Long-range chromatin regulatory interactions in vivo

Abstract

Communication between distal chromosomal elements is essential for control of many nuclear processes. For example, genes in higher eukaryotes often require distant enhancer sequences for high-level expression. The mechanisms proposed for long-range enhancer action fall into two basic categories. Non-contact models propose that enhancers act at a distance to create a favorable environment for gene transcription, or act as entry sites or nucleation points for factors that ultimately communicate with the gene. Contact models propose that communication occurs through direct interaction between the distant enhancer and the gene by various mechanisms that 'loop out' the intervening sequences. Although much attention has focused on contact models, the existence and nature of long-range interactions is still controversial and speculative, as there is no direct evidence that distant sequences physically interact in vivo. Here, we report the development of a widely applicable in situ technique to tag and recover chromatin in the immediate vicinity of an actively transcribed gene. We show that the classical enhancer element, HS2 of the prototypical locus control region (LCR) of the beta-globin gene cluster, is in close physical proximity to an actively transcribed HBB (beta-globin) gene located over 50 kb away in vivo, suggesting a direct regulatory interaction. The results give unprecedented insight into the in vivo structure of the LCR-gene interface and provide the first direct evidence of long-range enhancer communication.

Fetal hemoglobin chemical inducers for treatment of hemoglobinopathies

“…The role of cis-acting elements in the regulation of γ-globin gene expression was explored through RNA-TRAP and chromosome conformation capture (3-C) experiments in transgenic mice carrying the entire or selected regions of the human β-globin locus. RNA TRAP experiments provided evidence that HS2 is in close proximity to the actively transcribed β-globin gene, in agreement with genetic data suggesting that HS2 is the most prominent enhancer element in the β-globin LCR [4]. In this context, particularly significant were the 3-C experiments carried out in transgenic mice carrying the entire human β-globin locus: These mice show a switch in the association of HS2 and HS3 sites in the βLCR from contacts with embryonic and fetal genes in yolk sac cells to contacts with the adult human β-globin in adult-type erythroid cells [5].…”

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

“…Though there are a host of interesting examples of transcriptional regulation that involve DNA looping, we focus almost exclusively on the dissection of the role of looping in 85 Repression and activation 210 Gal repressor 85 Repression 115 Deo repressor 85 Repression 270, 599, 869 Nag repressor 86 Repression 93 NtrC 87 Activation 110-140 l repressor 84,88 Repression and activation $2400 XylR 89 Activation $150 PapI 87,90 Activation $100 -globin locus 91,92 Activation 40,000-60,000 RXR 93 Activation 30-500 SpGCF1 94 Activation, domain intercommunication 50-2500 HSTF 95 Activation 23 p53 96 Repression and activation 50-3000 Sp1 [97][98][99] Activation $1,800 c-Myb and C/EBP 100 Activation $80…”

Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elements

“…www.genome.org RNA-TRAP showed that the expressed globin gene interacted most strongly with HS2 (Carter et al 2002).…”

“…This locus was selected because several looping interactions have previously been detected by 3C as well as by a second method, RNA-TRAP (Carter et al 2002;Tolhuis et al 2002), and therefore detection of these looping interactions using 5C can be used to validate the new method.…”