dev. 17:2003;664-675 This paper shows that the scs and scs′ insulators interact with each other in vivo. This interaction is mediated by the Zw5 and BEAF32 proteins associated with each element. Loop formation is confirmed by 3C and illustrates how insulators could subdivide the chromosome into autonomous functional units (loops).
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This study identifies the first endogenous functional Su(Hw) insulator, which is located between the yellow gene and the Achaete-scute gene complex. This insulator contains two Su(Hw) binding sites that are required for the insulator function. The Su(Hw) and Mod(mdg4) proteins participate in proper regulation of the Achaete-scute gene complex.
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Golovnin A., Birukova I., Romanova O., Silicheva M., Parshikov A., Savitskaya E., Pirrotta V., Georgiev P. An endogenous Su(Hw) insulator separates the yellow gene from the Achaete-scute complex in Drosophila. Development. 130:2003;3249-3258 This study identifies the first endogenous functional Su(Hw) insulator, which is located between the yellow gene and the Achaete-scute gene complex. This insulator contains two Su(Hw) binding sites that are required for the insulator function. The Su(Hw) and Mod(mdg4) proteins participate in proper regulation of the Achaete-scute gene complex.
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Pirrotta, V.7
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Visualization of chromatin domains created by the gypsy insulator of Drosophila
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Here, the authors have studied the spatial organisation of the chromosome X region containing the cut locus flanked by two endogenous Su(Hw) binding sites. Using FISH they show that the intervening DNA is arranged in a loop, with the two insulators located at the base. Furthermore, the insertion of an additional gypsy insulator in the centre of the loop results in the formation of two smaller loops. These results suggest that the gypsy insulator modifies nuclear organisation by creating chromatin loops.
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Byrd K., Corces V.G. Visualization of chromatin domains created by the gypsy insulator of Drosophila. J Cell Biol. 162:2003;565-574 Here, the authors have studied the spatial organisation of the chromosome X region containing the cut locus flanked by two endogenous Su(Hw) binding sites. Using FISH they show that the intervening DNA is arranged in a loop, with the two insulators located at the base. Furthermore, the insertion of an additional gypsy insulator in the centre of the loop results in the formation of two smaller loops. These results suggest that the gypsy insulator modifies nuclear organisation by creating chromatin loops.
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Repression of the scalloped gene by a Fab-7 mini-white transgene integration 18kb away is shown to be dependent on the endogenous Fab-7 element and/or of the presence of another Fab-7 element elsewhere in the genome. FISH analysis shows that this repression is mediated by a physical co-localisation of the endogenous Fab-7 and the transgene in embryonic nuclei. This interaction depends strongly on the chromatin components of the PcG, on DNA sequence homology and also on the nuclear compartmentalisation of chromosomal domains.
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